https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=John+RipolloneProteopedia - User contributions [en]2026-09-24T07:33:33ZUser contributionsMediaWiki 1.43.8https://proteopedia.org/index.php?title=Hen_Egg-White_(HEW)_Lysozyme&diff=1222773Hen Egg-White (HEW) Lysozyme2011-03-31T01:35:01Z<p>John Ripollone: </p>
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<div>'''Introduction'''<br />
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Lysozyme - also known as muramidase, or glycoside hydrolase - is a powerful enzyme of biological significance found in abundance in tears, saliva, and human milk. In humans, it is encoded in the ''LYZ'' gene. Although it is responsible for the initial digestion of starches in the mouth, it is most widely identified as a non-specific defense in gram positive bacteria and in many species of fungi. Due to its antibacterial effects, it is a strong component of the innate immune system, and is an important part of an infant's diet to ward off diarrheal diseases. Since it is a small, easily available, and highly stable protein containing only 129 amino acid residues, it has been subject to extensive research regarding its function and structure. Hen Egg White (HEW) Lysozyme is shown below.<br />
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===History===<br />
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Lysozyme is an enzyme known for its unique ability to degrade the polysaccharide architecture of many kinds of cell walls, normally for the purpose of protection against bacterial infection<ref>Lysozyme. 2010. Citizendium.org. http://en.citizendium.org/wiki/Lysozyme</ref>. Its effects were first noticed by Laschtschenko in 1909. It was officially characterized and termed “lysozyme” by Alexander Fleming, the same person credited for the accidental discovery of penicillin. <br />
The characterization of lysozyme in 1922 by Alexander Fleming was providential in that the undertaken experiment related to the discovery of lysozyme was not geared toward any knowledge of such a protein as lysozyme <ref>Lysozyme. 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. During the unrelated experiment, nasal drippings were inadvertently introduced to a petri dish containing a bacterial culture, which culture consequently exhibited the results of an as yet unknown enzymatic reaction. The observation of this unknown reaction led to further research on the components of this reaction as well as to the corresponding identification of the newfound "lysozyme." Fleming's discovery was complemented by David C. Phillips' 1965 description of the three-dimensional structure of lysozyme via a 200 pm resolution model obtained from X-ray crystallography <ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. Phillips' work was especially groundbreaking since Phillips had managed to successfully elucidate the structure of an enzyme via X-ray crystallography - a feat that had never before been accomplished<ref>Bugg, T. 1997. An Introduction to Enzyme and Coenzyme Chemistry. Blackwell Science Ltd., Oxford </ref>. Phillips' research also led to the first sufficiently described enzymatic mechanism of catalytic action <ref>1967. Proc R Soc Lond B Bio 167 (1009): 389–401.</ref>. Thus, Phillips' elucidation of the function of lysozyme led Phillips to reach a more general conclusion on the diversity of enzymatic chemical action in relation to enzymatic structure. Clearly, the findings of Phillips as well as the more general historical development of the understanding of the structure and function of lysozyme have been paramount to the more general realm of enzyme chemistry.<br />
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[[Image:nag-nam2.jpg|thumb|left|350px|Lysozyme Cleavage Site]]<br />
<ref>Image from: http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm</ref> <br />
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'''Function'''<br />
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Lysozyme is known for damaging bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid (NAM) and N-acetyl-D-glucosamine (NAG) residues in peptidoglycan, and between N-acetyl-D-glucosamine residues in chitodextrins. In this way, lysozyme is efficient in lysing the cell walls of both bacteria and fungi. The location of cleavage for lysozyme on this architectural theme is the β(1-4) glycosidic linkage connecting the C1 carbon of NAM to the C4 carbon of NAG. <br />
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The particular substrate of preference for this cleavage type is a (NAG-NAM)₃ hexasaccharide, within which substrate occurs the<br />
cleaving target glycosidic bond, NAM₄-β-O-NAG₅. The individual hexasaccharide binding units are designated A-F, with NAM₄-β-O-NAG₅ glycosidic bond cleavage preference corresponding to a D-E unit glycosidic bond cleavage preference. <br />
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= Enzymatic Activity of Lysozyme =<br />
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Enzymes are designed to attract and to bind specific substrates. The active site of and lysozyme and its specific ligands are described in the following sections<br />
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==Mechanistic Features==<br />
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'''Zymogen of Lysozyme: Enzymatic Precursor'''<br />
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Zymogens are inactive enzyme precursors. Enzymes are developed in an inactive way to prevent the enzyme from digesting the cell that produced it. This process also prevents the enzyme from becoming active in the wrong portion of the body. Lysozyme's zymogen, simply titled “pre-lysozyme,” was sequenced in 1977 by R D Palmiter, J Gagnon, L H Ericsson and K A Walsh, and has since been sequenced much more extensively. <br />
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[[Image:jrip.jpg|thumb|left|350px|Mechanism of Lysozyme]]<br />
<ref>Image from: http://www.google.com/imgres?imgurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/pics-and-strucs/lysozyme-mech.gif&imgrefurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm&usg=__ormapG4XKg-tR5GrMSOdSMTV4vE=&h=603&w=801&sz=7&hl=en&start=17&zoom=1&tbnid=nvr9gvFrUILDkM:&tbnh=143&tbnw=189&prev=/images%3Fq%3DThe%2Blysozyme%2Breaction%2Bmechanism%26um%3D1%26hl%3Den%26sa%3DN%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C304&um=1&itbs=1&iact=hc&vpx=521&vpy=349&dur=448&hovh=191&hovw=254&tx=140&ty=48&ei=JQ_LTPKzLIjCsAPkzt2KDg&oei=IA_LTP74OsG78gapm-GFAQ&esq=2&page=2&ndsp=18&ved=1t:429,r:2,s:17&biw=1280&bih=647</ref><br />
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'''Mechanism'''<br />
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The lysozyme mechanism of action results in the hydrolysis of a glycoside (hence the familial distinction of lysozyme as a glycosylase<ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>), which corresponds to the conversion of an acetal to a hemiacetal, which reaction (general degradation of glycosidic bond to units "capped" by newly formed hydroxyl groups) necessitates acid catalysis, since the conversion of acetal to hemiacetal involves the protonation of the reactant oxygen prior to actual bond cleavage. <ref>Pratt, C.W., Voet, D., Voet, J.G. Fundamentals of Biochemistry - Life at the Molecular Level - Third Edition. Voet, Voet and Pratt, 2008.</ref>. Furthermore, the transition state obtained from this protonation is a covalent, oxonium ion, intermediate that must obtain resonance stabilization. The need for some means of acid catalysis and covalent resonance stabilization is adequately provided by the Glu 35 and Asp 52 residues of lysozyme, respectively. The reaction mechanism of lysozyme is demonstrated below. In the following image, the reaction begins at the upper left-hand side, and proceeds according to reaction arrows.<br />
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As seen to the left, lysozyme works by hydrolyzing the glycosidic bond, distorting the bond between the NAM and NAG. This produces a glycosyl enzyme intermediate, which reacts with a water molecule to produce the product and the unchanged enzyme.<br />
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'''Active Site'''<br />
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The <scene name='Sandbox_39/Active_site/1'>active site</scene> of lysozyme is formulated as a prominent cleft outlined by the two aforementioned catalytic amino acids, Glu 35 and Asp 52. The active site is geometrically bent to augment ligand binding, and the two amino acids interact with the ligand in the binding site. Asp52 is depicted in green, and Glu35 is depicted in purple. <br />
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<applet load='1hew' size='350' frame='true' align='right' caption='' /><br />
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==Binding==<br />
'''Ligands''' <br />
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A <scene name='Sandbox_39/Ligands_1/1'>ligand</scene> is able to bind to the active site of an enzyme to form a biologically relevant complex. The model to the right shows a space-filling model of lysozyme with the protein distinguishable in brown and the ligand distinguishable in green. Another model of the ligand can be seen in this <br />
<scene name='Sandbox_39/Ribbon_ligand/1'>ribbon diagram</scene>, with the ligand protruding as a space-filling model from the active site. Here, it is clear that the ligand is a polysaccharide. <br />
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The lysozyme reaction is characterized by hydrolysis of the beta (1-4) glycosidic bond between NAM and NAG. Lysozyme has a very specific active site, which can bind only six sugar rings from a polysaccharide chain. Once lysozyme binds to this chain, it hydrolyzes them. These six sugar rings represent the ligand of lysozyme. The lysozyme then distorts the fourth sugar in the six-membered complex, producing stress on the molecule and breaking the glycosidic bond.<br />
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The amino acid side-chains Glu35 and Asp52 are critical to the activity of this enzyme. Glu35 acts as a proton donor to the glycosidic bond, cleaving the C-O bond in the substrate, and Asp52 acts as a nucleophile to generate a glycosyl enzyme intermediate. The glycosyl enzyme intermediate then reacts with a water molecule to give the product of hydrolysis. <br />
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'''Inhibitors''' <br />
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Lysozyme is best inhibited by small saccharides which act competitively with the natural substrate. The smaller saccharides will bind to the first three binding sites of the cleft (sites A-C), but will not reach sites D and E, where the enzyme cuts the glycosidic bond. So, the competitive inhibitor will stick in the cleft, not allowing the substrate to bind to the enzyme complex.<ref>http://mcdb-webarchive.mcdb.ucsb.edu/sears/biochemistry/tw-enz/lysozyme/HEWL/lysozyme-overview.htm</ref> Several known inhibitors of lysozyme are: SDS, N-acetyl-D-glucosamine, and various alcohols and oxidizing agents.<ref>http://www.worthington-biochem.com/ly/default.html</ref> <br />
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<applet load='1hew' size='350' frame='true' align='left' caption='' /><br />
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= Composition and Structure of Lysozyme =<br />
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All proteins consist of carbon, hydrogen, nitrogen, oxygen, and sulfur, as do most organic molecules. Enzymes are composed in such a way as to maximize their reactivity with their desired substrate, increasing the efficiency of biological reactions. The <scene name='Sandbox_39/Elements/1'>composition of lysozyme</scene> can be seen on the left, with the carbon atoms outlined in gray, oxygen atoms in red, nitrogen atoms in blue, sulfur atoms in yellow, and the three-letter abbreviation for the <scene name='Sandbox_39/Amino_acid_residues/1'>amino acid residues</scene> in purple.<br />
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Lysozyme, like all proteins, also contains a <scene name='Sandbox_39/C_and_n_terminal_residues/1'> 3'C and 5'N terminal </scene>, and these can be seen by following the colors of the rainbow across the molecule. Starting at the red end, the 3' C terminal end, one can work the entire way through to the 5' N terminal end, showing the folding pattern and chain of the protein.<br />
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== Secondary Structure ==<br />
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Lysozyme contains five <scene name='Sandbox_38/A/2'>alpha helical</scene> regions and five regions containing <scene name='Sandbox_38/B/1'>beta sheets</scene> as displayed in this <scene name='Sandbox_38/Alphab/1'>image</scene>. Linking these secondary structures, a number of beta turns and a large number of random coils make up the remainder of the polypeptide backbone. The polypeptide backbone of lysozyme involved in the 3 antiparallel beta sheets display the beta hairpin motif of supersecondary structure. This depiction of lysozyme contains an antiparallel beta-pleated sheet, which contributes greatly to the stability of the molecule by providing the correct alignment of hydrogen bonds. Lysozyme also contains a great deal of random coil, which is seen in the white regions of the molecule.<br />
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==Amino Acid Residues==<br />
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The amino acids present in the lysozyme polypeptide sequence have a direct influence not only on primary structure, but also on the secondary and tertiary structures, which can be influenced by polarity and charge of the sidechains. The various amino acid <scene name='Sandbox_38/Aminoi/1'>residues</scene> differ in their properties because of the great variety of side chains present on each amino acid. Polar and nonpolar (and charged and uncharged) side chains lead to various degrees of hydrophobicity and hydrophilicity, which affects protein folding. In lysozyme, these <scene name='Sandbox_38/Sc/1'>side chains</scene> are displayed for each amino acid residue.<br />
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= Bonding Interactions =<br />
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'''Disulfide Bonding in Lysozyme'''<br />
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Lysozyme contains four <scene name='Sandbox_39/Disulfide_bonds/1'>disulfide bonds</scene> involving eight cysteine residues, which are highlighted in yellow on the left. Disulfide bonds are intramolecular forces that stabilize the tertiary structure of many proteins. Disulfide bonds are present in four locations in lysozyme: between Cys 6 and Cys 127, between Cys 30 and Cys 115, between Cys 64 and Cys 80 and between Cys 76 and Cys 94. <br />
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'''Hydrogen Bonding''' <br />
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In all proteins <scene name='Sandbox_39/Hydrogen_bonds/2'>hydrogen bonds</scene> are essential for stability. In this ribbon diagram, the hydrogen bonds can be seen between the secondary structures of lysozyme highlighted in orange. Since the double bonds of the alpha carbons in the main chain of lysozyme cause torsional strain, lysozyme is limited to very specific hydrogen bonding between the amino acid residues. This representation clearly shows how crucial hydrogen bonding is to help maintain the stability of the protein. <br />
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<applet load='1hew' size='350' frame='true' align='left' caption='' /><br />
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= Intermolecular Interactions =<br />
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'''Hydrophobicity'''<br />
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Lysozyme contains both hydrophobic and hydrophilic regions ( <scene name='Sandbox_39/Hydrophobicity/2'>Hydrophobicity</scene> ). The hydrophilic effect, or the desire for proteins to be at a specific position regarding water, is the single most important determinant of protein folding. These regions can be displayed with the hydrophobic regions in gray and the polar, hydrophillic regions in purple. This coloration highlights the location of these regions, showing that the majority of the hydrophobic regions are inside of the protein and that the majority of the hydrophillic regions are on the outside of the protein.<br />
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'''Polarity'''<br />
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The nature of the amino acid sidechains in the lysozyme polypeptide sequence leads to regions of varying hydrophobicities and polarities of the enzyme structure. The presence of certain regions of hydrophilicity and hydrophobicity is a driving force in determining protein structure when folding. The varying polarities of the side chains influence the locations of residues in the enzyme structure. Nonpolar residues appear blue, and polar residues appear red in the following <scene name='Sandbox_38/Non_polar_blue/1'>polarity</scene> display of lysozyme. Nonpolar residues will display hydrophobic tendencies occurring mostly on the interior of the enzyme while polar residues will increase in abundance on the surface of the protein in order to increase contact with the aqueous solvent so as to satisfy their hydrophilic nature. By observing a space-filled structural depiction of <scene name='Sandbox_38/Non_polar_blu/1'>lysozyme polarity</scene> with polar molecules colored red and nonpolar molecules colored blue the influence of polarity on nucleotide arrangement and protein folding is evident, with the blue (nonpolar) regions inside the red (polar) regions. The presence of <scene name='Sandbox_39/Water/1'>water</scene> interacting with the various hydrophilic residues is depicted to further display how polarity affects structure. Water is depicted as yellow, and the polar and nonpolar regions remain their respective color.<br />
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'''Charge'''<br />
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Charges of the various regions of the lysozyme structure display a hydrophilic nature and thus also affect the location of that region of polypeptides and the overall folding of the protein. Charged regions of the protein will display hydrophilic tendencies and therefore will most often be located on the surface of the lysozyme molecule where they can interact with the aqueous solvent. Non-charged portions will display hydrophobic tendencies and be located on the interior of the molecule. The effect of various <scene name='Sandbox_38/Rb/1'>charges</scene> on protein structure can be visualized with charged molecules represented by red anionic and blue cationic regions, and uncharged regions colored in grey. This depiction of lysozyme uses a spacefill representation of lysozyme to depict <scene name='Sandbox_38/Chargeddd/1'>charges</scene>.<br />
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= Applications of Lysozyme =<br />
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Since lysozyme has been widely recognized for its antibacterial and antifungal properties, it has a wide variety of uses both in biochemical and pharmaceutical applications. In molecular biology, lysozyme is often used in the alkaline-lysis procedure for extracting and isolating plasmid DNA. It is used extensively in the pharmaceutical field for destroying gram-positive bacteria, and can be used to support already-existing immune defenses to fight bacterial infections. This enzyme is particularly important for preventing bacterial diseases in infants. Because of its antibacterial properties, lysozyme can also be used in the food industry to help prevent spoilage of foods.<br />
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= Discovery and Applications of Hen Egg-White Lysozyme=<br />
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<applet load='aln_1H6M_to_1HEW_2.pdb' size='300' frame='true' align='right' caption=' Hen Egg White (HEW) Lysozyme containing a trisaccharide of N-acetylglucosamine (NAG) bound to the active site, PDBid 1HEW' scene='User:Judy_Voet/Lysozyme/Lysozyme1/16' /><br />
Lysozyme was the first enzyme whose X-ray structure was determined <ref> PMID 5840126</ref><ref>Phillips, D. C. The hen egg white lysozyme molecule. Proc. Natl Acad. Sci. USA 57, 483-495 (1967)</ref>. This <scene name='User:Judy_Voet/Lysozyme/Lysozyme1/15'>scene </scene> shows Hen Egg White (HEW) lysozyme containing a trisaccharide of N-acetylglucosamine (NAG) bound to a cleft in the enzyme. David Phillips, who determined the structure in 1965, saw that the cleft was large enough to fit three more saccharide units. <br />
He therefore built a model extending the trisaccharide to a <br />
<scene name='User:Judy_Voet/Lysozyme/Lysozyme1_hexamer/7'>hexasaccharide</scene> that fits into the cleft, labeling the sugar subsites A-F<ref> coordinates of the model kindly provided by Louise Johnson</ref>. Alternately click on <scene name='User:Judy_Voet/Lysozyme/Lysozyme1/15'>trisaccharide</scene> and <scene name='User:Judy_Voet/Lysozyme/Lysozyme1_hexamer/7'>hexasaccharide</scene> to turn the modeled portion of the hexasaccharide on and off.<br />
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The interesting thing about the model was that the only way that the hexasaccharide would fit into the cleft was if the 4th saccharide (in subsite D) was strained into a <scene name='User:Judy_Voet/Lysozyme/Half-chair/2'>half-chair conformation</scene>. This conformation is what would be necessary for the formation of an oxocarbenium ion (oxionium ion). When the model was studied, <scene name='User:Judy_Voet/Lysozyme/Glu_35/1'>Glu 35</scene> was found to be in an ideal location to act as a general acid catalyst, 3.34 Angstroms from the bridging oxygen between the 4th and 5th saccharide units. <scene name='User:Judy_Voet/Lysozyme/Asp_52/2'>Asp 52</scene> appeared to be too far away (2.69 angstroms) in the static lysozyme structure to have formed a covalent bond with C1 of the half-chair model in the D site, and no covalent intermediate had ever been detected, so Phillips proposed that it acted as an electrostatic stabilizer of the oxonium ion (referred to as The Phillips Mechanism).<br />
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<applet load='aln_1H6M_to_1HEW_2.pdb' size='200' frame='true' align='left' caption='NAG-2-deoxy-2-fluoro-glucosyl fluoride (NAG2FGlcF) bound to Glu35Gln HEW Lysozyme PDBid 1H6M' scene='User:Judy_Voet/Lysozyme/1h6m/3'/><br />
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Then, in 2001, Stephen Withers published <scene name='User:Judy_Voet/Lysozyme/1h6m/3'>1H6M</scene>,<ref>PMID 11518970</ref> in which Glu 35 had been mutated to Gln to remove the general acid catalyst. The substrate contained NAG-2-fluoro-glucosyl fluoride (NAG2FGlcF). The fluoro group on C-1 does not require acid catalysis to be a good leaving group, and the remaining saccharide, in the absence of the acid necessary to catalyse the second step of the reaction, was demonstrated to form a <scene name='User:Judy_Voet/Lysozyme/Covalent/1'> covalent intermediate</scene>. In this <scene name='User:Judy_Voet/Lysozyme/Superposition/2'>superposition</scene> of the half chair model with 1HEW (greens) and the covalent intermediate in 1H6M (blues), note the relatively small motions of Asp 52 and C1 of the sugar ring in going from the model to the covalent intermediate. to observe the motion from the <scene name='User:Judy_Voet/Lysozyme/Asp52_halfchair/1'>half-chair</scene> to the <scene name='User:Judy_Voet/Lysozyme/Covalent/2'>covalent intermediate</scene> just toggle between the two green links. <br />
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== 3D Structures of Lysozyme ==<br />
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===Lys===<br />
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[[2x0a]], [[3iju]], [[3ijv]], [[3a8z]], [[2w1y]], [[2w1m]], [[2w1x]], [[2w1l]], [[3e3d]], [[3exd]], [[2zq3]], [[2zq4]], [[3b72]], [[3b6l]], [[2z12]], [[2z18]], [[2z19]], [[2vb1]], [[2hu3]], [[2hub]], [[2htx]], [[2hu1]], [[2yvb]], [[2epe]], [[2g4p]], [[2g4q]], [[2cgi]], [[2b5z]], [[2d4k]], [[2d91]], [[2f2n]], [[2fbb]], [[2c8o]], [[2c8p]], [[2a6u]], [[2aub]], [[2blx]], [[2bly]], [[2a7d]], [[2a7f]], [[1wtm]], [[1wtn]], [[1w6z]], [[1vdp]], [[1vdq]], [[1vds]], [[1vdt]], [[1ved]], [[1v7t]], [[1ps5]], [[2cds]], [[1lj3]], [[1lj4]], [[1lje]], [[1ljf]], [[1ljg]], [[1ljh]], [[1lji]], [[1ljj]], [[1ljk]], [[1jis]], [[1jit]], [[1jiy]], [[1jj0]], [[1jj1]], [[1jj3]], [[1iee]], [[1qio]], [[1f0w]], [[1f10]], [[1dpx]], [[1c10]], [[1qtk]], [[1lz8]], [[1lz9]], [[1bhz]], [[1bgi]], [[1bwh]], [[1bwi]], [[1bwj]], [[1bvx]], [[1hsw]], [[1hsx]], [[1lpi]], [[4lzt]], [[3lzt]], [[1aki]], [[1jpo]], [[1rfp]], [[193l]], [[194l]], [[5lym]], [[1lza]], [[3lyt]], [[4lyt]], [[5lyt]], [[6lyt]], [[2lzt]], [[1lzt]], [[1lzh]], [[2lzh]], [[7lyz]], [[1lyz]], [[2lyz]], [[3lyz]], [[4lyz]], [[5lyz]], [[6lyz]] - HEWL – chicken<BR /><br />
[[1xei]], [[1xej]], [[1xek]], [[1uco]], [[1lma]], [[4lym]] – HEWL low hydration<BR /><br />
[[1lsa]], [[1lsb]], [[1lsc]], [[1lsd]], [[1lse]], [[1lsf]], [[1lys]] – HEWL temperature influence<BR /><br />
[[2lym]], [[3lym]] – HEWL pressure influence<BR /><br />
[[132l]] – HEWL methylated<BR /><br />
[[1rcm]] – HEWL 3 S-S form<BR /><br />
[[2xbr]], [[2xbs]]- HEWL– Raman crystallography<BR /><br />
[[2zwb]], [[1io5]], [[1lzn]] - HEWL– Neutron<BR /><br />
[[1gxv]], [[1gxx]], [[1e8l]] - HEWL- NMR<BR /><br />
[[2hs7]], [[2hso]], [[2hs9]]- HEWL– Powder diffraction<BR /><br />
[[1ir7]], [[1ir8]], [[1ir9]], [[1ioq]], [[1ior]], [[1ios]], [[1iot]], [[1flq]], [[1flu]], [[1flw]], [[1fly]], [[1fn5]], [[1kxw]], [[1kxx]], [[1kxy]], [[1uia]], [[1uib]], [[1uic]], [[1uid]], [[1uie]], [[1uif]], [[1uig]], [[1uih]], [[1lsm]], [[1lsn]], [[1hel]], [[1hem]], [[1hen]], [[1heo]], [[1hep]], [[1heq]], [[1her]] – HEWL (mutant)<BR /><br />
[[1lyo]], [[2lyo]], [[3lyo]], [[4lyo]] – HEWL cross-linked<BR /><br />
[[1xft]] - tuLys – turkey - Powder diffraction<BR /><br />
[[1jse]], [[1tew]], [[135l]], [[2lz2]], [[1lz2]] – tuLys<BR /><br />
[[3lz2]] – tuLys - Laue<BR /><br />
[[3ab6]] – Lys + NAG3 – Hard clam<BR /><br />
[[2x8r]] – Lys GH25 – ''Aspergillus fumigatus''<BR /><br />
[[3mgw]] – Lys G – Atlantic salmon<BR /><br />
[[3gxk]], [[3gxr]] – Lys G + NAG – Atlantic cod<BR /><br />
[[2fbd]] – HfLys 1<BR /><br />
[[3cb7]] – HfLys 2 <BR /><br />
[[2zij]], [[2zik]], [[2zil]], [[2nwd]], [[1iwt]], [[1iwu]], [[1iwv]], [[1iww]], [[1iwx]], [[1iwy]], [[1iwz]], [[1jwr]], [[1jsf]], [[1rex]], [[1lz1]] – hLys – human<BR /><br />
[[1w08]], [[1ix0]], [[1ioc]], [[1ip1]], [[1ip2]], [[1ip3]], [[1ip4]], [[1ip5]], [[1ip6]], [[1ip7]], [[1qsw]], [[1gev]], [[1gez]], [[1gf0]], [[1gf3]], [[1gf4]], [[1gf5]], [[1gf6]], [[1gf7]], [[1i1z]], [[1i20]], [[1i22]], [[1gfr]], [[1gft]], [[1gfu]], [[1gfv]], [[1gf8]], [[1gf9]], [[1gfa]], [[1gfe]], [[1gfg]], [[1gfh]], [[1gfj]], [[1gfk]], [[1inu]], [[1gdx]], [[1ge0]], [[1ge1]], [[1ge2]], [[1ge3]], [[1ge4]], [[1gdw]], [[1gaz]], [[1gb0]], [[1gb2]], [[1gb3]], [[1gb5]], [[1gb6]], [[1gb7]], [[1gb8]], [[1gb9]], [[1gbo]], [[1gbw]], [[1gbx]], [[1gby]], [[1gbz]], [[1gay]], [[1eq4]], [[1eq5]], [[1eqe]], [[1c7p]], [[1di3]], [[1di4]], [[1di5]], [[1c43]], [[1c45]], [[1c46]], [[1ckg]], [[1cj6]], [[1cj7]], [[1cj8]], [[1cj9]], [[1ckc]], [[1ckd]], [[1ckf]], [[1ckh]], [[1b5z]], [[1b70]], [[1b7q]], [[1b7r]], [[1b7s]], [[1b7l]], [[1b7m]], [[1b7n]], [[1b7p]], [[1b5u]], [[1b5v]], [[1b5w]], [[1b5x]], [[1b5y]], [[1bb3]], [[1bb4]], [[2bqa]], [[2bqb]], [[2bqc]], [[2bqd]], [[2bqe]], [[2bqf]], [[2bqg]], [[2bqh]], [[2bqi]], [[2bqj]], [[2bqk]], [[2bql]], [[2bqm]], [[2bqn]], [[2bqo]], [[2mea]], [[2meb]], [[2mec]], [[2med]], [[2mee]], [[2mef]], [[2meg]], [[2meh]], [[2mei]], [[1wqm]], [[1wqn]], [[1wqo]], [[1wqp]], [[1wqq]], [[1wqr]], [[2heb]], [[2hea]], [[2hec]], [[2hed]], [[2hee]], [[2hef]], [[1jka]], [[1jkb]], [[1jkc]], [[1jkd]], [[1loz]], [[1lyy]], [[1oua]], [[1oub]], [[1ouc]], [[1oud]], [[1oue]], [[1ouf]], [[1oug]], [[1ouh]], [[1oui]], [[1ouj]], [[207l]], [[208l ]], [[1yam]], [[1yan]], [[1yao]], [[1yap]], [[1yaq]], [[1lmt]], [[1lhh]], [[1lhi]], [[1lhj]], [[1lhk]], [[1lhl]], [[133l]], [[134l]], [[1lz4]], [[1lz5]], [[1lz6]], [[1laa]], [[1tay]], [[1tby]], [[1tcy]], [[1tdy]], [[2lhm]], [[3lhm]] – hLys (mutant)<BR /><br />
[[1iy3]], [[1iy4]] – hLys - NMR<BR /><br />
[[2z2f]] – Lys – Bovine<BR /><br />
[[2cwi]], [[1el1]], [[1qqy]] – dLys - dog<BR /><br />
[[2z2e]] – dLys (mutant) <BR /><br />
[[1i56]] – dLys – NMR<BR /><br />
[[2dqa]] – Lys – ''Tapes japonica''<BR /><br />
[[2gv0]] – Lys – Soft-shelled turtle<BR /><br />
[[1ivm]] – mLys M – NMR – mouse<BR /><br />
[[1jfx]] – Lys – ''Streptomyces coelicolor''<BR /><br />
[[1gd6]] – Lys – ''Bombyx mori''<BR /><br />
[[1jug]] – Lys – Echidna<BR /><br />
[[1dkj]] – BqLys – Bobwhite quail<BR /><br />
[[2ihl]] – Lys – Japanese quail<BR /><br />
[[1gbs]] – BsLys – Black swan<BR /><br />
[[1lmn]] – RtLys – Rainbow trout<BR /><br />
[[2eql]] – Lys – horse<BR /><br />
[[1ghl]] – phLys – pheasant<BR /><br />
[[1hhl]] – GfLys – Guinea fowl<BR /><br />
[[1lhm]] – Lys (mutant) – yeast<BR /><br />
<br />
===Lys small molecules complexes===<br />
<br />
[[3fe0]], [[2d4i]], [[2d4j]], [[1v7s]] - HEWL+ D2O<BR /><br />
[[3m3u]] – HEWL Trp fluorescence<BR /><br />
[[2xjw]] - HEWL + CO <BR /><br />
[[1hf4]], [[1lks]] – HEWL + NO3<BR /><br />
[[3a34]], [[3ems]] - HEWL + arginine<BR /><br />
[[2xth]] – cLys + inhibitor K2PtBr6<BR /><br />
[[3a90]], [[3a91]], [[3a92]], [[3a93]], [[3a94]], [[3a95]], [[3a96]], [[3kam]], [[2pc2]], [[2bpu]], [[1t3p]], [[1h87]] – HEWL + rare earth<BR /><br />
[[2d6b]], [[2hg0]], [[1vat]], [[1gwd]], [[1b2k]], [[1lkr]], [[1azf]], [[8lyz]]- HEWL+ halogen<BR /><br />
[[1vat]] - HEWL + Xe<BR /><br />
[[1n4f]] - HEWL + As<BR /><br />
[[2i6z]] - HEWL + Pt drug<BR /><br />
[[2zyp]] - HEWL + poly (allyl amine)<BR /><br />
[[2f30]], [[2f4a]] – HEWL + urea derivative<BR /><br />
[[2f4g]], [[1ykx]], [[1yky]], [[1ykz]], [[1yl0]], [[1yl1]], [[1z55]] - HEWL + alcohol<BR /><br />
[[1dpw]] – HEWL + MPD<BR /><br />
[[1lcn]] – HEWL + SCN<BR /><br />
[[2zxs]] - HEWL with glycine-amide<BR /><br />
[[2h9j]], [[2h9k]], [[1yik]], [[1yil]] - HEWL + cyclam derivative<BR /><br />
[[1b0d]] – HEWL + p-toluene-sulfonate<BR /><br />
[[2q0m]] - HEWL + tricarbonylmanganese<BR /><br />
[[2war]] – HEWL (mutant) + chitopentaose<BR /><br />
[[2h5z]] – HfLys 1 + chitotetraose – House fly<BR /><br />
[[1hnl]] – hLys + glutathione<BR /><br />
[[1dkk]] – BqLys + NO3<BR /><br />
<br />
===Lys complex with glucoside===<br />
<br />
[[3a3q]] – HEWL (mutant) + NAG<BR /><br />
[[1sf4]], [[1sf6]], [[1sf7]], [[1sfb]], [[1sfg]], [[1ja2]], [[1ja4]], [[1ja6]], [[1ja7]] – HEWL + NAG oligosaccharide – Powder diffraction<BR /><br />
[[1ubz]], [[1d6p]], [[1d6q]], [[1bb5]] – hLys (mutant) + glycoside<BR /><br />
[[1uc0]], [[1re2]], [[1rem]], [[1rey]], [[1rez]], [[1lzr]], [[1lzs]] - hLys + glycoside<BR /><br />
[[1ljn]], [[1jef]], [[1lzy]] – tuLys + glycoside<BR /><br />
[[1h6m]], [[1at5]], [[1at6]], [[1lzb]], [[1lzc]], [[1lzd]], [[1lze]], [[1lzg]], [[1hew ]]– HEWL + glycoside<BR /><br />
[[1lsy]], [[1lsz]] - HEWL (mutant) + glycoside<BR /><br />
[[1bb6]], [[1bb7]] – RtLys + glycoside<BR /><br />
[[1lmc]] – RtLys + bulgecin<BR /><br />
[[1lmo]], [[1lmp]], [[1lmq]] – RtLys + glucoside<BR /><br />
[[1lsp]] – BsLys + bulgecin <BR /><br />
[[153l]], [[154l]] – Lys +glucoside – goose<BR /><br />
<br />
===Phage Lys===<br />
<br />
[[2oe4]], [[2oe7]], [[2oe9]], [[2oea]], [[1swz]], [[1cx6]], [[1qtc]], [[1qtd]], [[1qth]], [[1qsb]], [[1qs5]], [[1qs9]], [[1qtb]], [[256l]], [[206l]], [[167l]], [[168l]], [[169l]], [[170l]], [[171l]], [[172l]], [[173l]], [[174l]], [[175l]], [[176l]], [[177l]], [[178l]], [[181l]], [[182l]], [[183l]], [[184l]], [[185l]], [[186l]], [[187l]], [[188l]], [[1nhb]], [[137l]], [[216l]], [[152l]], [[149l]], [[150l]], [[151l]], [[1lyd]], [[2lzm]] - T4Lys – Enterobacteria phage T4<BR /><br />
[[138l]] – T4Lys cross-linked<BR /><br />
[[4lzm]], [[5lzm]], [[6lzm]], [[7lzm]] – T4Lys ionic strength<BR /><br />
[[3l2x]], [[3k2r]], [[3g3v]], [[3g3w]], [[3g3x]], [[2q9d]], [[2q9e]], [[2igc]], [[2ntg]], [[2nth]], [[2ou8]], [[2ou9]], [[1zur]], [[1zwn]], [[1zyt]], [[2cuu]], [[2a4t]] – T4Lys (mutant) spin labeled<BR /><br />
[[3l64]], [[3hwl]], [[3jr6]], [[3gui]], [[3c7w]], [[3c7y]], [[3c7z]], [[3c80]], [[3c81]], [[3c82]], [[3c83]], [[3c8q]], [[3c8r]], [[3c8s]], [[3cdo]], [[3cdq]], [[3cdr]], [[3cdt]], [[3cdv]], [[3f8v]], [[3f9l]], [[3fa0]], [[3fad]], [[3fi5]], [[3dke]], [[3dmv]], [[2o4w]], [[2o79]], [[2o7a]], [[2huk]], [[2hul]], [[2hum]], [[2b7x]], [[2b6t]], [[2b6w]], [[2b6x]], [[2b6y]], [[2b6z]], [[2b70]], [[2b72]], [[2b73]], [[2b74]], [[2b75]], [[1sx7]], [[1swy]], [[1sx2]], [[1t6h]], [[1ssw]], [[1ssy]], [[1t8f]], [[1t8g]], [[1t8a]], [[1t97]], [[1p56]], [[1p5c]], [[1p2l]], [[1p2r]], [[1p36]], [[1p37]], [[1p3n]], [[1p46]], [[1p64]], [[1p6y]], [[1p7s]], [[1pqd]], [[1pqi]], [[1pqj]], [[1pqk]], [[1pqm]], [[1pqo]], [[1oyu]], [[1ks3]], [[1kw5]], [[1kw7]], [[1ky0]], [[1ky1]], [[1l0j]], [[1l0k]], [[1lw9]], [[1lwg]], [[1lwk]], [[1lpy]], [[1llh]], [[1lgu]], [[1li6]], [[1jtm]], [[1jtn]], [[1jqu]], [[1kni]], [[1g06]], [[1g07]], [[1g0g]], [[1g0j]], [[1g0k]], [[1g0l]], [[1g0m]], [[1g0p]], [[1g0q]], [[1g1v]], [[1g1w]], [[1i6s]], [[257l]], [[258l]], [[260l]], [[1epy]], [[1b6i]], [[1cu6]], [[1d9w]], [[1ctw]], [[1cu0]], [[1cu2]], [[1cu3]], [[1cu5]], [[1cv1]], [[1cv4]], [[1cv5]], [[1cv6]], [[1cvk]], [[1cx7]], [[1d2w]], [[1d2y]], [[1d3f]], [[1d3j]], [[1d3m]], [[1d3n]], [[1cv3]], [[1qt3]], [[1qt4]], [[1qt5]], [[1qt6]], [[1qt7]], [[1qt8]], [[1qtv]], [[1qtz]], [[1qud]], [[1qug]], [[1quh]], [[1quo]], [[1qsq]], [[261l]], [[262l]], [[259l]], [[220l]], [[222l]], [[223l]], [[225l]], [[226l]], [[227l]], [[228l]], [[229l]], [[235l]], [[236l]], [[237l]], [[238l]], [[239l]], [[240l]], [[241l]], [[242l]], [[243l]], [[244l]], [[245l]], [[246l]], [[247l]], [[248l]], [[249l]], [[250l]], [[251l]], [[252l]], [[253l]], [[254l]], [[255l]], [[230l]], [[231l]], [[232l]], [[233l]], [[234l]], [[209l]], [[210l]], [[211l]], [[212l]], [[213l]], [[214l]], [[215l]], [[218l]], [[219l]], [[180l]], [[195l]], [[196l]], [[197l]], [[198l]], [[199l]], [[200l]], [[190l]], [[191l]], [[192l]], [[189l]], [[155l]], [[156l]], [[157l]], [[158l]], [[159l]], [[160l]], [[161l]], [[162l]], [[163l]], [[164l]], [[165l]], [[166l]], [[129l]], [[130l]], [[131l]], [[140l]], [[141l]], [[142l]], [[143l]], [[144l]], [[145l]], [[146l]], [[147l]], [[201l]], [[205l]], [[221l]], [[224l]], [[102l]], [[103l]], [[104l]], [[107l]], [[108l]], [[109l]], [[110l]], [[111l]], [[112l]], [[113l]], [[114l]], [[115l]], [[118l]], [[119l]], [[120l]], [[122l]], [[123l]], [[125l]], [[126l]], [[127l]], [[128l]], [[1dya]], [[1dyb]], [[1dyc]], [[1dyd]], [[1dye]], [[1dyf]], [[1dyg]], [[1l00]], [[1l85]], [[1l86]], [[1l87]], [[1l88]], [[1l89]], [[1l90]], [[1l91]], [[1l92]], [[1l93]], [[1l94]], [[1l95]], [[1l96]], [[1l97]], [[1l98]], [[1l99]], [[1lye]], [[1lyf]], [[1lyg]], [[1lyh]], [[1lyi]], [[1lyj]], [[217l]], [[1tla]], [[1l77]], [[1l79]], [[1l80]], [[1l81]], [[1l82]], [[2l78]], [[1l36]], [[1l37]], [[1l38]], [[1l39]], [[1l40]], [[1l41]], [[1l42]], [[1l43]], [[1l44]], [[1l45]], [[1l46]], [[1l47]], [[1l48]], [[1l49]], [[1l50]], [[1l51]], [[1l52]], [[1l53]], [[1l54]], [[1l55]], [[1l56]], [[1l57]], [[1l58]], [[1l59]], [[1l60]], [[1l61]], [[1l62]], [[1l63]], [[1l64]], [[1l65]], [[1l66]], [[1l67]], [[1l68]], [[1l69]], [[1l70]], [[1l71]], [[1l72]], [[1l73]], [[1l74]], [[1l75]], [[1l76]], [[1l17]], [[1l18]], [[1l19]], [[1l20]], [[1l21]], [[1l22]], [[1l23]], [[1l24]], [[1l25]], [[1l26]], [[1l27]], [[1l28]], [[1l29]], [[1l30]], [[1l31]], [[1l32]], [[1l33]], [[1l34]], [[1l35]], [[3lzm]], [[1l01]], [[1l02]], [[1l03]], [[1l04]], [[1l05]], [[1l06]], [[1l07]], [[1l08]], [[1l09]], [[1l10]], [[1l11]], [[1l12]], [[1l13]], [[1l14]], [[1l15]], [[1l16]] – T4Lys (mutant)<BR /><br />
[[1c60]], [[1c61]], [[1c62]], [[1c63]], [[1c64]], [[1c65]], [[1c66]], [[1c67]], [[1c68]], [[1c69]], [[1c6a]], [[1c6b]], [[1c6c]], [[1c6d]], [[1c6e]], [[1c6f]], [[1c6g]], [[1c6h]], [[1c6i]], [[1c6j]], [[1c6k]], [[1c6l]], [[1c6m]], [[1c6n]], [[1c6p]], [[1c6q]], [[1c6t]] - T4Lys (mutant) + noble gas<BR /><br />
[[3ht6]], [[3ht7]], [[3ht8]], [[3ht9]], [[3htb]], [[3hu8]], [[3huq]], [[3guj]], [[3guk]], [[3gul]], [[3gum]], [[3gun]], [[3guo]], [[3gup]], [[3dmx]], [[3dmz]], [[3dn0]], [[3dn1]], [[3dn2]], [[3dn3]], [[3dn4]], [[3dn6]], [[3dn8]], [[3dna]], [[2rb1]], [[2ray]], [[2raz]], [[2rb0]], [[2rb2]], [[2rbn]], [[2rbo]], [[2rbq]], [[2rbr]], [[2rbs]], [[2oty]],[[2otz]], [[1owy]], [[1owz]], [[1ov5]], [[1ov7]], [[1ovh]], [[1ovj]], [[1ovk]], [[1lgw]], [[1lgx]], [[1li2]], [[1li3]], [[1l83]], [[1l84]] – T4Lys (mutant) + benzene derivative<BR /><br />
[[3htd]], [[3htf]], [[3htg]], [[3hu9]], [[3hua]], [[3huk]], [[3hh3]], [[3hh4]], [[3hh5]], [[3hh6]], [[2rbp]], [[2ou0]], [[2f2q]], [[2f32]], [[2f47]], [[1xep]] – T4Lys (mutant) + inhibitor<BR /><br />
[[148l]] - T4Lys (mutant) + glucoside<BR /><br />
[[3d3d]], [[1d9u]] – lamLys + chitohexasaccharide<BR /><br />
[[1am7]] – lamLys - Enterobacteria phage λ<BR /><br />
[[2anv]], [[2anx]] – Lys (mutant)]] - Enterobacteria phage p22<BR /><br />
[[1xjt]], [[1xju]] - Lys - Enterobacteria phage p1<BR /><br />
[[1lba]] - T7Lys - Enterobacteria phage T7<BR /><br />
<br />
===Lys protein complex===<br />
<br />
[[3m18]], [[3g3a]], [[3g3b]] - HEWL + Variable lymphocyte receptor – Marine lamprey<BR /><br />
[[3a67]], [[3a6b]], [[3a6c]], [[2yss]], [[2eiz]], [[2dqc]], [[2dqd]], [[2dqe]], [[2dqf]], [[2dqg]], [[2dqh]], [[2dqi]], [[2dqj]], [[1j1o]], [[1j1p]], [[1j1x]], [[1ic4]], [[1ic5]], [[1ic7]] – HEWL + mLys antibody HYHEL-10 (mutant)<BR /><br />
[[1xgp]], [[1xgq]], [[1xgr]], [[1xgt]], [[1xgu]] – HEWL + mLys antibody HYHEL-63 <BR /><br />
[[3d9a]], [[2eks]], [[1ua6]], [[1c08]], [[3hfm]] – HEWL + mLys antibody HYHEL-10<BR /><br />
[[1uac]] - tuLys C + mLys antibody HYHEL-10<BR /><br />
[[1yqv]], [[2iff]] – HEWL + mLys antibody HYHEL-5<BR /><br />
[[1bql]] – BqLys + mLys antibody HYHEL-5<BR /><br />
[[1ndg]] – HEWL + mLys antibody HYHEL-8<BR /><br />
[[1ndm]] – HEWL + mLys antibody HYHEL-26<BR /><br />
[[1dqj]] - HEWL + mLys antibody HYHEL-63<BR /><br />
[[1nby]], [[1nbz]] – HEWL (mutant) + mLys antibody HYHEL-63<BR /><br />
[[1g7h]], [[1g7i]], [[1g7j]], [[1g7l]], [[1g7m]], [[1kip]], [[1kiq]], [[1kir]] – HEWL + mAnti-HEWL monoclonal antibody (mutant)<BR /><br />
[[1mlc]], [[1vfb]] - HEWL + mIGG1-κ D44.1 FAB<BR /><br />
[[1a2y]] - HEWL (mutant) + mIGG1-κ D1.3 FV<BR /><br />
[[1fdl]] - HEWL + mIGG1-κ D1.3 FAB<BR /><br />
[[1jhl]] – phLys + mIGG1-κ D11.15 FV <BR /><br />
[[1fbi]] – GfLys + mIGG1 F9.13.7 FAB<BR /><br />
[[2znw]], [[2znx]] – HEWL + hSCFV10 antibody<BR /><br />
[[1bvk]] - HEWL + hAnti Lys FV antibody<BR /><br />
[[1dzb]] – tuLys + mSCFV 1F9<BR /><br />
[[1zv5]], [[1zvh]], [[1zvy]], [[1zmy]], [[1ri8]], [[1rjc]], [[1xfp]], [[1jtp]], [[1jtt]], [[1jto]], [[1mel]] - HEWL + cAntibody heavy chain domain – camel<BR /><br />
[[1op9]] - hLys C + cAntibody heavy chain domain<BR /> <br />
[[3otp]] – HEWL + EcProtease DO – ''Escherichia coli''<BR /><br />
[[3f6z]] - HEWL + MLIC – ''Pseudomonas aeruginosa''<BR /><br />
[[3eba]] – hLys C + hCABHUL6<BR /><br />
[[2qb0]], [[2qar]] – T4Lys/E80 TELSAM domain<BR /><br />
[[2i25]], [[2i26]] - HEWL +NsAntigen receptor PBLA8 variable domain – Nurse shark<BR /><br />
[[1sq2]], [[1t6v]] – HEWL +NsNew Antigen receptor variable domain<BR /><br />
[[1gpq]] – HEWL + EcInhibitor of Vertebrate Lys<BR /><br />
[[1aro]] – T7Lys + T7 RNA polymerase<BR /><br />
<br />
===Some Useful External Links===<br />
[http://en.wikipedia.org/wiki/Lysozyme Lysozyme]<br />
<br />
[http://en.wikipedia.org/wiki/Glycoside_hydrolase#Retaining_glycoside_hydrolases Retaining Glycoside Hydrolases]<br />
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===References===<br />
<references/><br />
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The rain in spain stays mainly in the plain.</div>John Ripollonehttps://proteopedia.org/index.php?title=Sandbox_51&diff=1222764Sandbox 512011-03-31T01:21:54Z<p>John Ripollone: </p>
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= Introduction =<br />
<br />
Lysozyme - also known as muramidase, or glycoside hydrolase - is a powerful enzyme of biological significance found in abundance in tears, saliva, and human milk. In humans, it is encoded in the ''LYZ'' gene. Although it is responsible for the initial digestion of starches in the mouth, it is most widely identified as a non-specific defense in gram positive bacteria and in many species of fungi. Due to its antibacterial effects, it is a strong component of the innate immune system, and is an important part of an infant's diet to ward off diarrheal diseases. Since it is a small, easily available, and highly stable protein containing only 129 amino acid residues, it has been subject to extensive research regarding its function and structure. Hen Egg White (HEW) Lysozyme is shown below.<br />
<br />
'''History'''<br />
<br />
Lysozyme is an enzyme known for its unique ability to degrade the polysaccharide architecture of many kinds of cell walls, normally for the purpose of protection against bacterial infection<ref>Lysozyme. 2010. Citizendium.org. http://en.citizendium.org/wiki/Lysozyme</ref>. Its effects were first noticed by Laschtschenko in 1909. It was officially characterized and termed “lysozyme” by Alexander Fleming, the same person credited for the accidental discovery of penicillin. <br />
The characterization of lysozyme in 1922 by Alexander Fleming was providential in that the undertaken experiment related to the discovery of lysozyme was not geared toward any knowledge of such a protein as lysozyme <ref>Lysozyme. 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. During the unrelated experiment, nasal drippings were inadvertently introduced to a petri dish containing a bacterial culture, which culture consequently exhibited the results of an as yet unknown enzymatic reaction. The observation of this unknown reaction led to further research on the components of this reaction as well as to the corresponding identification of the newfound "lysozyme." Fleming's discovery was complemented by David C. Phillips' 1965 description of the three-dimensional structure of lysozyme via a 200 pm resolution model obtained from X-ray crystallography <ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. Phillips' work was especially groundbreaking since Phillips had managed to successfully elucidate the structure of an enzyme via X-ray crystallography - a feat that had never before been accomplished<ref>Bugg, T. 1997. An Introduction to Enzyme and Coenzyme Chemistry. Blackwell Science Ltd., Oxford </ref>. Phillips' research also led to the first sufficiently described enzymatic mechanism of catalytic action <ref>1967. Proc R Soc Lond B Bio 167 (1009): 389–401.</ref>. Thus, Phillips' elucidation of the function of lysozyme led Phillips to reach a more general conclusion on the diversity of enzymatic chemical action in relation to enzymatic structure. Clearly, the findings of Phillips as well as the more general historical development of the understanding of the structure and function of lysozyme have been paramount to the more general realm of enzyme chemistry.<br />
<br />
<br />
[[Image:nag-nam2.jpg|thumb|left|350px|Lysozyme Cleavage Site]]<br />
<ref>Image from: http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm</ref> <br />
<br />
'''Function'''<br />
<br />
Lysozyme is known for damaging bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid (NAM) and N-acetyl-D-glucosamine (NAG) residues in peptidoglycan, and between N-acetyl-D-glucosamine residues in chitodextrins. In this way, lysozyme is efficient in lysing the cell walls of both bacteria and fungi. The location of cleavage for lysozyme on this architectural theme is the β(1-4) glycosidic linkage connecting the C1 carbon of NAM to the C4 carbon of NAG. <br />
<br />
The particular substrate of preference for this cleavage type is a (NAG-NAM)₃ hexasaccharide, within which substrate occurs the<br />
cleaving target glycosidic bond, NAM₄-β-O-NAG₅. The individual hexasaccharide binding units are designated A-F, with NAM₄-β-O-NAG₅ glycosidic bond cleavage preference corresponding to a D-E unit glycosidic bond cleavage preference. <br />
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<br />
= Enzymatic Activity of Lysozyme =<br />
<br />
Enzymes are designed to attract and to bind specific substrates. The active site of and lysozyme and its specific ligands are described in the following sections<br />
<br />
==Mechanistic Features==<br />
<br />
'''Zymogen of Lysozyme: Enzymatic Precursor'''<br />
<br />
Zymogens are inactive enzyme precursors. Enzymes are developed in an inactive way to prevent the enzyme from digesting the cell that produced it. This process also prevents the enzyme from becoming active in the wrong portion of the body. Lysozyme's zymogen, simply titled “pre-lysozyme,” was sequenced in 1977 by R D Palmiter, J Gagnon, L H Ericsson and K A Walsh, and has since been sequenced much more extensively. <br />
<br />
<br />
[[Image:jrip.jpg|thumb|left|350px|Mechanism of Lysozyme]]<br />
<ref>Image from: http://www.google.com/imgres?imgurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/pics-and-strucs/lysozyme-mech.gif&imgrefurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm&usg=__ormapG4XKg-tR5GrMSOdSMTV4vE=&h=603&w=801&sz=7&hl=en&start=17&zoom=1&tbnid=nvr9gvFrUILDkM:&tbnh=143&tbnw=189&prev=/images%3Fq%3DThe%2Blysozyme%2Breaction%2Bmechanism%26um%3D1%26hl%3Den%26sa%3DN%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C304&um=1&itbs=1&iact=hc&vpx=521&vpy=349&dur=448&hovh=191&hovw=254&tx=140&ty=48&ei=JQ_LTPKzLIjCsAPkzt2KDg&oei=IA_LTP74OsG78gapm-GFAQ&esq=2&page=2&ndsp=18&ved=1t:429,r:2,s:17&biw=1280&bih=647</ref><br />
<br />
'''Mechanism'''<br />
<br />
The lysozyme mechanism of action results in the hydrolysis of a glycoside (hence the familial distinction of lysozyme as a glycosylase<ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>), which corresponds to the conversion of an acetal to a hemiacetal, which reaction (general degradation of glycosidic bond to units "capped" by newly formed hydroxyl groups) necessitates acid catalysis, since the conversion of acetal to hemiacetal involves the protonation of the reactant oxygen prior to actual bond cleavage. <ref>Pratt, C.W., Voet, D., Voet, J.G. Fundamentals of Biochemistry - Life at the Molecular Level - Third Edition. Voet, Voet and Pratt, 2008.</ref>. Furthermore, the transition state obtained from this protonation is a covalent, oxonium ion, intermediate that must obtain resonance stabilization. The need for some means of acid catalysis and covalent resonance stabilization is adequately provided by the Glu 35 and Asp 52 residues of lysozyme, respectively. The reaction mechanism of lysozyme is demonstrated below. In the following image, the reaction begins at the upper left-hand side, and proceeds according to reaction arrows.<br />
<br />
As seen to the left, lysozyme works by hydrolyzing the glycosidic bond, distorting the bond between the NAM and NAG. This produces a glycosyl enzyme intermediate, which reacts with a water molecule to produce the product and the unchanged enzyme.<br />
<br />
'''Active Site'''<br />
<br />
The <scene name='Sandbox_39/Active_site/1'>active site</scene> of lysozyme is formulated as a prominent cleft outlined by the two aforementioned catalytic amino acids, Glu 35 and Asp 52. The active site is geometrically bent to augment ligand binding, and the two amino acids interact with the ligand in the binding site. Asp52 is depicted in green, and Glu35 is depicted in purple. <br />
<br />
<applet load='1hew' size='350' frame='true' align='right' caption='' /><br />
<br />
==Binding==<br />
'''Ligands''' <br />
<br />
A <scene name='Sandbox_39/Ligands_1/1'>ligand</scene> is able to bind to the active site of an enzyme to form a biologically relevant complex. The model to the right shows a space-filling model of lysozyme with the protein distinguishable in brown and the ligand distinguishable in green. Another model of the ligand can be seen in this <br />
<scene name='Sandbox_39/Ribbon_ligand/1'>ribbon diagram</scene>, with the ligand protruding as a space-filling model from the active site. Here, it is clear that the ligand is a polysaccharide. <br />
<br />
The lysozyme reaction is characterized by hydrolysis of the beta (1-4) glycosidic bond between NAM and NAG. Lysozyme has a very specific active site, which can bind only six sugar rings from a polysaccharide chain. Once lysozyme binds to this chain, it hydrolyzes them. These six sugar rings represent the ligand of lysozyme. The lysozyme then distorts the fourth sugar in the six-membered complex, producing stress on the molecule and breaking the glycosidic bond.<br />
<br />
The amino acid side-chains Glu35 and Asp52 are critical to the activity of this enzyme. Glu35 acts as a proton donor to the glycosidic bond, cleaving the C-O bond in the substrate, and Asp52 acts as a nucleophile to generate a glycosyl enzyme intermediate. The glycosyl enzyme intermediate then reacts with a water molecule to give the product of hydrolysis. <br />
<br />
<br />
'''Inhibitors''' <br />
<br />
Lysozyme is best inhibited by small saccharides which act competitively with the natural substrate. The smaller saccharides will bind to the first three binding sites of the cleft (sites A-C), but will not reach sites D and E, where the enzyme cuts the glycosidic bond. So, the competitive inhibitor will stick in the cleft, not allowing the substrate to bind to the enzyme complex.<ref>http://mcdb-webarchive.mcdb.ucsb.edu/sears/biochemistry/tw-enz/lysozyme/HEWL/lysozyme-overview.htm</ref> Several known inhibitors of lysozyme are: SDS, N-acetyl-D-glucosamine, and various alcohols and oxidizing agents.<ref>http://www.worthington-biochem.com/ly/default.html</ref> <br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='left' caption='' /><br />
<br />
= Composition and Structure of Lysozyme =<br />
<br />
All proteins consist of carbon, hydrogen, nitrogen, oxygen, and sulfur, as do most organic molecules. Enzymes are composed in such a way as to maximize their reactivity with their desired substrate, increasing the efficiency of biological reactions. The <scene name='Sandbox_39/Elements/1'>composition of lysozyme</scene> can be seen on the left, with the carbon atoms outlined in gray, oxygen atoms in red, nitrogen atoms in blue, sulfur atoms in yellow, and the three-letter abbreviation for the <scene name='Sandbox_39/Amino_acid_residues/1'>amino acid residues</scene> in purple.<br />
<br />
Lysozyme, like all proteins, also contains a <scene name='Sandbox_39/C_and_n_terminal_residues/1'> 3'C and 5'N terminal </scene>, and these can be seen by following the colors of the rainbow across the molecule. Starting at the red end, the 3' C terminal end, one can work the entire way through to the 5' N terminal end, showing the folding pattern and chain of the protein.<br />
<br />
== Secondary Structure ==<br />
<br />
Lysozyme contains five <scene name='Sandbox_38/A/2'>alpha helical</scene> regions and five regions containing <scene name='Sandbox_38/B/1'>beta sheets</scene> as displayed in this <scene name='Sandbox_38/Alphab/1'>image</scene>. Linking these secondary structures, a number of beta turns and a large number of random coils make up the remainder of the polypeptide backbone. The polypeptide backbone of lysozyme involved in the 3 antiparallel beta sheets display the beta hairpin motif of supersecondary structure. This depiction of lysozyme contains an antiparallel beta-pleated sheet, which contributes greatly to the stability of the molecule by providing the correct alignment of hydrogen bonds. Lysozyme also contains a great deal of random coil, which is seen in the white regions of the molecule.<br />
<br />
<br />
<br />
<br />
<br />
==Amino Acid Residues==<br />
<br />
The amino acids present in the lysozyme polypeptide sequence have a direct influence not only on primary structure, but also on the secondary and tertiary structures, which can be influenced by polarity and charge of the sidechains. The various amino acid <scene name='Sandbox_38/Aminoi/1'>residues</scene> differ in their properties because of the great variety of side chains present on each amino acid. Polar and nonpolar (and charged and uncharged) side chains lead to various degrees of hydrophobicity and hydrophilicity, which affects protein folding. In lysozyme, these <scene name='Sandbox_38/Sc/1'>side chains</scene> are displayed for each amino acid residue.<br />
<br />
= Bonding Interactions =<br />
<br />
'''Disulfide Bonding in Lysozyme'''<br />
<br />
Lysozyme contains four <scene name='Sandbox_39/Disulfide_bonds/1'>disulfide bonds</scene> involving eight cysteine residues, which are highlighted in yellow on the left. Disulfide bonds are intramolecular forces that stabilize the tertiary structure of many proteins. Disulfide bonds are present in four locations in lysozyme: between Cys 6 and Cys 127, between Cys 30 and Cys 115, between Cys 64 and Cys 80 and between Cys 76 and Cys 94. <br />
<br />
'''Hydrogen Bonding''' <br />
<br />
In all proteins <scene name='Sandbox_39/Hydrogen_bonds/2'>hydrogen bonds</scene> are essential for stability. In this ribbon diagram, the hydrogen bonds can be seen between the secondary structures of lysozyme highlighted in orange. Since the double bonds of the alpha carbons in the main chain of lysozyme cause torsional strain, lysozyme is limited to very specific hydrogen bonding between the amino acid residues. This representation clearly shows how crucial hydrogen bonding is to help maintain the stability of the protein. <br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='left' caption='' /><br />
<br />
= Intermolecular Interactions =<br />
<br />
'''Hydrophobicity'''<br />
<br />
Lysozyme contains both hydrophobic and hydrophilic regions ( <scene name='Sandbox_39/Hydrophobicity/2'>Hydrophobicity</scene> ). The hydrophilic effect, or the desire for proteins to be at a specific position regarding water, is the single most important determinant of protein folding. These regions can be displayed with the hydrophobic regions in gray and the polar, hydrophillic regions in purple. This coloration highlights the location of these regions, showing that the majority of the hydrophobic regions are inside of the protein and that the majority of the hydrophillic regions are on the outside of the protein.<br />
<br />
<br />
'''Polarity'''<br />
<br />
The nature of the amino acid sidechains in the lysozyme polypeptide sequence leads to regions of varying hydrophobicities and polarities of the enzyme structure. The presence of certain regions of hydrophilicity and hydrophobicity is a driving force in determining protein structure when folding. The varying polarities of the side chains influence the locations of residues in the enzyme structure. Nonpolar residues appear blue, and polar residues appear red in the following <scene name='Sandbox_38/Non_polar_blue/1'>polarity</scene> display of lysozyme. Nonpolar residues will display hydrophobic tendencies occurring mostly on the interior of the enzyme while polar residues will increase in abundance on the surface of the protein in order to increase contact with the aqueous solvent so as to satisfy their hydrophilic nature. By observing a space-filled structural depiction of <scene name='Sandbox_38/Non_polar_blu/1'>lysozyme polarity</scene> with polar molecules colored red and nonpolar molecules colored blue the influence of polarity on nucleotide arrangement and protein folding is evident, with the blue (nonpolar) regions inside the red (polar) regions. The presence of <scene name='Sandbox_39/Water/1'>water</scene> interacting with the various hydrophilic residues is depicted to further display how polarity affects structure. Water is depicted as yellow, and the polar and nonpolar regions remain their respective color.<br />
<br />
<br />
'''Charge'''<br />
<br />
Charges of the various regions of the lysozyme structure display a hydrophilic nature and thus also affect the location of that region of polypeptides and the overall folding of the protein. Charged regions of the protein will display hydrophilic tendencies and therefore will most often be located on the surface of the lysozyme molecule where they can interact with the aqueous solvent. Non-charged portions will display hydrophobic tendencies and be located on the interior of the molecule. The effect of various <scene name='Sandbox_38/Rb/1'>charges</scene> on protein structure can be visualized with charged molecules represented by red anionic and blue cationic regions, and uncharged regions colored in grey. This depiction of lysozyme uses a spacefill representation of lysozyme to depict <scene name='Sandbox_38/Chargeddd/1'>charges</scene>.<br />
<br />
= Applications of Lysozyme =<br />
<br />
Since lysozyme has been widely recognized for its antibacterial and antifungal properties, it has a wide variety of uses both in biochemical and pharmaceutical applications. In molecular biology, lysozyme is often used in the alkaline-lysis procedure for extracting and isolating plasmid DNA. It is used extensively in the pharmaceutical field for destroying gram-positive bacteria, and can be used to support already-existing immune defenses to fight bacterial infections. This enzyme is particularly important for preventing bacterial diseases in infants. Because of its antibacterial properties, lysozyme can also be used in the food industry to help prevent spoilage of foods.<br />
<br />
= References =<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Sandbox_51&diff=1222763Sandbox 512011-03-31T01:21:24Z<p>John Ripollone: </p>
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<br />
= Introduction =<br />
<br />
Lysozyme - also known as muramidase, or glycoside hydrolase - is a powerful enzyme of biological significance found in abundance in tears, saliva, and human milk. In humans, it is encoded in the ''LYZ'' gene. Although it is responsible for the initial digestion of starches in the mouth, it is most widely identified as a non-specific defense in gram positive bacteria and in many species of fungi. Due to its antibacterial effects, it is a strong component of the innate immune system, and is an important part of an infant's diet to ward off diarrheal diseases. Since it is a small, easily available, and highly stable protein containing only 129 amino acid residues, it has been subject to extensive research regarding its function and structure. Hen Egg White (HEW) Lysozyme is shown below.<br />
<br />
'''History'''<br />
<br />
Lysozyme is an enzyme known for its unique ability to degrade the polysaccharide architecture of many kinds of cell walls, normally for the purpose of protection against bacterial infection<ref>Lysozyme. 2010. Citizendium.org. http://en.citizendium.org/wiki/Lysozyme</ref>. Its effects were first noticed by Laschtschenko in 1909. It was officially characterized and termed “lysozyme” by Alexander Fleming, the same person credited for the accidental discovery of penicillin. <br />
The characterization of lysozyme in 1922 by Alexander Fleming was providential in that the undertaken experiment related to the discovery of lysozyme was not geared toward any knowledge of such a protein as lysozyme <ref>Lysozyme. 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. During the unrelated experiment, nasal drippings were inadvertently introduced to a petri dish containing a bacterial culture, which culture consequently exhibited the results of an as yet unknown enzymatic reaction. The observation of this unknown reaction led to further research on the components of this reaction as well as to the corresponding identification of the newfound "lysozyme." Fleming's discovery was complemented by David C. Phillips' 1965 description of the three-dimensional structure of lysozyme via a 200 pm resolution model obtained from X-ray crystallography <ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. Phillips' work was especially groundbreaking since Phillips had managed to successfully elucidate the structure of an enzyme via X-ray crystallography - a feat that had never before been accomplished<ref>Bugg, T. 1997. An Introduction to Enzyme and Coenzyme Chemistry. Blackwell Science Ltd., Oxford </ref>. Phillips' research also led to the first sufficiently described enzymatic mechanism of catalytic action <ref>1967. Proc R Soc Lond B Bio 167 (1009): 389–401.</ref>. Thus, Phillips' elucidation of the function of lysozyme led Phillips to reach a more general conclusion on the diversity of enzymatic chemical action in relation to enzymatic structure. Clearly, the findings of Phillips as well as the more general historical development of the understanding of the structure and function of lysozyme have been paramount to the more general realm of enzyme chemistry.<br />
<br />
<br />
[[Image:nag-nam2.jpg|thumb|left|350px|Lysozyme Cleavage Site]]<br />
<ref>Image from: http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm</ref> <br />
<br />
'''Function'''<br />
<br />
Lysozyme is known for damaging bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid (NAM) and N-acetyl-D-glucosamine (NAG) residues in peptidoglycan, and between N-acetyl-D-glucosamine residues in chitodextrins. In this way, lysozyme is efficient in lysing the cell walls of both bacteria and fungi. The location of cleavage for lysozyme on this architectural theme is the β(1-4) glycosidic linkage connecting the C1 carbon of NAM to the C4 carbon of NAG. <br />
<br />
The particular substrate of preference for this cleavage type is a (NAG-NAM)₃ hexasaccharide, within which substrate occurs the<br />
cleaving target glycosidic bond, NAM₄-β-O-NAG₅. The individual hexasaccharide binding units are designated A-F, with NAM₄-β-O-NAG₅ glycosidic bond cleavage preference corresponding to a D-E unit glycosidic bond cleavage preference. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
= Enzymatic Activity of Lysozyme =<br />
<br />
Enzymes are designed to attract and to bind specific substrates. The active site of and lysozyme and its specific ligands are described in the following sections<br />
<br />
==Mechanistic Features==<br />
<br />
'''Zymogen of Lysozyme: Enzymatic Precursor'''<br />
<br />
Zymogens are inactive enzyme precursors. Enzymes are developed in an inactive way to prevent the enzyme from digesting the cell that produced it. This process also prevents the enzyme from becoming active in the wrong portion of the body. Lysozyme's zymogen, simply titled “pre-lysozyme,” was sequenced in 1977 by R D Palmiter, J Gagnon, L H Ericsson and K A Walsh, and has since been sequenced much more extensively. <br />
<br />
<br />
[[Image:jrip.jpg|thumb|left|350px|Mechanism of Lysozyme]]<br />
<ref>Image from: http://www.google.com/imgres?imgurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/pics-and-strucs/lysozyme-mech.gif&imgrefurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm&usg=__ormapG4XKg-tR5GrMSOdSMTV4vE=&h=603&w=801&sz=7&hl=en&start=17&zoom=1&tbnid=nvr9gvFrUILDkM:&tbnh=143&tbnw=189&prev=/images%3Fq%3DThe%2Blysozyme%2Breaction%2Bmechanism%26um%3D1%26hl%3Den%26sa%3DN%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C304&um=1&itbs=1&iact=hc&vpx=521&vpy=349&dur=448&hovh=191&hovw=254&tx=140&ty=48&ei=JQ_LTPKzLIjCsAPkzt2KDg&oei=IA_LTP74OsG78gapm-GFAQ&esq=2&page=2&ndsp=18&ved=1t:429,r:2,s:17&biw=1280&bih=647</ref><br />
<br />
'''Mechanism'''<br />
<br />
The lysozyme mechanism of action results in the hydrolysis of a glycoside (hence the familial distinction of lysozyme as a glycosylase<ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>), which corresponds to the conversion of an acetal to a hemiacetal, which reaction (general degradation of glycosidic bond to units "capped" by newly formed hydroxyl groups) necessitates acid catalysis, since the conversion of acetal to hemiacetal involves the protonation of the reactant oxygen prior to actual bond cleavage. <ref>Pratt, C.W., Voet, D., Voet, J.G. Fundamentals of Biochemistry - Life at the Molecular Level - Third Edition. Voet, Voet and Pratt, 2008.</ref>. Furthermore, the transition state obtained from this protonation is a covalent, oxonium ion, intermediate that must obtain resonance stabilization. The need for some means of acid catalysis and covalent resonance stabilization is adequately provided by the Glu 35 and Asp 52 residues of lysozyme, respectively. The reaction mechanism of lysozyme is demonstrated below. In the following image, the reaction begins at the upper left-hand side, and proceeds according to reaction arrows.<br />
<br />
As seen to the left, lysozyme works by hydrolyzing the glycosidic bond, distorting the bond between the NAM and NAG. This produces a glycosyl enzyme intermediate, which reacts with a water molecule to produce the product and the unchanged enzyme.<br />
<br />
'''Active Site'''<br />
<br />
The <scene name='Sandbox_39/Active_site/1'>active site</scene> of lysozyme is formulated as a prominent cleft outlined by the two aforementioned catalytic amino acids, Glu 35 and Asp 52. The active site is geometrically bent to augment ligand binding, and the two amino acids interact with the ligand in the binding site. Asp52 is depicted in green, and Glu35 is depicted in purple. <br />
<br />
<applet load='1hew' size='350' frame='true' align='right' caption='' /><br />
<br />
==Binding==<br />
'''Ligands''' <br />
<br />
A <scene name='Sandbox_39/Ligands_1/1'>ligand</scene> is able to bind to the active site of an enzyme to form a biologically relevant complex. The model to the right shows a space-filling model of lysozyme with the protein distinguishable in brown and the ligand distinguishable in green. Another model of the ligand can be seen in this <br />
<scene name='Sandbox_39/Ribbon_ligand/1'>ribbon diagram</scene>, with the ligand protruding as a space-filling model from the active site. Here, it is clear that the ligand is a polysaccharide. <br />
<br />
The lysozyme reaction is characterized by hydrolysis of the beta (1-4) glycosidic bond between NAM and NAG. Lysozyme has a very specific active site, which can bind only six sugar rings from a polysaccharide chain. Once lysozyme binds to this chain, it hydrolyzes them. These six sugar rings represent the ligand of lysozyme. The lysozyme then distorts the fourth sugar in the six-membered complex, producing stress on the molecule and breaking the glycosidic bond.<br />
<br />
The amino acid side-chains Glu35 and Asp52 are critical to the activity of this enzyme. Glu35 acts as a proton donor to the glycosidic bond, cleaving the C-O bond in the substrate, and Asp52 acts as a nucleophile to generate a glycosyl enzyme intermediate. The glycosyl enzyme intermediate then reacts with a water molecule to give the product of hydrolysis. <br />
<br />
<br />
'''Inhibitors''' <br />
<br />
Lysozyme is best inhibited by small saccharides which act competitively with the natural substrate. The smaller saccharides will bind to the first three binding sites of the cleft (sites A-C), but will not reach sites D and E, where the enzyme cuts the glycosidic bond. So, the competitive inhibitor will stick in the cleft, not allowing the substrate to bind to the enzyme complex.<ref>http://mcdb-webarchive.mcdb.ucsb.edu/sears/biochemistry/tw-enz/lysozyme/HEWL/lysozyme-overview.htm</ref> Several known inhibitors of lysozyme are: SDS, N-acetyl-D-glucosamine, and various alcohols and oxidizing agents.<ref>http://www.worthington-biochem.com/ly/default.html</ref> <br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='left' caption='' /><br />
<br />
= Composition and Structure of Lysozyme =<br />
<br />
All proteins consist of carbon, hydrogen, nitrogen, oxygen, and sulfur, as do most organic molecules. Enzymes are composed in such a way as to maximize their reactivity with their desired substrate, increasing the efficiency of biological reactions. The <scene name='Sandbox_39/Elements/1'>composition of lysozyme</scene> can be seen on the left, with the carbon atoms outlined in gray, oxygen atoms in red, nitrogen atoms in blue, sulfur atoms in yellow, and the three-letter abbreviation for the <scene name='Sandbox_39/Amino_acid_residues/1'>amino acid residues</scene> in purple.<br />
<br />
Lysozyme, like all proteins, also contains a <scene name='Sandbox_39/C_and_n_terminal_residues/1'> 3'C and 5'N terminal </scene>, and these can be seen by following the colors of the rainbow across the molecule. Starting at the red end, the 3' C terminal end, one can work the entire way through to the 5' N terminal end, showing the folding pattern and chain of the protein.<br />
<br />
== Secondary Structure ==<br />
<br />
Lysozyme contains five <scene name='Sandbox_38/A/2'>alpha helical</scene> regions and five regions containing <scene name='Sandbox_38/B/1'>beta sheets</scene> as displayed in this <scene name='Sandbox_38/Alphab/1'>image</scene>. Linking these secondary structures, a number of beta turns and a large number of random coils make up the remainder of the polypeptide backbone. The polypeptide backbone of lysozyme involved in the 3 antiparallel beta sheets display the beta hairpin motif of supersecondary structure. This depiction of lysozyme contains an antiparallel beta-pleated sheet, which contributes greatly to the stability of the molecule by providing the correct alignment of hydrogen bonds. Lysozyme also contains a great deal of random coil, which is seen in the white regions of the molecule.<br />
<br />
<br />
<br />
<br />
<br />
==Amino Acid Residues==<br />
<br />
The amino acids present in the lysozyme polypeptide sequence have a direct influence not only on primary structure, but also on the secondary and tertiary structures, which can be influenced by polarity and charge of the sidechains. The various amino acid <scene name='Sandbox_38/Aminoi/1'>residues</scene> differ in their properties because of the great variety of side chains present on each amino acid. Polar and nonpolar (and charged and uncharged) side chains lead to various degrees of hydrophobicity and hydrophilicity, which affects protein folding. In lysozyme, these <scene name='Sandbox_38/Sc/1'>side chains</scene> are displayed for each amino acid residue.<br />
<br />
= Bonding Interactions =<br />
<br />
'''Disulfide Bonding in Lysozyme'''<br />
<br />
Lysozyme contains four <scene name='Sandbox_39/Disulfide_bonds/1'>disulfide bonds</scene> involving eight cysteine residues, which are highlighted in yellow on the left. Disulfide bonds are intramolecular forces that stabilize the tertiary structure of many proteins. Disulfide bonds are present in four locations in lysozyme: between Cys 6 and Cys 127, between Cys 30 and Cys 115, between Cys 64 and Cys 80 and between Cys 76 and Cys 94. <br />
<br />
'''Hydrogen Bonding''' <br />
<br />
In all proteins <scene name='Sandbox_39/Hydrogen_bonds/2'>hydrogen bonds</scene> are essential for stability. In this ribbon diagram, the hydrogen bonds can be seen between the secondary structures of lysozyme highlighted in orange. Since the double bonds of the alpha carbons in the main chain of lysozyme cause torsional strain, lysozyme is limited to very specific hydrogen bonding between the amino acid residues. This representation clearly shows how crucial hydrogen bonding is to help maintain the stability of the protein. <br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='left' caption='' /><br />
<br />
= Intermolecular Interactions =<br />
<br />
'''Hydrophobicity'''<br />
<br />
Lysozyme contains both hydrophobic and hydrophilic regions ( <scene name='Sandbox_39/Hydrophobicity/2'>Hydrophobicity</scene> ). The hydrophilic effect, or the desire for proteins to be at a specific position regarding water, is the single most important determinant of protein folding. These regions can be displayed with the hydrophobic regions in gray and the polar, hydrophillic regions in purple. This coloration highlights the location of these regions, showing that the majority of the hydrophobic regions are inside of the protein and that the majority of the hydrophillic regions are on the outside of the protein.<br />
<br />
<br />
'''Polarity'''<br />
<br />
The nature of the amino acid sidechains in the lysozyme polypeptide sequence leads to regions of varying hydrophobicities and polarities of the enzyme structure. The presence of certain regions of hydrophilicity and hydrophobicity is a driving force in determining protein structure when folding. The varying polarities of the side chains influence the locations of residues in the enzyme structure. Nonpolar residues appear blue, and polar residues appear red in the following <scene name='Sandbox_38/Non_polar_blue/1'>polarity</scene> display of lysozyme. Nonpolar residues will display hydrophobic tendencies occurring mostly on the interior of the enzyme while polar residues will increase in abundance on the surface of the protein in order to increase contact with the aqueous solvent so as to satisfy their hydrophilic nature. By observing a space-filled structural depiction of <scene name='Sandbox_38/Non_polar_blu/1'>lysozyme polarity</scene> with polar molecules colored red and nonpolar molecules colored blue the influence of polarity on nucleotide arrangement and protein folding is evident, with the blue (nonpolar) regions inside the red (polar) regions. The presence of <scene name='Sandbox_39/Water/1'>water</scene> interacting with the various hydrophilic residues is depicted to further display how polarity affects structure. Water is depicted as yellow, and the polar and nonpolar regions remain their respective color.<br />
<br />
<br />
'''Charge'''<br />
<br />
Charges of the various regions of the lysozyme structure display a hydrophilic nature and thus also affect the location of that region of polypeptides and the overall folding of the protein. Charged regions of the protein will display hydrophilic tendencies and therefore will most often be located on the surface of the lysozyme molecule where they can interact with the aqueous solvent. Non-charged portions will display hydrophobic tendencies and be located on the interior of the molecule. The effect of various <scene name='Sandbox_38/Rb/1'>charges</scene> on protein structure can be visualized with charged molecules represented by red anionic and blue cationic regions, and uncharged regions colored in grey. This depiction of lysozyme uses a spacefill representation of lysozyme to depict <scene name='Sandbox_38/Chargeddd/1'>charges</scene>.<br />
<br />
<br />
<br />
= Applications of Lysozyme =<br />
<br />
Since lysozyme has been widely recognized for its antibacterial and antifungal properties, it has a wide variety of uses both in biochemical and pharmaceutical applications. In molecular biology, lysozyme is often used in the alkaline-lysis procedure for extracting and isolating plasmid DNA. It is used extensively in the pharmaceutical field for destroying gram-positive bacteria, and can be used to support already-existing immune defenses to fight bacterial infections. This enzyme is particularly important for preventing bacterial diseases in infants. Because of its antibacterial properties, lysozyme can also be used in the food industry to help prevent spoilage of foods.<br />
<br />
= References =<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Sandbox_51&diff=1222761Sandbox 512011-03-31T01:20:43Z<p>John Ripollone: </p>
<hr />
<div><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
{{Template:Oberholser_Sandbox_Reservation}}<br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
<br />
= Introduction =<br />
<br />
Lysozyme - also known as muramidase, or glycoside hydrolase - is a powerful enzyme of biological significance found in abundance in tears, saliva, and human milk. In humans, it is encoded in the ''LYZ'' gene. Although it is responsible for the initial digestion of starches in the mouth, it is most widely identified as a non-specific defense in gram positive bacteria and in many species of fungi. Due to its antibacterial effects, it is a strong component of the innate immune system, and is an important part of an infant's diet to ward off diarrheal diseases. Since it is a small, easily available, and highly stable protein containing only 129 amino acid residues, it has been subject to extensive research regarding its function and structure. Hen Egg White (HEW) Lysozyme is shown below.<br />
<br />
'''History'''<br />
<br />
Lysozyme is an enzyme known for its unique ability to degrade the polysaccharide architecture of many kinds of cell walls, normally for the purpose of protection against bacterial infection<ref>Lysozyme. 2010. Citizendium.org. http://en.citizendium.org/wiki/Lysozyme</ref>. Its effects were first noticed by Laschtschenko in 1909. It was officially characterized and termed “lysozyme” by Alexander Fleming, the same person credited for the accidental discovery of penicillin. <br />
The characterization of lysozyme in 1922 by Alexander Fleming was providential in that the undertaken experiment related to the discovery of lysozyme was not geared toward any knowledge of such a protein as lysozyme <ref>Lysozyme. 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. During the unrelated experiment, nasal drippings were inadvertently introduced to a petri dish containing a bacterial culture, which culture consequently exhibited the results of an as yet unknown enzymatic reaction. The observation of this unknown reaction led to further research on the components of this reaction as well as to the corresponding identification of the newfound "lysozyme." Fleming's discovery was complemented by David C. Phillips' 1965 description of the three-dimensional structure of lysozyme via a 200 pm resolution model obtained from X-ray crystallography <ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. Phillips' work was especially groundbreaking since Phillips had managed to successfully elucidate the structure of an enzyme via X-ray crystallography - a feat that had never before been accomplished<ref>Bugg, T. 1997. An Introduction to Enzyme and Coenzyme Chemistry. Blackwell Science Ltd., Oxford </ref>. Phillips' research also led to the first sufficiently described enzymatic mechanism of catalytic action <ref>1967. Proc R Soc Lond B Bio 167 (1009): 389–401.</ref>. Thus, Phillips' elucidation of the function of lysozyme led Phillips to reach a more general conclusion on the diversity of enzymatic chemical action in relation to enzymatic structure. Clearly, the findings of Phillips as well as the more general historical development of the understanding of the structure and function of lysozyme have been paramount to the more general realm of enzyme chemistry.<br />
<br />
<br />
[[Image:nag-nam2.jpg|thumb|left|350px|Lysozyme Cleavage Site]]<br />
<ref>Image from: http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm</ref> <br />
<br />
'''Function'''<br />
<br />
Lysozyme is known for damaging bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid (NAM) and N-acetyl-D-glucosamine (NAG) residues in peptidoglycan, and between N-acetyl-D-glucosamine residues in chitodextrins. In this way, lysozyme is efficient in lysing the cell walls of both bacteria and fungi. The location of cleavage for lysozyme on this architectural theme is the β(1-4) glycosidic linkage connecting the C1 carbon of NAM to the C4 carbon of NAG. <br />
<br />
The particular substrate of preference for this cleavage type is a (NAG-NAM)₃ hexasaccharide, within which substrate occurs the<br />
cleaving target glycosidic bond, NAM₄-β-O-NAG₅. The individual hexasaccharide binding units are designated A-F, with NAM₄-β-O-NAG₅ glycosidic bond cleavage preference corresponding to a D-E unit glycosidic bond cleavage preference. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
= Enzymatic Activity of Lysozyme =<br />
<br />
Enzymes are designed to attract and to bind specific substrates. The active site of and lysozyme and its specific ligands are described in the following sections<br />
<br />
==Mechanistic Features==<br />
<br />
'''Zymogen of Lysozyme: Enzymatic Precursor'''<br />
<br />
Zymogens are inactive enzyme precursors. Enzymes are developed in an inactive way to prevent the enzyme from digesting the cell that produced it. This process also prevents the enzyme from becoming active in the wrong portion of the body. Lysozyme's zymogen, simply titled “pre-lysozyme,” was sequenced in 1977 by R D Palmiter, J Gagnon, L H Ericsson and K A Walsh, and has since been sequenced much more extensively. <br />
<br />
<br />
[[Image:jrip.jpg|thumb|left|350px|Mechanism of Lysozyme]]<br />
<ref>Image from: http://www.google.com/imgres?imgurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/pics-and-strucs/lysozyme-mech.gif&imgrefurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm&usg=__ormapG4XKg-tR5GrMSOdSMTV4vE=&h=603&w=801&sz=7&hl=en&start=17&zoom=1&tbnid=nvr9gvFrUILDkM:&tbnh=143&tbnw=189&prev=/images%3Fq%3DThe%2Blysozyme%2Breaction%2Bmechanism%26um%3D1%26hl%3Den%26sa%3DN%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C304&um=1&itbs=1&iact=hc&vpx=521&vpy=349&dur=448&hovh=191&hovw=254&tx=140&ty=48&ei=JQ_LTPKzLIjCsAPkzt2KDg&oei=IA_LTP74OsG78gapm-GFAQ&esq=2&page=2&ndsp=18&ved=1t:429,r:2,s:17&biw=1280&bih=647</ref><br />
<br />
'''Mechanism'''<br />
<br />
The lysozyme mechanism of action results in the hydrolysis of a glycoside (hence the familial distinction of lysozyme as a glycosylase<ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>), which corresponds to the conversion of an acetal to a hemiacetal, which reaction (general degradation of glycosidic bond to units "capped" by newly formed hydroxyl groups) necessitates acid catalysis, since the conversion of acetal to hemiacetal involves the protonation of the reactant oxygen prior to actual bond cleavage. <ref>Pratt, C.W., Voet, D., Voet, J.G. Fundamentals of Biochemistry - Life at the Molecular Level - Third Edition. Voet, Voet and Pratt, 2008.</ref>. Furthermore, the transition state obtained from this protonation is a covalent, oxonium ion, intermediate that must obtain resonance stabilization. The need for some means of acid catalysis and covalent resonance stabilization is adequately provided by the Glu 35 and Asp 52 residues of lysozyme, respectively. The reaction mechanism of lysozyme is demonstrated below. In the following image, the reaction begins at the upper left-hand side, and proceeds according to reaction arrows.<br />
<br />
As seen to the left, lysozyme works by hydrolyzing the glycosidic bond, distorting the bond between the NAM and NAG. This produces a glycosyl enzyme intermediate, which reacts with a water molecule to produce the product and the unchanged enzyme.<br />
<br />
'''Active Site'''<br />
<br />
The <scene name='Sandbox_39/Active_site/1'>active site</scene> of lysozyme is formulated as a prominent cleft outlined by the two aforementioned catalytic amino acids, Glu 35 and Asp 52. The active site is geometrically bent to augment ligand binding, and the two amino acids interact with the ligand in the binding site. Asp52 is depicted in green, and Glu35 is depicted in purple. <br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='right' caption='' /><br />
<br />
==Binding==<br />
'''Ligands''' <br />
<br />
A <scene name='Sandbox_39/Ligands_1/1'>ligand</scene> is able to bind to the active site of an enzyme to form a biologically relevant complex. The model to the right shows a space-filling model of lysozyme with the protein distinguishable in brown and the ligand distinguishable in green. Another model of the ligand can be seen in this <br />
<scene name='Sandbox_39/Ribbon_ligand/1'>ribbon diagram</scene>, with the ligand protruding as a space-filling model from the active site. Here, it is clear that the ligand is a polysaccharide. <br />
<br />
The lysozyme reaction is characterized by hydrolysis of the beta (1-4) glycosidic bond between NAM and NAG. Lysozyme has a very specific active site, which can bind only six sugar rings from a polysaccharide chain. Once lysozyme binds to this chain, it hydrolyzes them. These six sugar rings represent the ligand of lysozyme. The lysozyme then distorts the fourth sugar in the six-membered complex, producing stress on the molecule and breaking the glycosidic bond.<br />
<br />
The amino acid side-chains Glu35 and Asp52 are critical to the activity of this enzyme. Glu35 acts as a proton donor to the glycosidic bond, cleaving the C-O bond in the substrate, and Asp52 acts as a nucleophile to generate a glycosyl enzyme intermediate. The glycosyl enzyme intermediate then reacts with a water molecule to give the product of hydrolysis. <br />
<br />
<br />
'''Inhibitors''' <br />
<br />
Lysozyme is best inhibited by small saccharides which act competitively with the natural substrate. The smaller saccharides will bind to the first three binding sites of the cleft (sites A-C), but will not reach sites D and E, where the enzyme cuts the glycosidic bond. So, the competitive inhibitor will stick in the cleft, not allowing the substrate to bind to the enzyme complex.<ref>http://mcdb-webarchive.mcdb.ucsb.edu/sears/biochemistry/tw-enz/lysozyme/HEWL/lysozyme-overview.htm</ref> Several known inhibitors of lysozyme are: SDS, N-acetyl-D-glucosamine, and various alcohols and oxidizing agents.<ref>http://www.worthington-biochem.com/ly/default.html</ref> <br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='left' caption='' /><br />
<br />
= Composition and Structure of Lysozyme =<br />
<br />
All proteins consist of carbon, hydrogen, nitrogen, oxygen, and sulfur, as do most organic molecules. Enzymes are composed in such a way as to maximize their reactivity with their desired substrate, increasing the efficiency of biological reactions. The <scene name='Sandbox_39/Elements/1'>composition of lysozyme</scene> can be seen on the left, with the carbon atoms outlined in gray, oxygen atoms in red, nitrogen atoms in blue, sulfur atoms in yellow, and the three-letter abbreviation for the <scene name='Sandbox_39/Amino_acid_residues/1'>amino acid residues</scene> in purple.<br />
<br />
Lysozyme, like all proteins, also contains a <scene name='Sandbox_39/C_and_n_terminal_residues/1'> 3'C and 5'N terminal </scene>, and these can be seen by following the colors of the rainbow across the molecule. Starting at the red end, the 3' C terminal end, one can work the entire way through to the 5' N terminal end, showing the folding pattern and chain of the protein.<br />
<br />
== Secondary Structure ==<br />
<br />
Lysozyme contains five <scene name='Sandbox_38/A/2'>alpha helical</scene> regions and five regions containing <scene name='Sandbox_38/B/1'>beta sheets</scene> as displayed in this <scene name='Sandbox_38/Alphab/1'>image</scene>. Linking these secondary structures, a number of beta turns and a large number of random coils make up the remainder of the polypeptide backbone. The polypeptide backbone of lysozyme involved in the 3 antiparallel beta sheets display the beta hairpin motif of supersecondary structure. This depiction of lysozyme contains an antiparallel beta-pleated sheet, which contributes greatly to the stability of the molecule by providing the correct alignment of hydrogen bonds. Lysozyme also contains a great deal of random coil, which is seen in the white regions of the molecule.<br />
<br />
<br />
<br />
<br />
<br />
==Amino Acid Residues==<br />
<br />
The amino acids present in the lysozyme polypeptide sequence have a direct influence not only on primary structure, but also on the secondary and tertiary structures, which can be influenced by polarity and charge of the sidechains. The various amino acid <scene name='Sandbox_38/Aminoi/1'>residues</scene> differ in their properties because of the great variety of side chains present on each amino acid. Polar and nonpolar (and charged and uncharged) side chains lead to various degrees of hydrophobicity and hydrophilicity, which affects protein folding. In lysozyme, these <scene name='Sandbox_38/Sc/1'>side chains</scene> are displayed for each amino acid residue.<br />
<br />
= Bonding Interactions =<br />
<br />
'''Disulfide Bonding in Lysozyme'''<br />
<br />
Lysozyme contains four <scene name='Sandbox_39/Disulfide_bonds/1'>disulfide bonds</scene> involving eight cysteine residues, which are highlighted in yellow on the left. Disulfide bonds are intramolecular forces that stabilize the tertiary structure of many proteins. Disulfide bonds are present in four locations in lysozyme: between Cys 6 and Cys 127, between Cys 30 and Cys 115, between Cys 64 and Cys 80 and between Cys 76 and Cys 94. <br />
<br />
'''Hydrogen Bonding''' <br />
<br />
In all proteins <scene name='Sandbox_39/Hydrogen_bonds/2'>hydrogen bonds</scene> are essential for stability. In this ribbon diagram, the hydrogen bonds can be seen between the secondary structures of lysozyme highlighted in orange. Since the double bonds of the alpha carbons in the main chain of lysozyme cause torsional strain, lysozyme is limited to very specific hydrogen bonding between the amino acid residues. This representation clearly shows how crucial hydrogen bonding is to help maintain the stability of the protein. <br />
<br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='left' caption='' /><br />
<br />
= Intermolecular Interactions =<br />
<br />
'''Hydrophobicity'''<br />
<br />
Lysozyme contains both hydrophobic and hydrophilic regions ( <scene name='Sandbox_39/Hydrophobicity/2'>Hydrophobicity</scene> ). The hydrophilic effect, or the desire for proteins to be at a specific position regarding water, is the single most important determinant of protein folding. These regions can be displayed with the hydrophobic regions in gray and the polar, hydrophillic regions in purple. This coloration highlights the location of these regions, showing that the majority of the hydrophobic regions are inside of the protein and that the majority of the hydrophillic regions are on the outside of the protein.<br />
<br />
<br />
'''Polarity'''<br />
<br />
The nature of the amino acid sidechains in the lysozyme polypeptide sequence leads to regions of varying hydrophobicities and polarities of the enzyme structure. The presence of certain regions of hydrophilicity and hydrophobicity is a driving force in determining protein structure when folding. The varying polarities of the side chains influence the locations of residues in the enzyme structure. Nonpolar residues appear blue, and polar residues appear red in the following <scene name='Sandbox_38/Non_polar_blue/1'>polarity</scene> display of lysozyme. Nonpolar residues will display hydrophobic tendencies occurring mostly on the interior of the enzyme while polar residues will increase in abundance on the surface of the protein in order to increase contact with the aqueous solvent so as to satisfy their hydrophilic nature. By observing a space-filled structural depiction of <scene name='Sandbox_38/Non_polar_blu/1'>lysozyme polarity</scene> with polar molecules colored red and nonpolar molecules colored blue the influence of polarity on nucleotide arrangement and protein folding is evident, with the blue (nonpolar) regions inside the red (polar) regions. The presence of <scene name='Sandbox_39/Water/1'>water</scene> interacting with the various hydrophilic residues is depicted to further display how polarity affects structure. Water is depicted as yellow, and the polar and nonpolar regions remain their respective color.<br />
<br />
<br />
'''Charge'''<br />
<br />
Charges of the various regions of the lysozyme structure display a hydrophilic nature and thus also affect the location of that region of polypeptides and the overall folding of the protein. Charged regions of the protein will display hydrophilic tendencies and therefore will most often be located on the surface of the lysozyme molecule where they can interact with the aqueous solvent. Non-charged portions will display hydrophobic tendencies and be located on the interior of the molecule. The effect of various <scene name='Sandbox_38/Rb/1'>charges</scene> on protein structure can be visualized with charged molecules represented by red anionic and blue cationic regions, and uncharged regions colored in grey. This depiction of lysozyme uses a spacefill representation of lysozyme to depict <scene name='Sandbox_38/Chargeddd/1'>charges</scene>.<br />
<br />
<br />
<br />
= Applications of Lysozyme =<br />
<br />
Since lysozyme has been widely recognized for its antibacterial and antifungal properties, it has a wide variety of uses both in biochemical and pharmaceutical applications. In molecular biology, lysozyme is often used in the alkaline-lysis procedure for extracting and isolating plasmid DNA. It is used extensively in the pharmaceutical field for destroying gram-positive bacteria, and can be used to support already-existing immune defenses to fight bacterial infections. This enzyme is particularly important for preventing bacterial diseases in infants. Because of its antibacterial properties, lysozyme can also be used in the food industry to help prevent spoilage of foods.<br />
<br />
= References =<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Sandbox_51&diff=1222759Sandbox 512011-03-31T01:19:59Z<p>John Ripollone: </p>
<hr />
<div><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
{{Template:Oberholser_Sandbox_Reservation}}<br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
= '''Lysozyme''' =<br />
<br />
= Introduction =<br />
<br />
Lysozyme - also known as muramidase, or glycoside hydrolase - is a powerful enzyme of biological significance found in abundance in tears, saliva, and human milk. In humans, it is encoded in the ''LYZ'' gene. Although it is responsible for the initial digestion of starches in the mouth, it is most widely identified as a non-specific defense in gram positive bacteria and in many species of fungi. Due to its antibacterial effects, it is a strong component of the innate immune system, and is an important part of an infant's diet to ward off diarrheal diseases. Since it is a small, easily available, and highly stable protein containing only 129 amino acid residues, it has been subject to extensive research regarding its function and structure. Hen Egg White (HEW) Lysozyme is shown below.<br />
<br />
'''History'''<br />
<br />
Lysozyme is an enzyme known for its unique ability to degrade the polysaccharide architecture of many kinds of cell walls, normally for the purpose of protection against bacterial infection<ref>Lysozyme. 2010. Citizendium.org. http://en.citizendium.org/wiki/Lysozyme</ref>. Its effects were first noticed by Laschtschenko in 1909. It was officially characterized and termed “lysozyme” by Alexander Fleming, the same person credited for the accidental discovery of penicillin. <br />
The characterization of lysozyme in 1922 by Alexander Fleming was providential in that the undertaken experiment related to the discovery of lysozyme was not geared toward any knowledge of such a protein as lysozyme <ref>Lysozyme. 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. During the unrelated experiment, nasal drippings were inadvertently introduced to a petri dish containing a bacterial culture, which culture consequently exhibited the results of an as yet unknown enzymatic reaction. The observation of this unknown reaction led to further research on the components of this reaction as well as to the corresponding identification of the newfound "lysozyme." Fleming's discovery was complemented by David C. Phillips' 1965 description of the three-dimensional structure of lysozyme via a 200 pm resolution model obtained from X-ray crystallography <ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. Phillips' work was especially groundbreaking since Phillips had managed to successfully elucidate the structure of an enzyme via X-ray crystallography - a feat that had never before been accomplished<ref>Bugg, T. 1997. An Introduction to Enzyme and Coenzyme Chemistry. Blackwell Science Ltd., Oxford </ref>. Phillips' research also led to the first sufficiently described enzymatic mechanism of catalytic action <ref>1967. Proc R Soc Lond B Bio 167 (1009): 389–401.</ref>. Thus, Phillips' elucidation of the function of lysozyme led Phillips to reach a more general conclusion on the diversity of enzymatic chemical action in relation to enzymatic structure. Clearly, the findings of Phillips as well as the more general historical development of the understanding of the structure and function of lysozyme have been paramount to the more general realm of enzyme chemistry.<br />
<br />
<br />
[[Image:nag-nam2.jpg|thumb|left|350px|Lysozyme Cleavage Site]]<br />
<ref>Image from: http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm</ref> <br />
<br />
'''Function'''<br />
<br />
Lysozyme is known for damaging bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid (NAM) and N-acetyl-D-glucosamine (NAG) residues in peptidoglycan, and between N-acetyl-D-glucosamine residues in chitodextrins. In this way, lysozyme is efficient in lysing the cell walls of both bacteria and fungi. The location of cleavage for lysozyme on this architectural theme is the β(1-4) glycosidic linkage connecting the C1 carbon of NAM to the C4 carbon of NAG. <br />
<br />
The particular substrate of preference for this cleavage type is a (NAG-NAM)₃ hexasaccharide, within which substrate occurs the<br />
cleaving target glycosidic bond, NAM₄-β-O-NAG₅. The individual hexasaccharide binding units are designated A-F, with NAM₄-β-O-NAG₅ glycosidic bond cleavage preference corresponding to a D-E unit glycosidic bond cleavage preference. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
= Enzymatic Activity of Lysozyme =<br />
<br />
Enzymes are designed to attract and to bind specific substrates. The active site of and lysozyme and its specific ligands are described in the following sections<br />
<br />
==Mechanistic Features==<br />
<br />
'''Zymogen of Lysozyme: Enzymatic Precursor'''<br />
<br />
Zymogens are inactive enzyme precursors. Enzymes are developed in an inactive way to prevent the enzyme from digesting the cell that produced it. This process also prevents the enzyme from becoming active in the wrong portion of the body. Lysozyme's zymogen, simply titled “pre-lysozyme,” was sequenced in 1977 by R D Palmiter, J Gagnon, L H Ericsson and K A Walsh, and has since been sequenced much more extensively. <br />
<br />
<br />
[[Image:jrip.jpg|thumb|left|350px|Mechanism of Lysozyme]]<br />
<ref>Image from: http://www.google.com/imgres?imgurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/pics-and-strucs/lysozyme-mech.gif&imgrefurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm&usg=__ormapG4XKg-tR5GrMSOdSMTV4vE=&h=603&w=801&sz=7&hl=en&start=17&zoom=1&tbnid=nvr9gvFrUILDkM:&tbnh=143&tbnw=189&prev=/images%3Fq%3DThe%2Blysozyme%2Breaction%2Bmechanism%26um%3D1%26hl%3Den%26sa%3DN%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C304&um=1&itbs=1&iact=hc&vpx=521&vpy=349&dur=448&hovh=191&hovw=254&tx=140&ty=48&ei=JQ_LTPKzLIjCsAPkzt2KDg&oei=IA_LTP74OsG78gapm-GFAQ&esq=2&page=2&ndsp=18&ved=1t:429,r:2,s:17&biw=1280&bih=647</ref><br />
<br />
'''Mechanism'''<br />
<br />
The lysozyme mechanism of action results in the hydrolysis of a glycoside (hence the familial distinction of lysozyme as a glycosylase<ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>), which corresponds to the conversion of an acetal to a hemiacetal, which reaction (general degradation of glycosidic bond to units "capped" by newly formed hydroxyl groups) necessitates acid catalysis, since the conversion of acetal to hemiacetal involves the protonation of the reactant oxygen prior to actual bond cleavage. <ref>Pratt, C.W., Voet, D., Voet, J.G. Fundamentals of Biochemistry - Life at the Molecular Level - Third Edition. Voet, Voet and Pratt, 2008.</ref>. Furthermore, the transition state obtained from this protonation is a covalent, oxonium ion, intermediate that must obtain resonance stabilization. The need for some means of acid catalysis and covalent resonance stabilization is adequately provided by the Glu 35 and Asp 52 residues of lysozyme, respectively. The reaction mechanism of lysozyme is demonstrated below. In the following image, the reaction begins at the upper left-hand side, and proceeds according to reaction arrows.<br />
<br />
As seen to the left, lysozyme works by hydrolyzing the glycosidic bond, distorting the bond between the NAM and NAG. This produces a glycosyl enzyme intermediate, which reacts with a water molecule to produce the product and the unchanged enzyme.<br />
<br />
'''Active Site'''<br />
<br />
The <scene name='Sandbox_39/Active_site/1'>active site</scene> of lysozyme is formulated as a prominent cleft outlined by the two aforementioned catalytic amino acids, Glu 35 and Asp 52. The active site is geometrically bent to augment ligand binding, and the two amino acids interact with the ligand in the binding site. Asp52 is depicted in green, and Glu35 is depicted in purple. <br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='right' caption='' /><br />
<br />
==Binding==<br />
'''Ligands''' <br />
<br />
A <scene name='Sandbox_39/Ligands_1/1'>ligand</scene> is able to bind to the active site of an enzyme to form a biologically relevant complex. The model to the right shows a space-filling model of lysozyme with the protein distinguishable in brown and the ligand distinguishable in green. Another model of the ligand can be seen in this <br />
<scene name='Sandbox_39/Ribbon_ligand/1'>ribbon diagram</scene>, with the ligand protruding as a space-filling model from the active site. Here, it is clear that the ligand is a polysaccharide. <br />
<br />
The lysozyme reaction is characterized by hydrolysis of the beta (1-4) glycosidic bond between NAM and NAG. Lysozyme has a very specific active site, which can bind only six sugar rings from a polysaccharide chain. Once lysozyme binds to this chain, it hydrolyzes them. These six sugar rings represent the ligand of lysozyme. The lysozyme then distorts the fourth sugar in the six-membered complex, producing stress on the molecule and breaking the glycosidic bond.<br />
<br />
The amino acid side-chains Glu35 and Asp52 are critical to the activity of this enzyme. Glu35 acts as a proton donor to the glycosidic bond, cleaving the C-O bond in the substrate, and Asp52 acts as a nucleophile to generate a glycosyl enzyme intermediate. The glycosyl enzyme intermediate then reacts with a water molecule to give the product of hydrolysis. <br />
<br />
<br />
'''Inhibitors''' <br />
<br />
Lysozyme is best inhibited by small saccharides which act competitively with the natural substrate. The smaller saccharides will bind to the first three binding sites of the cleft (sites A-C), but will not reach sites D and E, where the enzyme cuts the glycosidic bond. So, the competitive inhibitor will stick in the cleft, not allowing the substrate to bind to the enzyme complex.<ref>http://mcdb-webarchive.mcdb.ucsb.edu/sears/biochemistry/tw-enz/lysozyme/HEWL/lysozyme-overview.htm</ref> Several known inhibitors of lysozyme are: SDS, N-acetyl-D-glucosamine, and various alcohols and oxidizing agents.<ref>http://www.worthington-biochem.com/ly/default.html</ref> <br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='left' caption='' /><br />
<br />
= Composition and Structure of Lysozyme =<br />
<br />
All proteins consist of carbon, hydrogen, nitrogen, oxygen, and sulfur, as do most organic molecules. Enzymes are composed in such a way as to maximize their reactivity with their desired substrate, increasing the efficiency of biological reactions. The <scene name='Sandbox_39/Elements/1'>composition of lysozyme</scene> can be seen on the left, with the carbon atoms outlined in gray, oxygen atoms in red, nitrogen atoms in blue, sulfur atoms in yellow, and the three-letter abbreviation for the <scene name='Sandbox_39/Amino_acid_residues/1'>amino acid residues</scene> in purple.<br />
<br />
Lysozyme, like all proteins, also contains a <scene name='Sandbox_39/C_and_n_terminal_residues/1'> 3'C and 5'N terminal </scene>, and these can be seen by following the colors of the rainbow across the molecule. Starting at the red end, the 3' C terminal end, one can work the entire way through to the 5' N terminal end, showing the folding pattern and chain of the protein.<br />
<br />
== Secondary Structure ==<br />
<br />
Lysozyme contains five <scene name='Sandbox_38/A/2'>alpha helical</scene> regions and five regions containing <scene name='Sandbox_38/B/1'>beta sheets</scene> as displayed in this <scene name='Sandbox_38/Alphab/1'>image</scene>. Linking these secondary structures, a number of beta turns and a large number of random coils make up the remainder of the polypeptide backbone. The polypeptide backbone of lysozyme involved in the 3 antiparallel beta sheets display the beta hairpin motif of supersecondary structure. This depiction of lysozyme contains an antiparallel beta-pleated sheet, which contributes greatly to the stability of the molecule by providing the correct alignment of hydrogen bonds. Lysozyme also contains a great deal of random coil, which is seen in the white regions of the molecule.<br />
<br />
<br />
<br />
<br />
<br />
==Amino Acid Residues==<br />
<br />
The amino acids present in the lysozyme polypeptide sequence have a direct influence not only on primary structure, but also on the secondary and tertiary structures, which can be influenced by polarity and charge of the sidechains. The various amino acid <scene name='Sandbox_38/Aminoi/1'>residues</scene> differ in their properties because of the great variety of side chains present on each amino acid. Polar and nonpolar (and charged and uncharged) side chains lead to various degrees of hydrophobicity and hydrophilicity, which affects protein folding. In lysozyme, these <scene name='Sandbox_38/Sc/1'>side chains</scene> are displayed for each amino acid residue.<br />
<br />
= Bonding Interactions =<br />
<br />
'''Disulfide Bonding in Lysozyme'''<br />
<br />
Lysozyme contains four <scene name='Sandbox_39/Disulfide_bonds/1'>disulfide bonds</scene> involving eight cysteine residues, which are highlighted in yellow on the left. Disulfide bonds are intramolecular forces that stabilize the tertiary structure of many proteins. Disulfide bonds are present in four locations in lysozyme: between Cys 6 and Cys 127, between Cys 30 and Cys 115, between Cys 64 and Cys 80 and between Cys 76 and Cys 94. <br />
<br />
'''Hydrogen Bonding''' <br />
<br />
In all proteins <scene name='Sandbox_39/Hydrogen_bonds/2'>hydrogen bonds</scene> are essential for stability. In this ribbon diagram, the hydrogen bonds can be seen between the secondary structures of lysozyme highlighted in orange. Since the double bonds of the alpha carbons in the main chain of lysozyme cause torsional strain, lysozyme is limited to very specific hydrogen bonding between the amino acid residues. This representation clearly shows how crucial hydrogen bonding is to help maintain the stability of the protein. <br />
<br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='left' caption='' /><br />
<br />
= Intermolecular Interactions =<br />
<br />
'''Hydrophobicity'''<br />
<br />
Lysozyme contains both hydrophobic and hydrophilic regions ( <scene name='Sandbox_39/Hydrophobicity/2'>Hydrophobicity</scene> ). The hydrophilic effect, or the desire for proteins to be at a specific position regarding water, is the single most important determinant of protein folding. These regions can be displayed with the hydrophobic regions in gray and the polar, hydrophillic regions in purple. This coloration highlights the location of these regions, showing that the majority of the hydrophobic regions are inside of the protein and that the majority of the hydrophillic regions are on the outside of the protein.<br />
<br />
<br />
'''Polarity'''<br />
<br />
The nature of the amino acid sidechains in the lysozyme polypeptide sequence leads to regions of varying hydrophobicities and polarities of the enzyme structure. The presence of certain regions of hydrophilicity and hydrophobicity is a driving force in determining protein structure when folding. The varying polarities of the side chains influence the locations of residues in the enzyme structure. Nonpolar residues appear blue, and polar residues appear red in the following <scene name='Sandbox_38/Non_polar_blue/1'>polarity</scene> display of lysozyme. Nonpolar residues will display hydrophobic tendencies occurring mostly on the interior of the enzyme while polar residues will increase in abundance on the surface of the protein in order to increase contact with the aqueous solvent so as to satisfy their hydrophilic nature. By observing a space-filled structural depiction of <scene name='Sandbox_38/Non_polar_blu/1'>lysozyme polarity</scene> with polar molecules colored red and nonpolar molecules colored blue the influence of polarity on nucleotide arrangement and protein folding is evident, with the blue (nonpolar) regions inside the red (polar) regions. The presence of <scene name='Sandbox_39/Water/1'>water</scene> interacting with the various hydrophilic residues is depicted to further display how polarity affects structure. Water is depicted as yellow, and the polar and nonpolar regions remain their respective color.<br />
<br />
<br />
'''Charge'''<br />
<br />
Charges of the various regions of the lysozyme structure display a hydrophilic nature and thus also affect the location of that region of polypeptides and the overall folding of the protein. Charged regions of the protein will display hydrophilic tendencies and therefore will most often be located on the surface of the lysozyme molecule where they can interact with the aqueous solvent. Non-charged portions will display hydrophobic tendencies and be located on the interior of the molecule. The effect of various <scene name='Sandbox_38/Rb/1'>charges</scene> on protein structure can be visualized with charged molecules represented by red anionic and blue cationic regions, and uncharged regions colored in grey. This depiction of lysozyme uses a spacefill representation of lysozyme to depict <scene name='Sandbox_38/Chargeddd/1'>charges</scene>.<br />
<br />
<br />
<br />
= Applications of Lysozyme =<br />
<br />
Since lysozyme has been widely recognized for its antibacterial and antifungal properties, it has a wide variety of uses both in biochemical and pharmaceutical applications. In molecular biology, lysozyme is often used in the alkaline-lysis procedure for extracting and isolating plasmid DNA. It is used extensively in the pharmaceutical field for destroying gram-positive bacteria, and can be used to support already-existing immune defenses to fight bacterial infections. This enzyme is particularly important for preventing bacterial diseases in infants. Because of its antibacterial properties, lysozyme can also be used in the food industry to help prevent spoilage of foods.<br />
<br />
= References =<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Sandbox_51&diff=1222747Sandbox 512011-03-31T01:10:15Z<p>John Ripollone: </p>
<hr />
<div><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
{{Template:Oberholser_Sandbox_Reservation}}<br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
= '''Lysozyme''' =<br />
<br />
= Introduction =<br />
<br />
Lysozyme - also known as muramidase, or glycoside hydrolase - is a powerful enzyme of biological significance found in abundance in tears, saliva, and human milk. In humans, it is encoded in the ''LYZ'' gene. Although it is responsible for the initial digestion of starches in the mouth, it is most widely identified as a non-specific defense in gram positive bacteria and in many species of fungi. Due to its antibacterial effects, it is a strong component of the innate immune system, and is an important part of an infant's diet to ward off diarrheal diseases. Since it is a small, easily available, and highly stable protein containing only 129 amino acid residues, it has been subject to extensive research regarding its function and structure. Hen Egg White (HEW) Lysozyme is shown below.<br />
<br />
'''History'''<br />
<br />
Lysozyme is an enzyme known for its unique ability to degrade the polysaccharide architecture of many kinds of cell walls, normally for the purpose of protection against bacterial infection<ref>Lysozyme. 2010. Citizendium.org. http://en.citizendium.org/wiki/Lysozyme</ref>. Its effects were first noticed by Laschtschenko in 1909. It was officially characterized and termed “lysozyme” by Alexander Fleming, the same person credited for the accidental discovery of penicillin. <br />
The characterization of lysozyme in 1922 by Alexander Fleming was providential in that the undertaken experiment related to the discovery of lysozyme was not geared toward any knowledge of such a protein as lysozyme <ref>Lysozyme. 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. During the unrelated experiment, nasal drippings were inadvertently introduced to a petri dish containing a bacterial culture, which culture consequently exhibited the results of an as yet unknown enzymatic reaction. The observation of this unknown reaction led to further research on the components of this reaction as well as to the corresponding identification of the newfound "lysozyme." Fleming's discovery was complemented by David C. Phillips' 1965 description of the three-dimensional structure of lysozyme via a 200 pm resolution model obtained from X-ray crystallography <ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. Phillips' work was especially groundbreaking since Phillips had managed to successfully elucidate the structure of an enzyme via X-ray crystallography - a feat that had never before been accomplished<ref>Bugg, T. 1997. An Introduction to Enzyme and Coenzyme Chemistry. Blackwell Science Ltd., Oxford </ref>. Phillips' research also led to the first sufficiently described enzymatic mechanism of catalytic action <ref>1967. Proc R Soc Lond B Bio 167 (1009): 389–401.</ref>. Thus, Phillips' elucidation of the function of lysozyme led Phillips to reach a more general conclusion on the diversity of enzymatic chemical action in relation to enzymatic structure. Clearly, the findings of Phillips as well as the more general historical development of the understanding of the structure and function of lysozyme have been paramount to the more general realm of enzyme chemistry.<br />
<br />
<br />
[[Image:nag-nam2.jpg|thumb|left|350px|Lysozyme Cleavage Site]]<br />
<ref>Image from: http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm</ref> <br />
<br />
'''Function'''<br />
<br />
Lysozyme is known for damaging bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid (NAM) and N-acetyl-D-glucosamine (NAG) residues in peptidoglycan, and between N-acetyl-D-glucosamine residues in chitodextrins. In this way, lysozyme is efficient in lysing the cell walls of both bacteria and fungi. The location of cleavage for lysozyme on this architectural theme is the β(1-4) glycosidic linkage connecting the C1 carbon of NAM to the C4 carbon of NAG. <br />
<br />
The particular substrate of preference for this cleavage type is a (NAG-NAM)₃ hexasaccharide, within which substrate occurs the<br />
cleaving target glycosidic bond, NAM₄-β-O-NAG₅. The individual hexasaccharide binding units are designated A-F, with NAM₄-β-O-NAG₅ glycosidic bond cleavage preference corresponding to a D-E unit glycosidic bond cleavage preference. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='right' caption='' /><br />
<br />
<br />
= Enzymatic Activity of Lysozyme =<br />
<br />
Enzymes are designed to attract and to bind specific substrates. The active site of and lysozyme and its specific ligands are described in the following sections<br />
<br />
'''Active Site'''<br />
<br />
The <scene name='Sandbox_39/Active_site/1'>active site</scene> of lysozyme is formulated as a prominent cleft outlined by the two aforementioned catalytic amino acids, Glu 35 and Asp 52. The active site is geometrically bent to augment ligand binding, and the two amino acids interact with the ligand in the binding site. Asp52 is depicted in green, and Glu35 is depicted in purple. <br />
<br />
'''Ligands''' <br />
<br />
A <scene name='Sandbox_39/Ligands_1/1'>ligand</scene> is able to bind to the active site of an enzyme to form a biologically relevant complex. The model to the right shows a space-filling model of lysozyme with the protein distinguishable in brown and the ligand distinguishable in green. Another model of the ligand can be seen in this <br />
<scene name='Sandbox_39/Ribbon_ligand/1'>ribbon diagram</scene>, with the ligand protruding as a space-filling model from the active site. Here, it is clear that the ligand is a polysaccharide. <br />
<br />
The lysozyme reaction is characterized by hydrolysis of the beta (1-4) glycosidic bond between NAM and NAG. Lysozyme has a very specific active site, which can bind only six sugar rings from a polysaccharide chain. Once lysozyme binds to this chain, it hydrolyzes them. These six sugar rings represent the ligand of lysozyme. The lysozyme then distorts the fourth sugar in the six-membered complex, producing stress on the molecule and breaking the glycosidic bond.<br />
<br />
The amino acid side-chains Glu35 and Asp52 are critical to the activity of this enzyme. Glu35 acts as a proton donor to the glycosidic bond, cleaving the C-O bond in the substrate, and Asp52 acts as a nucleophile to generate a glycosyl enzyme intermediate. The glycosyl enzyme intermediate then reacts with a water molecule to give the product of hydrolysis. <br />
<br />
[[Image:jrip.jpg|thumb|left|350px|Mechanism of Lysozyme]]<br />
<ref>Image from: http://www.google.com/imgres?imgurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/pics-and-strucs/lysozyme-mech.gif&imgrefurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm&usg=__ormapG4XKg-tR5GrMSOdSMTV4vE=&h=603&w=801&sz=7&hl=en&start=17&zoom=1&tbnid=nvr9gvFrUILDkM:&tbnh=143&tbnw=189&prev=/images%3Fq%3DThe%2Blysozyme%2Breaction%2Bmechanism%26um%3D1%26hl%3Den%26sa%3DN%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C304&um=1&itbs=1&iact=hc&vpx=521&vpy=349&dur=448&hovh=191&hovw=254&tx=140&ty=48&ei=JQ_LTPKzLIjCsAPkzt2KDg&oei=IA_LTP74OsG78gapm-GFAQ&esq=2&page=2&ndsp=18&ved=1t:429,r:2,s:17&biw=1280&bih=647</ref><br />
<br />
'''Mechanism'''<br />
<br />
The lysozyme mechanism of action results in the hydrolysis of a glycoside (hence the familial distinction of lysozyme as a glycosylase<ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>), which corresponds to the conversion of an acetal to a hemiacetal, which reaction (general degradation of glycosidic bond to units "capped" by newly formed hydroxyl groups) necessitates acid catalysis, since the conversion of acetal to hemiacetal involves the protonation of the reactant oxygen prior to actual bond cleavage. <ref>Pratt, C.W., Voet, D., Voet, J.G. Fundamentals of Biochemistry - Life at the Molecular Level - Third Edition. Voet, Voet and Pratt, 2008.</ref>. Furthermore, the transition state obtained from this protonation is a covalent, oxonium ion, intermediate that must obtain resonance stabilization. The need for some means of acid catalysis and covalent resonance stabilization is adequately provided by the Glu 35 and Asp 52 residues of lysozyme, respectively. The reaction mechanism of lysozyme is demonstrated below. In the following image, the reaction begins at the upper left-hand side, and proceeds according to reaction arrows.<br />
<br />
As seen to the left, lysozyme works by hydrolyzing the glycosidic bond, distorting the bond between the NAM and NAG. This produces a glycosyl enzyme intermediate, which reacts with a water molecule to produce the product and the unchanged enzyme.<br />
<br />
'''Inhibitors''' <br />
<br />
Lysozyme is best inhibited by small saccharides which act competitively with the natural substrate. The smaller saccharides will bind to the first three binding sites of the cleft (sites A-C), but will not reach sites D and E, where the enzyme cuts the glycosidic bond. So, the competitive inhibitor will stick in the cleft, not allowing the substrate to bind to the enzyme complex.<ref>http://mcdb-webarchive.mcdb.ucsb.edu/sears/biochemistry/tw-enz/lysozyme/HEWL/lysozyme-overview.htm</ref> Several known inhibitors of lysozyme are: SDS, N-acetyl-D-glucosamine, and various alcohols and oxidizing agents.<ref>http://www.worthington-biochem.com/ly/default.html</ref> <br />
<br />
=== Zymogen of Lysozyme: Enzymatic Precursor ===<br />
<br />
Zymogens are inactive enzyme precursors. Enzymes are developed in an inactive way to prevent the enzyme from digesting the cell that produced it. This process also prevents the enzyme from becoming active in the wrong portion of the body. Lysozyme's zymogen, simply titled “pre-lysozyme,” was sequenced in 1977 by R D Palmiter, J Gagnon, L H Ericsson and K A Walsh, and has since been sequenced much more extensively. <br />
<br />
<applet load='1hew' size='350' frame='true' align='right' caption='' /><br />
<br />
= Composition and Structure of Lysozyme =<br />
<br />
All proteins consist of carbon, hydrogen, nitrogen, oxygen, and sulfur, as do most organic molecules. Enzymes are composed in such a way as to maximize their reactivity with their desired substrate, increasing the efficiency of biological reactions. The <scene name='Sandbox_39/Elements/1'>composition of lysozyme</scene> can be seen on the left, with the carbon atoms outlined in gray, oxygen atoms in red, nitrogen atoms in blue, sulfur atoms in yellow, and the three-letter abbreviation for the <scene name='Sandbox_39/Amino_acid_residues/1'>amino acid residues</scene> in purple.<br />
<br />
Lysozyme, like all proteins, also contains a <scene name='Sandbox_39/C_and_n_terminal_residues/1'> 3'C and 5'N terminal </scene>, and these can be seen by following the colors of the rainbow across the molecule. Starting at the red end, the 3' C terminal end, one can work the entire way through to the 5' N terminal end, showing the folding pattern and chain of the protein.<br />
<br />
== Secondary Structure ==<br />
<br />
Lysozyme contains five <scene name='Sandbox_38/A/2'>alpha helical</scene> regions and five regions containing <scene name='Sandbox_38/B/1'>beta sheets</scene> as displayed in this <scene name='Sandbox_38/Alphab/1'>image</scene>. Linking these secondary structures, a number of beta turns and a large number of random coils make up the remainder of the polypeptide backbone. The polypeptide backbone of lysozyme involved in the 3 antiparallel beta sheets display the beta hairpin motif of supersecondary structure. This depiction of lysozyme contains an antiparallel beta-pleated sheet, which contributes greatly to the stability of the molecule by providing the correct alignment of hydrogen bonds. Lysozyme also contains a great deal of random coil, which is seen in the white regions of the molecule.<br />
<br />
==Amino Acid Residues==<br />
<br />
The amino acids present in the lysozyme polypeptide sequence have a direct influence not only on primary structure, but also on the secondary and tertiary structures, which can be influenced by polarity and charge of the sidechains. The various amino acid <scene name='Sandbox_38/Aminoi/1'>residues</scene> differ in their properties because of the great variety of side chains present on each amino acid. Polar and nonpolar (and charged and uncharged) side chains lead to various degrees of hydrophobicity and hydrophilicity, which affects protein folding. In lysozyme, these <scene name='Sandbox_38/Sc/1'>side chains</scene> are displayed for each amino acid residue.<br />
<br />
= Bonding Interactions =<br />
<br />
'''Disulfide Bonding in Lysozyme'''<br />
<br />
Lysozyme contains four <scene name='Sandbox_39/Disulfide_bonds/1'>disulfide bonds</scene> involving eight cysteine residues, which are highlighted in yellow on the left. Disulfide bonds are intramolecular forces that stabilize the tertiary structure of many proteins. Disulfide bonds are present in four locations in lysozyme: between Cys 6 and Cys 127, between Cys 30 and Cys 115, between Cys 64 and Cys 80 and between Cys 76 and Cys 94. <br />
<br />
'''Hydrogen Bonding''' <br />
<br />
In all proteins <scene name='Sandbox_39/Hydrogen_bonds/2'>hydrogen bonds</scene> are essential for stability. In this ribbon diagram, the hydrogen bonds can be seen between the secondary structures of lysozyme highlighted in orange. Since the double bonds of the alpha carbons in the main chain of lysozyme cause torsional strain, lysozyme is limited to very specific hydrogen bonding between the amino acid residues. This representation clearly shows how crucial hydrogen bonding is to help maintain the stability of the protein. <br />
<br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='left' caption='' /><br />
<br />
= Intermolecular Interactions =<br />
<br />
'''Hydrophobicity'''<br />
<br />
Lysozyme contains both hydrophobic and hydrophilic regions ( <scene name='Sandbox_39/Hydrophobicity/2'>Hydrophobicity</scene> ). The hydrophilic effect, or the desire for proteins to be at a specific position regarding water, is the single most important determinant of protein folding. These regions can be displayed with the hydrophobic regions in gray and the polar, hydrophillic regions in purple. This coloration highlights the location of these regions, showing that the majority of the hydrophobic regions are inside of the protein and that the majority of the hydrophillic regions are on the outside of the protein.<br />
<br />
<br />
'''Polarity'''<br />
<br />
The nature of the amino acid sidechains in the lysozyme polypeptide sequence leads to regions of varying hydrophobicities and polarities of the enzyme structure. The presence of certain regions of hydrophilicity and hydrophobicity is a driving force in determining protein structure when folding. The varying polarities of the side chains influence the locations of residues in the enzyme structure. Nonpolar residues appear blue, and polar residues appear red in the following <scene name='Sandbox_38/Non_polar_blue/1'>polarity</scene> display of lysozyme. Nonpolar residues will display hydrophobic tendencies occurring mostly on the interior of the enzyme while polar residues will increase in abundance on the surface of the protein in order to increase contact with the aqueous solvent so as to satisfy their hydrophilic nature. By observing a space-filled structural depiction of <scene name='Sandbox_38/Non_polar_blu/1'>lysozyme polarity</scene> with polar molecules colored red and nonpolar molecules colored blue the influence of polarity on nucleotide arrangement and protein folding is evident, with the blue (nonpolar) regions inside the red (polar) regions. The presence of <scene name='Sandbox_39/Water/1'>water</scene> interacting with the various hydrophilic residues is depicted to further display how polarity affects structure. Water is depicted as yellow, and the polar and nonpolar regions remain their respective color.<br />
<br />
<br />
'''Charge'''<br />
<br />
Charges of the various regions of the lysozyme structure display a hydrophilic nature and thus also affect the location of that region of polypeptides and the overall folding of the protein. Charged regions of the protein will display hydrophilic tendencies and therefore will most often be located on the surface of the lysozyme molecule where they can interact with the aqueous solvent. Non-charged portions will display hydrophobic tendencies and be located on the interior of the molecule. The effect of various <scene name='Sandbox_38/Rb/1'>charges</scene> on protein structure can be visualized with charged molecules represented by red anionic and blue cationic regions, and uncharged regions colored in grey. This depiction of lysozyme uses a spacefill representation of lysozyme to depict <scene name='Sandbox_38/Chargeddd/1'>charges</scene>.<br />
<br />
<br />
<br />
= Applications of Lysozyme =<br />
<br />
Since lysozyme has been widely recognized for its antibacterial and antifungal properties, it has a wide variety of uses both in biochemical and pharmaceutical applications. In molecular biology, lysozyme is often used in the alkaline-lysis procedure for extracting and isolating plasmid DNA. It is used extensively in the pharmaceutical field for destroying gram-positive bacteria, and can be used to support already-existing immune defenses to fight bacterial infections. This enzyme is particularly important for preventing bacterial diseases in infants. Because of its antibacterial properties, lysozyme can also be used in the food industry to help prevent spoilage of foods.<br />
<br />
= References =<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Sandbox_51&diff=1222745Sandbox 512011-03-31T01:09:14Z<p>John Ripollone: </p>
<hr />
<div><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
{{Template:Oberholser_Sandbox_Reservation}}<br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
= '''Lysozyme''' =<br />
<br />
=== Introduction ===<br />
<br />
Lysozyme - also known as muramidase, or glycoside hydrolase - is a powerful enzyme of biological significance found in abundance in tears, saliva, and human milk. In humans, it is encoded in the ''LYZ'' gene. Although it is responsible for the initial digestion of starches in the mouth, it is most widely identified as a non-specific defense in gram positive bacteria and in many species of fungi. Due to its antibacterial effects, it is a strong component of the innate immune system, and is an important part of an infant's diet to ward off diarrheal diseases. Since it is a small, easily available, and highly stable protein containing only 129 amino acid residues, it has been subject to extensive research regarding its function and structure. Hen Egg White (HEW) Lysozyme is shown below.<br />
<br />
=== History ===<br />
<br />
Lysozyme is an enzyme known for its unique ability to degrade the polysaccharide architecture of many kinds of cell walls, normally for the purpose of protection against bacterial infection<ref>Lysozyme. 2010. Citizendium.org. http://en.citizendium.org/wiki/Lysozyme</ref>. Its effects were first noticed by Laschtschenko in 1909. It was officially characterized and termed “lysozyme” by Alexander Fleming, the same person credited for the accidental discovery of penicillin. <br />
The characterization of lysozyme in 1922 by Alexander Fleming was providential in that the undertaken experiment related to the discovery of lysozyme was not geared toward any knowledge of such a protein as lysozyme <ref>Lysozyme. 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. During the unrelated experiment, nasal drippings were inadvertently introduced to a petri dish containing a bacterial culture, which culture consequently exhibited the results of an as yet unknown enzymatic reaction. The observation of this unknown reaction led to further research on the components of this reaction as well as to the corresponding identification of the newfound "lysozyme." Fleming's discovery was complemented by David C. Phillips' 1965 description of the three-dimensional structure of lysozyme via a 200 pm resolution model obtained from X-ray crystallography <ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. Phillips' work was especially groundbreaking since Phillips had managed to successfully elucidate the structure of an enzyme via X-ray crystallography - a feat that had never before been accomplished<ref>Bugg, T. 1997. An Introduction to Enzyme and Coenzyme Chemistry. Blackwell Science Ltd., Oxford </ref>. Phillips' research also led to the first sufficiently described enzymatic mechanism of catalytic action <ref>1967. Proc R Soc Lond B Bio 167 (1009): 389–401.</ref>. Thus, Phillips' elucidation of the function of lysozyme led Phillips to reach a more general conclusion on the diversity of enzymatic chemical action in relation to enzymatic structure. Clearly, the findings of Phillips as well as the more general historical development of the understanding of the structure and function of lysozyme have been paramount to the more general realm of enzyme chemistry.<br />
<br />
<br />
[[Image:nag-nam2.jpg|thumb|left|350px|Lysozyme Cleavage Site]]<br />
<ref>Image from: http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm</ref> <br />
<br />
=== Function ===<br />
<br />
Lysozyme is known for damaging bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid (NAM) and N-acetyl-D-glucosamine (NAG) residues in peptidoglycan, and between N-acetyl-D-glucosamine residues in chitodextrins. In this way, lysozyme is efficient in lysing the cell walls of both bacteria and fungi. The location of cleavage for lysozyme on this architectural theme is the β(1-4) glycosidic linkage connecting the C1 carbon of NAM to the C4 carbon of NAG. <br />
<br />
The particular substrate of preference for this cleavage type is a (NAG-NAM)₃ hexasaccharide, within which substrate occurs the<br />
cleaving target glycosidic bond, NAM₄-β-O-NAG₅. The individual hexasaccharide binding units are designated A-F, with NAM₄-β-O-NAG₅ glycosidic bond cleavage preference corresponding to a D-E unit glycosidic bond cleavage preference. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='right' caption='' /><br />
<br />
<br />
= Enzymatic Activity of Lysozyme =<br />
<br />
Enzymes are designed to attract and to bind specific substrates. The active site of and lysozyme and its specific ligands are described in the following sections<br />
<br />
'''Active Site'''<br />
<br />
The <scene name='Sandbox_39/Active_site/1'>active site</scene> of lysozyme is formulated as a prominent cleft outlined by the two aforementioned catalytic amino acids, Glu 35 and Asp 52. The active site is geometrically bent to augment ligand binding, and the two amino acids interact with the ligand in the binding site. Asp52 is depicted in green, and Glu35 is depicted in purple. <br />
<br />
'''Ligands''' <br />
<br />
A <scene name='Sandbox_39/Ligands_1/1'>ligand</scene> is able to bind to the active site of an enzyme to form a biologically relevant complex. The model to the right shows a space-filling model of lysozyme with the protein distinguishable in brown and the ligand distinguishable in green. Another model of the ligand can be seen in this <br />
<scene name='Sandbox_39/Ribbon_ligand/1'>ribbon diagram</scene>, with the ligand protruding as a space-filling model from the active site. Here, it is clear that the ligand is a polysaccharide. <br />
<br />
The lysozyme reaction is characterized by hydrolysis of the beta (1-4) glycosidic bond between NAM and NAG. Lysozyme has a very specific active site, which can bind only six sugar rings from a polysaccharide chain. Once lysozyme binds to this chain, it hydrolyzes them. These six sugar rings represent the ligand of lysozyme. The lysozyme then distorts the fourth sugar in the six-membered complex, producing stress on the molecule and breaking the glycosidic bond.<br />
<br />
The amino acid side-chains Glu35 and Asp52 are critical to the activity of this enzyme. Glu35 acts as a proton donor to the glycosidic bond, cleaving the C-O bond in the substrate, and Asp52 acts as a nucleophile to generate a glycosyl enzyme intermediate. The glycosyl enzyme intermediate then reacts with a water molecule to give the product of hydrolysis. <br />
<br />
[[Image:jrip.jpg|thumb|left|350px|Mechanism of Lysozyme]]<br />
<ref>Image from: http://www.google.com/imgres?imgurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/pics-and-strucs/lysozyme-mech.gif&imgrefurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm&usg=__ormapG4XKg-tR5GrMSOdSMTV4vE=&h=603&w=801&sz=7&hl=en&start=17&zoom=1&tbnid=nvr9gvFrUILDkM:&tbnh=143&tbnw=189&prev=/images%3Fq%3DThe%2Blysozyme%2Breaction%2Bmechanism%26um%3D1%26hl%3Den%26sa%3DN%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C304&um=1&itbs=1&iact=hc&vpx=521&vpy=349&dur=448&hovh=191&hovw=254&tx=140&ty=48&ei=JQ_LTPKzLIjCsAPkzt2KDg&oei=IA_LTP74OsG78gapm-GFAQ&esq=2&page=2&ndsp=18&ved=1t:429,r:2,s:17&biw=1280&bih=647</ref><br />
<br />
'''Mechanism'''<br />
<br />
The lysozyme mechanism of action results in the hydrolysis of a glycoside (hence the familial distinction of lysozyme as a glycosylase<ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>), which corresponds to the conversion of an acetal to a hemiacetal, which reaction (general degradation of glycosidic bond to units "capped" by newly formed hydroxyl groups) necessitates acid catalysis, since the conversion of acetal to hemiacetal involves the protonation of the reactant oxygen prior to actual bond cleavage. <ref>Pratt, C.W., Voet, D., Voet, J.G. Fundamentals of Biochemistry - Life at the Molecular Level - Third Edition. Voet, Voet and Pratt, 2008.</ref>. Furthermore, the transition state obtained from this protonation is a covalent, oxonium ion, intermediate that must obtain resonance stabilization. The need for some means of acid catalysis and covalent resonance stabilization is adequately provided by the Glu 35 and Asp 52 residues of lysozyme, respectively. The reaction mechanism of lysozyme is demonstrated below. In the following image, the reaction begins at the upper left-hand side, and proceeds according to reaction arrows.<br />
<br />
As seen to the left, lysozyme works by hydrolyzing the glycosidic bond, distorting the bond between the NAM and NAG. This produces a glycosyl enzyme intermediate, which reacts with a water molecule to produce the product and the unchanged enzyme.<br />
<br />
'''Inhibitors''' <br />
<br />
Lysozyme is best inhibited by small saccharides which act competitively with the natural substrate. The smaller saccharides will bind to the first three binding sites of the cleft (sites A-C), but will not reach sites D and E, where the enzyme cuts the glycosidic bond. So, the competitive inhibitor will stick in the cleft, not allowing the substrate to bind to the enzyme complex.<ref>http://mcdb-webarchive.mcdb.ucsb.edu/sears/biochemistry/tw-enz/lysozyme/HEWL/lysozyme-overview.htm</ref> Several known inhibitors of lysozyme are: SDS, N-acetyl-D-glucosamine, and various alcohols and oxidizing agents.<ref>http://www.worthington-biochem.com/ly/default.html</ref> <br />
<br />
=== Zymogen of Lysozyme: Enzymatic Precursor ===<br />
<br />
Zymogens are inactive enzyme precursors. Enzymes are developed in an inactive way to prevent the enzyme from digesting the cell that produced it. This process also prevents the enzyme from becoming active in the wrong portion of the body. Lysozyme's zymogen, simply titled “pre-lysozyme,” was sequenced in 1977 by R D Palmiter, J Gagnon, L H Ericsson and K A Walsh, and has since been sequenced much more extensively. <br />
<br />
<applet load='1hew' size='350' frame='true' align='right' caption='' /><br />
<br />
= Composition and Structure of Lysozyme =<br />
<br />
All proteins consist of carbon, hydrogen, nitrogen, oxygen, and sulfur, as do most organic molecules. Enzymes are composed in such a way as to maximize their reactivity with their desired substrate, increasing the efficiency of biological reactions. The <scene name='Sandbox_39/Elements/1'>composition of lysozyme</scene> can be seen on the left, with the carbon atoms outlined in gray, oxygen atoms in red, nitrogen atoms in blue, sulfur atoms in yellow, and the three-letter abbreviation for the <scene name='Sandbox_39/Amino_acid_residues/1'>amino acid residues</scene> in purple.<br />
<br />
Lysozyme, like all proteins, also contains a <scene name='Sandbox_39/C_and_n_terminal_residues/1'> 3'C and 5'N terminal </scene>, and these can be seen by following the colors of the rainbow across the molecule. Starting at the red end, the 3' C terminal end, one can work the entire way through to the 5' N terminal end, showing the folding pattern and chain of the protein.<br />
<br />
== Secondary Structure ==<br />
<br />
Lysozyme contains five <scene name='Sandbox_38/A/2'>alpha helical</scene> regions and five regions containing <scene name='Sandbox_38/B/1'>beta sheets</scene> as displayed in this <scene name='Sandbox_38/Alphab/1'>image</scene>. Linking these secondary structures, a number of beta turns and a large number of random coils make up the remainder of the polypeptide backbone. The polypeptide backbone of lysozyme involved in the 3 antiparallel beta sheets display the beta hairpin motif of supersecondary structure. This depiction of lysozyme contains an antiparallel beta-pleated sheet, which contributes greatly to the stability of the molecule by providing the correct alignment of hydrogen bonds. Lysozyme also contains a great deal of random coil, which is seen in the white regions of the molecule.<br />
<br />
==Amino Acid Residues==<br />
<br />
The amino acids present in the lysozyme polypeptide sequence have a direct influence not only on primary structure, but also on the secondary and tertiary structures, which can be influenced by polarity and charge of the sidechains. The various amino acid <scene name='Sandbox_38/Aminoi/1'>residues</scene> differ in their properties because of the great variety of side chains present on each amino acid. Polar and nonpolar (and charged and uncharged) side chains lead to various degrees of hydrophobicity and hydrophilicity, which affects protein folding. In lysozyme, these <scene name='Sandbox_38/Sc/1'>side chains</scene> are displayed for each amino acid residue.<br />
<br />
= Bonding Interactions =<br />
<br />
'''Disulfide Bonding in Lysozyme'''<br />
<br />
Lysozyme contains four <scene name='Sandbox_39/Disulfide_bonds/1'>disulfide bonds</scene> involving eight cysteine residues, which are highlighted in yellow on the left. Disulfide bonds are intramolecular forces that stabilize the tertiary structure of many proteins. Disulfide bonds are present in four locations in lysozyme: between Cys 6 and Cys 127, between Cys 30 and Cys 115, between Cys 64 and Cys 80 and between Cys 76 and Cys 94. <br />
<br />
'''Hydrogen Bonding''' <br />
<br />
In all proteins <scene name='Sandbox_39/Hydrogen_bonds/2'>hydrogen bonds</scene> are essential for stability. In this ribbon diagram, the hydrogen bonds can be seen between the secondary structures of lysozyme highlighted in orange. Since the double bonds of the alpha carbons in the main chain of lysozyme cause torsional strain, lysozyme is limited to very specific hydrogen bonding between the amino acid residues. This representation clearly shows how crucial hydrogen bonding is to help maintain the stability of the protein. <br />
<br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='left' caption='' /><br />
<br />
= Intermolecular Interactions =<br />
<br />
'''Hydrophobicity'''<br />
<br />
Lysozyme contains both hydrophobic and hydrophilic regions ( <scene name='Sandbox_39/Hydrophobicity/2'>Hydrophobicity</scene> ). The hydrophilic effect, or the desire for proteins to be at a specific position regarding water, is the single most important determinant of protein folding. These regions can be displayed with the hydrophobic regions in gray and the polar, hydrophillic regions in purple. This coloration highlights the location of these regions, showing that the majority of the hydrophobic regions are inside of the protein and that the majority of the hydrophillic regions are on the outside of the protein.<br />
<br />
<br />
'''Polarity'''<br />
<br />
The nature of the amino acid sidechains in the lysozyme polypeptide sequence leads to regions of varying hydrophobicities and polarities of the enzyme structure. The presence of certain regions of hydrophilicity and hydrophobicity is a driving force in determining protein structure when folding. The varying polarities of the side chains influence the locations of residues in the enzyme structure. Nonpolar residues appear blue, and polar residues appear red in the following <scene name='Sandbox_38/Non_polar_blue/1'>polarity</scene> display of lysozyme. Nonpolar residues will display hydrophobic tendencies occurring mostly on the interior of the enzyme while polar residues will increase in abundance on the surface of the protein in order to increase contact with the aqueous solvent so as to satisfy their hydrophilic nature. By observing a space-filled structural depiction of <scene name='Sandbox_38/Non_polar_blu/1'>lysozyme polarity</scene> with polar molecules colored red and nonpolar molecules colored blue the influence of polarity on nucleotide arrangement and protein folding is evident, with the blue (nonpolar) regions inside the red (polar) regions. The presence of <scene name='Sandbox_39/Water/1'>water</scene> interacting with the various hydrophilic residues is depicted to further display how polarity affects structure. Water is depicted as yellow, and the polar and nonpolar regions remain their respective color.<br />
<br />
<br />
'''Charge'''<br />
<br />
Charges of the various regions of the lysozyme structure display a hydrophilic nature and thus also affect the location of that region of polypeptides and the overall folding of the protein. Charged regions of the protein will display hydrophilic tendencies and therefore will most often be located on the surface of the lysozyme molecule where they can interact with the aqueous solvent. Non-charged portions will display hydrophobic tendencies and be located on the interior of the molecule. The effect of various <scene name='Sandbox_38/Rb/1'>charges</scene> on protein structure can be visualized with charged molecules represented by red anionic and blue cationic regions, and uncharged regions colored in grey. This depiction of lysozyme uses a spacefill representation of lysozyme to depict <scene name='Sandbox_38/Chargeddd/1'>charges</scene>.<br />
<br />
<br />
<br />
= Applications of Lysozyme =<br />
<br />
Since lysozyme has been widely recognized for its antibacterial and antifungal properties, it has a wide variety of uses both in biochemical and pharmaceutical applications. In molecular biology, lysozyme is often used in the alkaline-lysis procedure for extracting and isolating plasmid DNA. It is used extensively in the pharmaceutical field for destroying gram-positive bacteria, and can be used to support already-existing immune defenses to fight bacterial infections. This enzyme is particularly important for preventing bacterial diseases in infants. Because of its antibacterial properties, lysozyme can also be used in the food industry to help prevent spoilage of foods.<br />
<br />
= References =<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Sandbox_51&diff=1222741Sandbox 512011-03-31T01:06:39Z<p>John Ripollone: </p>
<hr />
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{{Template:Oberholser_Sandbox_Reservation}}<br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
= '''Lysozyme''' =<br />
<br />
=== Introduction ===<br />
<br />
Lysozyme - also known as muramidase, or glycoside hydrolase - is a powerful enzyme of biological significance found in abundance in tears, saliva, and human milk. In humans, it is encoded in the ''LYZ'' gene. Although it is responsible for the initial digestion of starches in the mouth, it is most widely identified as a non-specific defense in gram positive bacteria and in many species of fungi. Due to its antibacterial effects, it is a strong component of the innate immune system, and is an important part of an infant's diet to ward off diarrheal diseases. Since it is a small, easily available, and highly stable protein containing only 129 amino acid residues, it has been subject to extensive research regarding its function and structure. Hen Egg White (HEW) Lysozyme is shown below.<br />
<br />
=== History ===<br />
<br />
Lysozyme is an enzyme known for its unique ability to degrade the polysaccharide architecture of many kinds of cell walls, normally for the purpose of protection against bacterial infection<ref>Lysozyme. 2010. Citizendium.org. http://en.citizendium.org/wiki/Lysozyme</ref>. Its effects were first noticed by Laschtschenko in 1909. It was officially characterized and termed “lysozyme” by Alexander Fleming, the same person credited for the accidental discovery of penicillin. <br />
The characterization of lysozyme in 1922 by Alexander Fleming was providential in that the undertaken experiment related to the discovery of lysozyme was not geared toward any knowledge of such a protein as lysozyme <ref>Lysozyme. 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. During the unrelated experiment, nasal drippings were inadvertently introduced to a petri dish containing a bacterial culture, which culture consequently exhibited the results of an as yet unknown enzymatic reaction. The observation of this unknown reaction led to further research on the components of this reaction as well as to the corresponding identification of the newfound "lysozyme." Fleming's discovery was complemented by David C. Phillips' 1965 description of the three-dimensional structure of lysozyme via a 200 pm resolution model obtained from X-ray crystallography <ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. Phillips' work was especially groundbreaking since Phillips had managed to successfully elucidate the structure of an enzyme via X-ray crystallography - a feat that had never before been accomplished<ref>Bugg, T. 1997. An Introduction to Enzyme and Coenzyme Chemistry. Blackwell Science Ltd., Oxford </ref>. Phillips' research also led to the first sufficiently described enzymatic mechanism of catalytic action <ref>1967. Proc R Soc Lond B Bio 167 (1009): 389–401.</ref>. Thus, Phillips' elucidation of the function of lysozyme led Phillips to reach a more general conclusion on the diversity of enzymatic chemical action in relation to enzymatic structure. Clearly, the findings of Phillips as well as the more general historical development of the understanding of the structure and function of lysozyme have been paramount to the more general realm of enzyme chemistry.<br />
<br />
<br />
[[Image:nag-nam2.jpg|thumb|left|350px|Lysozyme Cleavage Site]]<br />
<ref>Image from: http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm</ref> <br />
<br />
=== Function===<br />
<br />
Lysozyme is known for damaging bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid (NAM) and N-acetyl-D-glucosamine (NAG) residues in peptidoglycan, and between N-acetyl-D-glucosamine residues in chitodextrins. In this way, lysozyme is efficient in lysing the cell walls of both bacteria and fungi. The location of cleavage for lysozyme on this architectural theme is the β(1-4) glycosidic linkage connecting the C1 carbon of NAM to the C4 carbon of NAG. <br />
<br />
The particular substrate of preference for this cleavage type is a (NAG-NAM)₃ hexasaccharide, within which substrate occurs the<br />
cleaving target glycosidic bond, NAM₄-β-O-NAG₅. The individual hexasaccharide binding units are designated A-F, with NAM₄-β-O-NAG₅ glycosidic bond cleavage preference corresponding to a D-E unit glycosidic bond cleavage preference. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='right' caption='' /><br />
<br />
<br />
= Enzymatic Activity of Lysozyme =<br />
<br />
Enzymes are designed to attract and to bind specific substrates. The active site of and lysozyme and its specific ligands are described in the following sections<br />
<br />
=== Active Site ===<br />
<br />
The <scene name='Sandbox_39/Active_site/1'>active site</scene> of lysozyme is formulated as a prominent cleft outlined by the two aforementioned catalytic amino acids, Glu 35 and Asp 52. The active site is geometrically bent to augment ligand binding, and the two amino acids interact with the ligand in the binding site. Asp52 is depicted in green, and Glu35 is depicted in purple. <br />
<br />
=== Ligands ===<br />
<br />
A <scene name='Sandbox_39/Ligands_1/1'>ligand</scene> is able to bind to the active site of an enzyme to form a biologically relevant complex. The model to the right shows a space-filling model of lysozyme with the protein distinguishable in brown and the ligand distinguishable in green. Another model of the ligand can be seen in this <br />
<scene name='Sandbox_39/Ribbon_ligand/1'>ribbon diagram</scene>, with the ligand protruding as a space-filling model from the active site. Here, it is clear that the ligand is a polysaccharide. <br />
<br />
The lysozyme reaction is characterized by hydrolysis of the beta (1-4) glycosidic bond between NAM and NAG. Lysozyme has a very specific active site, which can bind only six sugar rings from a polysaccharide chain. Once lysozyme binds to this chain, it hydrolyzes them. These six sugar rings represent the ligand of lysozyme. The lysozyme then distorts the fourth sugar in the six-membered complex, producing stress on the molecule and breaking the glycosidic bond.<br />
<br />
The amino acid side-chains Glu35 and Asp52 are critical to the activity of this enzyme. Glu35 acts as a proton donor to the glycosidic bond, cleaving the C-O bond in the substrate, and Asp52 acts as a nucleophile to generate a glycosyl enzyme intermediate. The glycosyl enzyme intermediate then reacts with a water molecule to give the product of hydrolysis. <br />
<br />
[[Image:jrip.jpg|thumb|left|350px|Mechanism of Lysozyme]]<br />
<ref>Image from: http://www.google.com/imgres?imgurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/pics-and-strucs/lysozyme-mech.gif&imgrefurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm&usg=__ormapG4XKg-tR5GrMSOdSMTV4vE=&h=603&w=801&sz=7&hl=en&start=17&zoom=1&tbnid=nvr9gvFrUILDkM:&tbnh=143&tbnw=189&prev=/images%3Fq%3DThe%2Blysozyme%2Breaction%2Bmechanism%26um%3D1%26hl%3Den%26sa%3DN%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C304&um=1&itbs=1&iact=hc&vpx=521&vpy=349&dur=448&hovh=191&hovw=254&tx=140&ty=48&ei=JQ_LTPKzLIjCsAPkzt2KDg&oei=IA_LTP74OsG78gapm-GFAQ&esq=2&page=2&ndsp=18&ved=1t:429,r:2,s:17&biw=1280&bih=647</ref><br />
<br />
=== Mechanism === <br />
<br />
The lysozyme mechanism of action results in the hydrolysis of a glycoside (hence the familial distinction of lysozyme as a glycosylase<ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>), which corresponds to the conversion of an acetal to a hemiacetal, which reaction (general degradation of glycosidic bond to units "capped" by newly formed hydroxyl groups) necessitates acid catalysis, since the conversion of acetal to hemiacetal involves the protonation of the reactant oxygen prior to actual bond cleavage. <ref>Pratt, C.W., Voet, D., Voet, J.G. Fundamentals of Biochemistry - Life at the Molecular Level - Third Edition. Voet, Voet and Pratt, 2008.</ref>. Furthermore, the transition state obtained from this protonation is a covalent, oxonium ion, intermediate that must obtain resonance stabilization. The need for some means of acid catalysis and covalent resonance stabilization is adequately provided by the Glu 35 and Asp 52 residues of lysozyme, respectively. The reaction mechanism of lysozyme is demonstrated below. In the following image, the reaction begins at the upper left-hand side, and proceeds according to reaction arrows.<br />
<br />
As seen to the left, lysozyme works by hydrolyzing the glycosidic bond, distorting the bond between the NAM and NAG. This produces a glycosyl enzyme intermediate, which reacts with a water molecule to produce the product and the unchanged enzyme.<br />
=== Inhibitors ===<br />
<br />
Lysozyme is best inhibited by small saccharides which act competitively with the natural substrate. The smaller saccharides will bind to the first three binding sites of the cleft (sites A-C), but will not reach sites D and E, where the enzyme cuts the glycosidic bond. So, the competitive inhibitor will stick in the cleft, not allowing the substrate to bind to the enzyme complex.<ref>http://mcdb-webarchive.mcdb.ucsb.edu/sears/biochemistry/tw-enz/lysozyme/HEWL/lysozyme-overview.htm</ref> Several known inhibitors of lysozyme are: SDS, N-acetyl-D-glucosamine, and various alcohols and oxidizing agents.<ref>http://www.worthington-biochem.com/ly/default.html</ref> <br />
<br />
=== Zymogen of Lysozyme: Enzymatic Precursor ===<br />
<br />
Zymogens are inactive enzyme precursors. Enzymes are developed in an inactive way to prevent the enzyme from digesting the cell that produced it. This process also prevents the enzyme from becoming active in the wrong portion of the body. Lysozyme's zymogen, simply titled “pre-lysozyme,” was sequenced in 1977 by R D Palmiter, J Gagnon, L H Ericsson and K A Walsh, and has since been sequenced much more extensively. <br />
<br />
<applet load='1hew' size='350' frame='true' align='right' caption='' /><br />
<br />
= Composition and Structure of Lysozyme =<br />
<br />
All proteins consist of carbon, hydrogen, nitrogen, oxygen, and sulfur, as do most organic molecules. Enzymes are composed in such a way as to maximize their reactivity with their desired substrate, increasing the efficiency of biological reactions. The <scene name='Sandbox_39/Elements/1'>composition of lysozyme</scene> can be seen on the left, with the carbon atoms outlined in gray, oxygen atoms in red, nitrogen atoms in blue, sulfur atoms in yellow, and the three-letter abbreviation for the <scene name='Sandbox_39/Amino_acid_residues/1'>amino acid residues</scene> in purple.<br />
<br />
Lysozyme, like all proteins, also contains a <scene name='Sandbox_39/C_and_n_terminal_residues/1'> 3'C and 5'N terminal </scene>, and these can be seen by following the colors of the rainbow across the molecule. Starting at the red end, the 3' C terminal end, one can work the entire way through to the 5' N terminal end, showing the folding pattern and chain of the protein.<br />
<br />
== Secondary Structure ==<br />
<br />
Lysozyme contains five <scene name='Sandbox_38/A/2'>alpha helical</scene> regions and five regions containing <scene name='Sandbox_38/B/1'>beta sheets</scene> as displayed in this <scene name='Sandbox_38/Alphab/1'>image</scene>. Linking these secondary structures, a number of beta turns and a large number of random coils make up the remainder of the polypeptide backbone. The polypeptide backbone of lysozyme involved in the 3 antiparallel beta sheets display the beta hairpin motif of supersecondary structure. This depiction of lysozyme contains an antiparallel beta-pleated sheet, which contributes greatly to the stability of the molecule by providing the correct alignment of hydrogen bonds. Lysozyme also contains a great deal of random coil, which is seen in the white regions of the molecule.<br />
<br />
==Amino Acid Residues==<br />
<br />
The amino acids present in the lysozyme polypeptide sequence have a direct influence not only on primary structure, but also on the secondary and tertiary structures, which can be influenced by polarity and charge of the sidechains. The various amino acid <scene name='Sandbox_38/Aminoi/1'>residues</scene> differ in their properties because of the great variety of side chains present on each amino acid. Polar and nonpolar (and charged and uncharged) side chains lead to various degrees of hydrophobicity and hydrophilicity, which affects protein folding. In lysozyme, these <scene name='Sandbox_38/Sc/1'>side chains</scene> are displayed for each amino acid residue.<br />
<br />
= Bonding Interactions =<br />
<br />
=== Disulfide Bonding in Lysozyme ===<br />
<br />
Lysozyme contains four <scene name='Sandbox_39/Disulfide_bonds/1'>disulfide bonds</scene> involving eight cysteine residues, which are highlighted in yellow on the left. Disulfide bonds are intramolecular forces that stabilize the tertiary structure of many proteins. Disulfide bonds are present in four locations in lysozyme: between Cys 6 and Cys 127, between Cys 30 and Cys 115, between Cys 64 and Cys 80 and between Cys 76 and Cys 94. <br />
<br />
=== Hydrogen Bonding ===<br />
<br />
In all proteins <scene name='Sandbox_39/Hydrogen_bonds/2'>hydrogen bonds</scene> are essential for stability. In this ribbon diagram, the hydrogen bonds can be seen between the secondary structures of lysozyme highlighted in orange. Since the double bonds of the alpha carbons in the main chain of lysozyme cause torsional strain, lysozyme is limited to very specific hydrogen bonding between the amino acid residues. This representation clearly shows how crucial hydrogen bonding is to help maintain the stability of the protein. <br />
<br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='left' caption='' /><br />
<br />
= Intermolecular Interactions =<br />
<br />
''Hydrophobicity''<br />
<br />
Lysozyme contains both hydrophobic and hydrophilic regions ( <scene name='Sandbox_39/Hydrophobicity/2'>Hydrophobicity</scene> ). The hydrophilic effect, or the desire for proteins to be at a specific position regarding water, is the single most important determinant of protein folding. These regions can be displayed with the hydrophobic regions in gray and the polar, hydrophillic regions in purple. This coloration highlights the location of these regions, showing that the majority of the hydrophobic regions are inside of the protein and that the majority of the hydrophillic regions are on the outside of the protein.<br />
<br />
<br />
''Polarity''<br />
<br />
The nature of the amino acid sidechains in the lysozyme polypeptide sequence leads to regions of varying hydrophobicities and polarities of the enzyme structure. The presence of certain regions of hydrophilicity and hydrophobicity is a driving force in determining protein structure when folding. The varying polarities of the side chains influence the locations of residues in the enzyme structure. Nonpolar residues appear blue, and polar residues appear red in the following <scene name='Sandbox_38/Non_polar_blue/1'>polarity</scene> display of lysozyme. Nonpolar residues will display hydrophobic tendencies occurring mostly on the interior of the enzyme while polar residues will increase in abundance on the surface of the protein in order to increase contact with the aqueous solvent so as to satisfy their hydrophilic nature. By observing a space-filled structural depiction of <scene name='Sandbox_38/Non_polar_blu/1'>lysozyme polarity</scene> with polar molecules colored red and nonpolar molecules colored blue the influence of polarity on nucleotide arrangement and protein folding is evident, with the blue (nonpolar) regions inside the red (polar) regions. The presence of <scene name='Sandbox_39/Water/1'>water</scene> interacting with the various hydrophilic residues is depicted to further display how polarity affects structure. Water is depicted as yellow, and the polar and nonpolar regions remain their respective color.<br />
<br />
<br />
''Charge''<br />
<br />
Charges of the various regions of the lysozyme structure display a hydrophilic nature and thus also affect the location of that region of polypeptides and the overall folding of the protein. Charged regions of the protein will display hydrophilic tendencies and therefore will most often be located on the surface of the lysozyme molecule where they can interact with the aqueous solvent. Non-charged portions will display hydrophobic tendencies and be located on the interior of the molecule. The effect of various <scene name='Sandbox_38/Rb/1'>charges</scene> on protein structure can be visualized with charged molecules represented by red anionic and blue cationic regions, and uncharged regions colored in grey. This depiction of lysozyme uses a spacefill representation of lysozyme to depict <scene name='Sandbox_38/Chargeddd/1'>charges</scene>.<br />
<br />
<br />
<br />
= Applications of Lysozyme =<br />
<br />
Since lysozyme has been widely recognized for its antibacterial and antifungal properties, it has a wide variety of uses both in biochemical and pharmaceutical applications. In molecular biology, lysozyme is often used in the alkaline-lysis procedure for extracting and isolating plasmid DNA. It is used extensively in the pharmaceutical field for destroying gram-positive bacteria, and can be used to support already-existing immune defenses to fight bacterial infections. This enzyme is particularly important for preventing bacterial diseases in infants. Because of its antibacterial properties, lysozyme can also be used in the food industry to help prevent spoilage of foods.<br />
<br />
= References =<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Sandbox_51&diff=1222739Sandbox 512011-03-31T01:04:15Z<p>John Ripollone: </p>
<hr />
<div><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
{{Template:Oberholser_Sandbox_Reservation}}<br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
= '''Lysozyme''' =<br />
<br />
=== Introduction ===<br />
<br />
Lysozyme - also known as muramidase, or glycoside hydrolase - is a powerful enzyme of biological significance found in abundance in tears, saliva, and human milk. In humans, it is encoded in the ''LYZ'' gene. Although it is responsible for the initial digestion of starches in the mouth, it is most widely identified as a non-specific defense in gram positive bacteria and in many species of fungi. Due to its antibacterial effects, it is a strong component of the innate immune system, and is an important part of an infant's diet to ward off diarrheal diseases. Since it is a small, easily available, and highly stable protein containing only 129 amino acid residues, it has been subject to extensive research regarding its function and structure. Hen Egg White (HEW) Lysozyme is shown below.<br />
<br />
=== History ===<br />
<br />
Lysozyme is an enzyme known for its unique ability to degrade the polysaccharide architecture of many kinds of cell walls, normally for the purpose of protection against bacterial infection<ref>Lysozyme. 2010. Citizendium.org. http://en.citizendium.org/wiki/Lysozyme</ref>. Its effects were first noticed by Laschtschenko in 1909. It was officially characterized and termed “lysozyme” by Alexander Fleming, the same person credited for the accidental discovery of penicillin. <br />
The characterization of lysozyme in 1922 by Alexander Fleming was providential in that the undertaken experiment related to the discovery of lysozyme was not geared toward any knowledge of such a protein as lysozyme <ref>Lysozyme. 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. During the unrelated experiment, nasal drippings were inadvertently introduced to a petri dish containing a bacterial culture, which culture consequently exhibited the results of an as yet unknown enzymatic reaction. The observation of this unknown reaction led to further research on the components of this reaction as well as to the corresponding identification of the newfound "lysozyme." Fleming's discovery was complemented by David C. Phillips' 1965 description of the three-dimensional structure of lysozyme via a 200 pm resolution model obtained from X-ray crystallography <ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. Phillips' work was especially groundbreaking since Phillips had managed to successfully elucidate the structure of an enzyme via X-ray crystallography - a feat that had never before been accomplished<ref>Bugg, T. 1997. An Introduction to Enzyme and Coenzyme Chemistry. Blackwell Science Ltd., Oxford </ref>. Phillips' research also led to the first sufficiently described enzymatic mechanism of catalytic action <ref>1967. Proc R Soc Lond B Bio 167 (1009): 389–401.</ref>. Thus, Phillips' elucidation of the function of lysozyme led Phillips to reach a more general conclusion on the diversity of enzymatic chemical action in relation to enzymatic structure. Clearly, the findings of Phillips as well as the more general historical development of the understanding of the structure and function of lysozyme have been paramount to the more general realm of enzyme chemistry.<br />
<br />
<br />
[[Image:nag-nam2.jpg|thumb|left|350px|Lysozyme Cleavage Site]]<br />
<ref>Image from: http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm</ref> <br />
<br />
=== Function===<br />
<br />
Lysozyme is known for damaging bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid (NAM) and N-acetyl-D-glucosamine (NAG) residues in peptidoglycan, and between N-acetyl-D-glucosamine residues in chitodextrins. In this way, lysozyme is efficient in lysing the cell walls of both bacteria and fungi. The location of cleavage for lysozyme on this architectural theme is the β(1-4) glycosidic linkage connecting the C1 carbon of NAM to the C4 carbon of NAG. <br />
<br />
The particular substrate of preference for this cleavage type is a (NAG-NAM)₃ hexasaccharide, within which substrate occurs the<br />
cleaving target glycosidic bond, NAM₄-β-O-NAG₅. The individual hexasaccharide binding units are designated A-F, with NAM₄-β-O-NAG₅ glycosidic bond cleavage preference corresponding to a D-E unit glycosidic bond cleavage preference. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='right' caption='' /><br />
<br />
<br />
= Enzymatic Activity of Lysozyme =<br />
<br />
Enzymes are designed to attract and to bind specific substrates. The active site of and lysozyme and its specific ligands are described in the following sections<br />
<br />
=== Active Site ===<br />
<br />
The <scene name='Sandbox_39/Active_site/1'>active site</scene> of lysozyme is formulated as a prominent cleft outlined by the two aforementioned catalytic amino acids, Glu 35 and Asp 52. The active site is geometrically bent to augment ligand binding, and the two amino acids interact with the ligand in the binding site. Asp52 is depicted in green, and Glu35 is depicted in purple. <br />
<br />
=== Ligands ===<br />
<br />
A <scene name='Sandbox_39/Ligands_1/1'>ligand</scene> is able to bind to the active site of an enzyme to form a biologically relevant complex. The model to the right shows a space-filling model of lysozyme with the protein distinguishable in brown and the ligand distinguishable in green. Another model of the ligand can be seen in this <br />
<scene name='Sandbox_39/Ribbon_ligand/1'>ribbon diagram</scene>, with the ligand protruding as a space-filling model from the active site. Here, it is clear that the ligand is a polysaccharide. <br />
<br />
The lysozyme reaction is characterized by hydrolysis of the beta (1-4) glycosidic bond between NAM and NAG. Lysozyme has a very specific active site, which can bind only six sugar rings from a polysaccharide chain. Once lysozyme binds to this chain, it hydrolyzes them. These six sugar rings represent the ligand of lysozyme. The lysozyme then distorts the fourth sugar in the six-membered complex, producing stress on the molecule and breaking the glycosidic bond.<br />
<br />
The amino acid side-chains Glu35 and Asp52 are critical to the activity of this enzyme. Glu35 acts as a proton donor to the glycosidic bond, cleaving the C-O bond in the substrate, and Asp52 acts as a nucleophile to generate a glycosyl enzyme intermediate. The glycosyl enzyme intermediate then reacts with a water molecule to give the product of hydrolysis. <br />
<br />
[[Image:jrip.jpg|thumb|left|350px|Mechanism of Lysozyme]]<br />
<ref>Image from: http://www.google.com/imgres?imgurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/pics-and-strucs/lysozyme-mech.gif&imgrefurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm&usg=__ormapG4XKg-tR5GrMSOdSMTV4vE=&h=603&w=801&sz=7&hl=en&start=17&zoom=1&tbnid=nvr9gvFrUILDkM:&tbnh=143&tbnw=189&prev=/images%3Fq%3DThe%2Blysozyme%2Breaction%2Bmechanism%26um%3D1%26hl%3Den%26sa%3DN%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C304&um=1&itbs=1&iact=hc&vpx=521&vpy=349&dur=448&hovh=191&hovw=254&tx=140&ty=48&ei=JQ_LTPKzLIjCsAPkzt2KDg&oei=IA_LTP74OsG78gapm-GFAQ&esq=2&page=2&ndsp=18&ved=1t:429,r:2,s:17&biw=1280&bih=647</ref><br />
<br />
=== Mechanism === <br />
<br />
The lysozyme mechanism of action results in the hydrolysis of a glycoside (hence the familial distinction of lysozyme as a glycosylase<ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>), which corresponds to the conversion of an acetal to a hemiacetal, which reaction (general degradation of glycosidic bond to units "capped" by newly formed hydroxyl groups) necessitates acid catalysis, since the conversion of acetal to hemiacetal involves the protonation of the reactant oxygen prior to actual bond cleavage. <ref>Pratt, C.W., Voet, D., Voet, J.G. Fundamentals of Biochemistry - Life at the Molecular Level - Third Edition. Voet, Voet and Pratt, 2008.</ref>. Furthermore, the transition state obtained from this protonation is a covalent, oxonium ion, intermediate that must obtain resonance stabilization. The need for some means of acid catalysis and covalent resonance stabilization is adequately provided by the Glu 35 and Asp 52 residues of lysozyme, respectively. The reaction mechanism of lysozyme is demonstrated below. In the following image, the reaction begins at the upper left-hand side, and proceeds according to reaction arrows.<br />
<br />
As seen to the left, lysozyme works by hydrolyzing the glycosidic bond, distorting the bond between the NAM and NAG. This produces a glycosyl enzyme intermediate, which reacts with a water molecule to produce the product and the unchanged enzyme.<br />
=== Inhibitors ===<br />
<br />
Lysozyme is best inhibited by small saccharides which act competitively with the natural substrate. The smaller saccharides will bind to the first three binding sites of the cleft (sites A-C), but will not reach sites D and E, where the enzyme cuts the glycosidic bond. So, the competitive inhibitor will stick in the cleft, not allowing the substrate to bind to the enzyme complex.<ref>http://mcdb-webarchive.mcdb.ucsb.edu/sears/biochemistry/tw-enz/lysozyme/HEWL/lysozyme-overview.htm</ref> Several known inhibitors of lysozyme are: SDS, N-acetyl-D-glucosamine, and various alcohols and oxidizing agents.<ref>http://www.worthington-biochem.com/ly/default.html</ref> <br />
<br />
=== Zymogen of Lysozyme: Enzymatic Precursor ===<br />
<br />
Zymogens are inactive enzyme precursors. Enzymes are developed in an inactive way to prevent the enzyme from digesting the cell that produced it. This process also prevents the enzyme from becoming active in the wrong portion of the body. Lysozyme's zymogen, simply titled “pre-lysozyme,” was sequenced in 1977 by R D Palmiter, J Gagnon, L H Ericsson and K A Walsh, and has since been sequenced much more extensively. <br />
<br />
<applet load='1hew' size='350' frame='true' align='right' caption='' /><br />
<br />
= Composition and Structure of Lysozyme =<br />
<br />
All proteins consist of carbon, hydrogen, nitrogen, oxygen, and sulfur, as do most organic molecules. Enzymes are composed in such a way as to maximize their reactivity with their desired substrate, increasing the efficiency of biological reactions. The <scene name='Sandbox_39/Elements/1'>composition of lysozyme</scene> can be seen on the left, with the carbon atoms outlined in gray, oxygen atoms in red, nitrogen atoms in blue, sulfur atoms in yellow, and the three-letter abbreviation for the <scene name='Sandbox_39/Amino_acid_residues/1'>amino acid residues</scene> in purple.<br />
<br />
Lysozyme, like all proteins, also contains a <scene name='Sandbox_39/C_and_n_terminal_residues/1'> 3'C and 5'N terminal </scene>, and these can be seen by following the colors of the rainbow across the molecule. Starting at the red end, the 3' C terminal end, one can work the entire way through to the 5' N terminal end, showing the folding pattern and chain of the protein.<br />
<br />
== Secondary Structure ==<br />
<br />
Lysozyme contains five <scene name='Sandbox_38/A/2'>alpha helical</scene> regions and five regions containing <scene name='Sandbox_38/B/1'>beta sheets</scene> as displayed in this <scene name='Sandbox_38/Alphab/1'>image</scene>. Linking these secondary structures, a number of beta turns and a large number of random coils make up the remainder of the polypeptide backbone. The polypeptide backbone of lysozyme involved in the 3 antiparallel beta sheets display the beta hairpin motif of supersecondary structure. This depiction of lysozyme contains an antiparallel beta-pleated sheet, which contributes greatly to the stability of the molecule by providing the correct alignment of hydrogen bonds. Lysozyme also contains a great deal of random coil, which is seen in the white regions of the molecule.<br />
<br />
==Amino Acid Residues==<br />
<br />
The amino acids present in the lysozyme polypeptide sequence have a direct influence not only on primary structure, but also on the secondary and tertiary structures, which can be influenced by polarity and charge of the sidechains. The various amino acid <scene name='Sandbox_38/Aminoi/1'>residues</scene> differ in their properties because of the great variety of side chains present on each amino acid. Polar and nonpolar (and charged and uncharged) side chains lead to various degrees of hydrophobicity and hydrophilicity, which affects protein folding. In lysozyme, these <scene name='Sandbox_38/Sc/1'>side chains</scene> are displayed for each amino acid residue.<br />
<br />
= Bonding Interactions =<br />
<br />
=== Disulfide Bonding in Lysozyme ===<br />
<br />
Lysozyme contains four <scene name='Sandbox_39/Disulfide_bonds/1'>disulfide bonds</scene> involving eight cysteine residues, which are highlighted in yellow on the left. Disulfide bonds are intramolecular forces that stabilize the tertiary structure of many proteins. Disulfide bonds are present in four locations in lysozyme: between Cys 6 and Cys 127, between Cys 30 and Cys 115, between Cys 64 and Cys 80 and between Cys 76 and Cys 94. <br />
<br />
=== Hydrogen Bonding ===<br />
<br />
In all proteins <scene name='Sandbox_39/Hydrogen_bonds/2'>hydrogen bonds</scene> are essential for stability. In this ribbon diagram, the hydrogen bonds can be seen between the secondary structures of lysozyme highlighted in orange. Since the double bonds of the alpha carbons in the main chain of lysozyme cause torsional strain, lysozyme is limited to very specific hydrogen bonding between the amino acid residues. This representation clearly shows how crucial hydrogen bonding is to help maintain the stability of the protein. <br />
<br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='left' caption='' /><br />
<br />
=== Hydrophobicity ===<br />
<br />
Lysozyme contains both hydrophobic and hydrophilic regions ( <scene name='Sandbox_39/Hydrophobicity/2'>Hydrophobicity</scene> ). The hydrophilic effect, or the desire for proteins to be at a specific position regarding water, is the single most important determinant of protein folding. These regions can be displayed with the hydrophobic regions in gray and the polar, hydrophillic regions in purple. This coloration highlights the location of these regions, showing that the majority of the hydrophobic regions are inside of the protein and that the majority of the hydrophillic regions are on the outside of the protein.<br />
<br />
<br />
====Polarity====<br />
<br />
The nature of the amino acid sidechains in the lysozyme polypeptide sequence leads to regions of varying hydrophobicities and polarities of the enzyme structure. The presence of certain regions of hydrophilicity and hydrophobicity is a driving force in determining protein structure when folding. The varying polarities of the side chains influence the locations of residues in the enzyme structure. Nonpolar residues appear blue, and polar residues appear red in the following <scene name='Sandbox_38/Non_polar_blue/1'>polarity</scene> display of lysozyme. Nonpolar residues will display hydrophobic tendencies occurring mostly on the interior of the enzyme while polar residues will increase in abundance on the surface of the protein in order to increase contact with the aqueous solvent so as to satisfy their hydrophilic nature. By observing a space-filled structural depiction of <scene name='Sandbox_38/Non_polar_blu/1'>lysozyme polarity</scene> with polar molecules colored red and nonpolar molecules colored blue the influence of polarity on nucleotide arrangement and protein folding is evident, with the blue (nonpolar) regions inside the red (polar) regions. The presence of <scene name='Sandbox_39/Water/1'>water</scene> interacting with the various hydrophilic residues is depicted to further display how polarity affects structure. Water is depicted as yellow, and the polar and nonpolar regions remain their respective color.<br />
<br />
<br />
====Charge====<br />
<br />
Charges of the various regions of the lysozyme structure display a hydrophilic nature and thus also affect the location of that region of polypeptides and the overall folding of the protein. Charged regions of the protein will display hydrophilic tendencies and therefore will most often be located on the surface of the lysozyme molecule where they can interact with the aqueous solvent. Non-charged portions will display hydrophobic tendencies and be located on the interior of the molecule. The effect of various <scene name='Sandbox_38/Rb/1'>charges</scene> on protein structure can be visualized with charged molecules represented by red anionic and blue cationic regions, and uncharged regions colored in grey. This depiction of lysozyme uses a spacefill representation of lysozyme to depict <scene name='Sandbox_38/Chargeddd/1'>charges</scene>.<br />
<br />
<br />
<br />
=== Hydrogen Bonding ===<br />
<br />
In all proteins <scene name='Sandbox_39/Hydrogen_bonds/2'>hydrogen bonds</scene> are essential for stability. In this ribbon diagram, the hydrogen bonds can be seen between the secondary structures of lysozyme highlighted in orange. Since the double bonds of the alpha carbons in the main chain of lysozyme cause torsional strain, lysozyme is limited to very specific hydrogen bonding between the amino acid residues. This representation clearly shows how crucial hydrogen bonding is to help maintain the stability of the protein. <br />
<br />
<br />
= Applications of Lysozyme =<br />
<br />
Since lysozyme has been widely recognized for its antibacterial and antifungal properties, it has a wide variety of uses both in biochemical and pharmaceutical applications. In molecular biology, lysozyme is often used in the alkaline-lysis procedure for extracting and isolating plasmid DNA. It is used extensively in the pharmaceutical field for destroying gram-positive bacteria, and can be used to support already-existing immune defenses to fight bacterial infections. This enzyme is particularly important for preventing bacterial diseases in infants. Because of its antibacterial properties, lysozyme can also be used in the food industry to help prevent spoilage of foods.<br />
<br />
= References =<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Sandbox_51&diff=1222737Sandbox 512011-03-31T01:01:51Z<p>John Ripollone: </p>
<hr />
<div><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
{{Template:Oberholser_Sandbox_Reservation}}<br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
= '''Lysozyme''' =<br />
<br />
=== Introduction ===<br />
<br />
Lysozyme - also known as muramidase, or glycoside hydrolase - is a powerful enzyme of biological significance found in abundance in tears, saliva, and human milk. In humans, it is encoded in the ''LYZ'' gene. Although it is responsible for the initial digestion of starches in the mouth, it is most widely identified as a non-specific defense in gram positive bacteria and in many species of fungi. Due to its antibacterial effects, it is a strong component of the innate immune system, and is an important part of an infant's diet to ward off diarrheal diseases. Since it is a small, easily available, and highly stable protein containing only 129 amino acid residues, it has been subject to extensive research regarding its function and structure. Hen Egg White (HEW) Lysozyme is shown below.<br />
<br />
=== History ===<br />
<br />
Lysozyme is an enzyme known for its unique ability to degrade the polysaccharide architecture of many kinds of cell walls, normally for the purpose of protection against bacterial infection<ref>Lysozyme. 2010. Citizendium.org. http://en.citizendium.org/wiki/Lysozyme</ref>. Its effects were first noticed by Laschtschenko in 1909. It was officially characterized and termed “lysozyme” by Alexander Fleming, the same person credited for the accidental discovery of penicillin. <br />
The characterization of lysozyme in 1922 by Alexander Fleming was providential in that the undertaken experiment related to the discovery of lysozyme was not geared toward any knowledge of such a protein as lysozyme <ref>Lysozyme. 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. During the unrelated experiment, nasal drippings were inadvertently introduced to a petri dish containing a bacterial culture, which culture consequently exhibited the results of an as yet unknown enzymatic reaction. The observation of this unknown reaction led to further research on the components of this reaction as well as to the corresponding identification of the newfound "lysozyme." Fleming's discovery was complemented by David C. Phillips' 1965 description of the three-dimensional structure of lysozyme via a 200 pm resolution model obtained from X-ray crystallography <ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. Phillips' work was especially groundbreaking since Phillips had managed to successfully elucidate the structure of an enzyme via X-ray crystallography - a feat that had never before been accomplished<ref>Bugg, T. 1997. An Introduction to Enzyme and Coenzyme Chemistry. Blackwell Science Ltd., Oxford </ref>. Phillips' research also led to the first sufficiently described enzymatic mechanism of catalytic action <ref>1967. Proc R Soc Lond B Bio 167 (1009): 389–401.</ref>. Thus, Phillips' elucidation of the function of lysozyme led Phillips to reach a more general conclusion on the diversity of enzymatic chemical action in relation to enzymatic structure. Clearly, the findings of Phillips as well as the more general historical development of the understanding of the structure and function of lysozyme have been paramount to the more general realm of enzyme chemistry.<br />
<br />
<br />
[[Image:nag-nam2.jpg|thumb|left|350px|Lysozyme Cleavage Site]]<br />
<ref>Image from: http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm</ref> <br />
<br />
=== Function===<br />
<br />
Lysozyme is known for damaging bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid (NAM) and N-acetyl-D-glucosamine (NAG) residues in peptidoglycan, and between N-acetyl-D-glucosamine residues in chitodextrins. In this way, lysozyme is efficient in lysing the cell walls of both bacteria and fungi. The location of cleavage for lysozyme on this architectural theme is the β(1-4) glycosidic linkage connecting the C1 carbon of NAM to the C4 carbon of NAG. <br />
<br />
The particular substrate of preference for this cleavage type is a (NAG-NAM)₃ hexasaccharide, within which substrate occurs the<br />
cleaving target glycosidic bond, NAM₄-β-O-NAG₅. The individual hexasaccharide binding units are designated A-F, with NAM₄-β-O-NAG₅ glycosidic bond cleavage preference corresponding to a D-E unit glycosidic bond cleavage preference. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='right' caption='' /><br />
<br />
<br />
= Enzymatic Activity of Lysozyme =<br />
<br />
Enzymes are designed to attract and to bind specific substrates. The active site of and lysozyme and its specific ligands are described in the following sections<br />
<br />
=== Active Site ===<br />
<br />
The <scene name='Sandbox_39/Active_site/1'>active site</scene> of lysozyme is formulated as a prominent cleft outlined by the two aforementioned catalytic amino acids, Glu 35 and Asp 52. The active site is geometrically bent to augment ligand binding, and the two amino acids interact with the ligand in the binding site. Asp52 is depicted in green, and Glu35 is depicted in purple. <br />
<br />
=== Ligands ===<br />
<br />
A <scene name='Sandbox_39/Ligands_1/1'>ligand</scene> is able to bind to the active site of an enzyme to form a biologically relevant complex. The model to the right shows a space-filling model of lysozyme with the protein distinguishable in brown and the ligand distinguishable in green. Another model of the ligand can be seen in this <br />
<scene name='Sandbox_39/Ribbon_ligand/1'>ribbon diagram</scene>, with the ligand protruding as a space-filling model from the active site. Here, it is clear that the ligand is a polysaccharide. <br />
<br />
The lysozyme reaction is characterized by hydrolysis of the beta (1-4) glycosidic bond between NAM and NAG. Lysozyme has a very specific active site, which can bind only six sugar rings from a polysaccharide chain. Once lysozyme binds to this chain, it hydrolyzes them. These six sugar rings represent the ligand of lysozyme. The lysozyme then distorts the fourth sugar in the six-membered complex, producing stress on the molecule and breaking the glycosidic bond.<br />
<br />
The amino acid side-chains Glu35 and Asp52 are critical to the activity of this enzyme. Glu35 acts as a proton donor to the glycosidic bond, cleaving the C-O bond in the substrate, and Asp52 acts as a nucleophile to generate a glycosyl enzyme intermediate. The glycosyl enzyme intermediate then reacts with a water molecule to give the product of hydrolysis. <br />
<br />
[[Image:jrip.jpg|thumb|left|350px|Mechanism of Lysozyme]]<br />
<ref>Image from: http://www.google.com/imgres?imgurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/pics-and-strucs/lysozyme-mech.gif&imgrefurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm&usg=__ormapG4XKg-tR5GrMSOdSMTV4vE=&h=603&w=801&sz=7&hl=en&start=17&zoom=1&tbnid=nvr9gvFrUILDkM:&tbnh=143&tbnw=189&prev=/images%3Fq%3DThe%2Blysozyme%2Breaction%2Bmechanism%26um%3D1%26hl%3Den%26sa%3DN%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C304&um=1&itbs=1&iact=hc&vpx=521&vpy=349&dur=448&hovh=191&hovw=254&tx=140&ty=48&ei=JQ_LTPKzLIjCsAPkzt2KDg&oei=IA_LTP74OsG78gapm-GFAQ&esq=2&page=2&ndsp=18&ved=1t:429,r:2,s:17&biw=1280&bih=647</ref><br />
<br />
=== Mechanism === <br />
<br />
The lysozyme mechanism of action results in the hydrolysis of a glycoside (hence the familial distinction of lysozyme as a glycosylase<ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>), which corresponds to the conversion of an acetal to a hemiacetal, which reaction (general degradation of glycosidic bond to units "capped" by newly formed hydroxyl groups) necessitates acid catalysis, since the conversion of acetal to hemiacetal involves the protonation of the reactant oxygen prior to actual bond cleavage. <ref>Pratt, C.W., Voet, D., Voet, J.G. Fundamentals of Biochemistry - Life at the Molecular Level - Third Edition. Voet, Voet and Pratt, 2008.</ref>. Furthermore, the transition state obtained from this protonation is a covalent, oxonium ion, intermediate that must obtain resonance stabilization. The need for some means of acid catalysis and covalent resonance stabilization is adequately provided by the Glu 35 and Asp 52 residues of lysozyme, respectively. The reaction mechanism of lysozyme is demonstrated below. In the following image, the reaction begins at the upper left-hand side, and proceeds according to reaction arrows.<br />
<br />
As seen to the left, lysozyme works by hydrolyzing the glycosidic bond, distorting the bond between the NAM and NAG. This produces a glycosyl enzyme intermediate, which reacts with a water molecule to produce the product and the unchanged enzyme.<br />
=== Inhibitors ===<br />
<br />
Lysozyme is best inhibited by small saccharides which act competitively with the natural substrate. The smaller saccharides will bind to the first three binding sites of the cleft (sites A-C), but will not reach sites D and E, where the enzyme cuts the glycosidic bond. So, the competitive inhibitor will stick in the cleft, not allowing the substrate to bind to the enzyme complex.<ref>http://mcdb-webarchive.mcdb.ucsb.edu/sears/biochemistry/tw-enz/lysozyme/HEWL/lysozyme-overview.htm</ref> Several known inhibitors of lysozyme are: SDS, N-acetyl-D-glucosamine, and various alcohols and oxidizing agents.<ref>http://www.worthington-biochem.com/ly/default.html</ref> <br />
<br />
=== Zymogen of Lysozyme: Enzymatic Precursor ===<br />
<br />
Zymogens are inactive enzyme precursors. Enzymes are developed in an inactive way to prevent the enzyme from digesting the cell that produced it. This process also prevents the enzyme from becoming active in the wrong portion of the body. Lysozyme's zymogen, simply titled “pre-lysozyme,” was sequenced in 1977 by R D Palmiter, J Gagnon, L H Ericsson and K A Walsh, and has since been sequenced much more extensively. <br />
<br />
<applet load='1hew' size='350' frame='true' align='right' caption='' /><br />
<br />
= Composition and Structure of Lysozyme =<br />
<br />
All proteins consist of carbon, hydrogen, nitrogen, oxygen, and sulfur, as do most organic molecules. Enzymes are composed in such a way as to maximize their reactivity with their desired substrate, increasing the efficiency of biological reactions. The <scene name='Sandbox_39/Elements/1'>composition of lysozyme</scene> can be seen on the left, with the carbon atoms outlined in gray, oxygen atoms in red, nitrogen atoms in blue, sulfur atoms in yellow, and the three-letter abbreviation for the <scene name='Sandbox_39/Amino_acid_residues/1'>amino acid residues</scene> in purple.<br />
<br />
Lysozyme, like all proteins, also contains a <scene name='Sandbox_39/C_and_n_terminal_residues/1'> 3'C and 5'N terminal </scene>, and these can be seen by following the colors of the rainbow across the molecule. Starting at the red end, the 3' C terminal end, one can work the entire way through to the 5' N terminal end, showing the folding pattern and chain of the protein.<br />
<br />
== Secondary Structure ==<br />
<br />
Lysozyme contains five <scene name='Sandbox_38/A/2'>alpha helical</scene> regions and five regions containing <scene name='Sandbox_38/B/1'>beta sheets</scene> as displayed in this <scene name='Sandbox_38/Alphab/1'>image</scene>. Linking these secondary structures, a number of beta turns and a large number of random coils make up the remainder of the polypeptide backbone. The polypeptide backbone of lysozyme involved in the 3 antiparallel beta sheets display the beta hairpin motif of supersecondary structure. This depiction of lysozyme contains an antiparallel beta-pleated sheet, which contributes greatly to the stability of the molecule by providing the correct alignment of hydrogen bonds. Lysozyme also contains a great deal of random coil, which is seen in the white regions of the molecule.<br />
<br />
==Amino Acid Residues==<br />
<br />
The amino acids present in the lysozyme polypeptide sequence have a direct influence not only on primary structure, but also on the secondary and tertiary structures, which can be influenced by polarity and charge of the sidechains. The various amino acid <scene name='Sandbox_38/Aminoi/1'>residues</scene> differ in their properties because of the great variety of side chains present on each amino acid. Polar and nonpolar (and charged and uncharged) side chains lead to various degrees of hydrophobicity and hydrophilicity, which affects protein folding. In lysozyme, these <scene name='Sandbox_38/Sc/1'>side chains</scene> are displayed for each amino acid residue.<br />
<br />
= Bonding Interactions =<br />
<br />
=== Disulfide Bonding in Lysozyme ===<br />
<br />
Lysozyme contains four <scene name='Sandbox_39/Disulfide_bonds/1'>disulfide bonds</scene> involving eight cysteine residues, which are highlighted in yellow on the left. Disulfide bonds are intramolecular forces that stabilize the tertiary structure of many proteins. Disulfide bonds are present in four locations in lysozyme: between Cys 6 and Cys 127, between Cys 30 and Cys 115, between Cys 64 and Cys 80 and between Cys 76 and Cys 94. <br />
<br />
=== Hydrogen Bonding ===<br />
<br />
In all proteins <scene name='Sandbox_39/Hydrogen_bonds/2'>hydrogen bonds</scene> are essential for stability. In this ribbon diagram, the hydrogen bonds can be seen between the secondary structures of lysozyme highlighted in orange. Since the double bonds of the alpha carbons in the main chain of lysozyme cause torsional strain, lysozyme is limited to very specific hydrogen bonding between the amino acid residues. This representation clearly shows how crucial hydrogen bonding is to help maintain the stability of the protein. <br />
<br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='left' caption='' /><br />
<br />
=== Hydrophobicity ===<br />
<br />
Lysozyme contains both hydrophobic and hydrophilic regions ( <scene name='Sandbox_39/Hydrophobicity/2'>Hydrophobicity</scene> ). The hydrophilic effect, or the desire for proteins to be at a specific position regarding water, is the single most important determinant of protein folding. These regions can be displayed with the hydrophobic regions in gray and the polar, hydrophillic regions in purple. This coloration highlights the location of these regions, showing that the majority of the hydrophobic regions are inside of the protein and that the majority of the hydrophillic regions are on the outside of the protein.<br />
<br />
Here, lysozyme can also be seen interacting with <scene name='Sandbox_39/Water/1'>water</scene>, demonstrating how water remains almost exclusively on the outside of the molecule where the polar residues reside. <br />
<br />
====Polarity====<br />
<br />
The nature of the amino acid sidechains in the lysozyme polypeptide sequence leads to regions of varying hydrophobicities and polarities of the enzyme structure. The presence of certain regions of hydrophilicity and hydrophobicity is a driving force in determining protein structure when folding. The varying polarities of the side chains influence the locations of residues in the enzyme structure. Nonpolar residues appear blue, and polar residues appear red in the following <scene name='Sandbox_38/Non_polar_blue/1'>polarity</scene> display of lysozyme. Nonpolar residues will display hydrophobic tendencies occurring mostly on the interior of the enzyme while polar residues will increase in abundance on the surface of the protein in order to increase contact with the aqueous solvent so as to satisfy their hydrophilic nature. By observing a space-filled structural depiction of <scene name='Sandbox_38/Non_polar_blu/1'>lysozyme polarity</scene> with polar molecules colored red and nonpolar molecules colored blue the influence of polarity on nucleotide arrangement and protein folding is evident, with the blue (nonpolar) regions inside the red (polar) regions. The presence of <scene name='Sandbox_38/Water/1'>water molecules</scene> interacting with the various hydrophilic residues is depicted to further display how polarity affects structure. Water is depicted as yellow, and the polar and nonpolar regions remain their respective color.<br />
<br />
<br />
====Charge====<br />
<br />
Charges of the various regions of the lysozyme structure display a hydrophilic nature and thus also affect the location of that region of polypeptides and the overall folding of the protein. Charged regions of the protein will display hydrophilic tendencies and therefore will most often be located on the surface of the lysozyme molecule where they can interact with the aqueous solvent. Non-charged portions will display hydrophobic tendencies and be located on the interior of the molecule. The effect of various <scene name='Sandbox_38/Rb/1'>charges</scene> on protein structure can be visualized with charged molecules represented by red anionic and blue cationic regions, and uncharged regions colored in grey. This depiction of lysozyme uses a spacefill representation of lysozyme to depict <scene name='Sandbox_38/Chargeddd/1'>charges</scene>.<br />
<br />
<br />
<br />
=== Hydrogen Bonding ===<br />
<br />
In all proteins <scene name='Sandbox_39/Hydrogen_bonds/2'>hydrogen bonds</scene> are essential for stability. In this ribbon diagram, the hydrogen bonds can be seen between the secondary structures of lysozyme highlighted in orange. Since the double bonds of the alpha carbons in the main chain of lysozyme cause torsional strain, lysozyme is limited to very specific hydrogen bonding between the amino acid residues. This representation clearly shows how crucial hydrogen bonding is to help maintain the stability of the protein. <br />
<br />
<br />
= Applications of Lysozyme =<br />
<br />
Since lysozyme has been widely recognized for its antibacterial and antifungal properties, it has a wide variety of uses both in biochemical and pharmaceutical applications. In molecular biology, lysozyme is often used in the alkaline-lysis procedure for extracting and isolating plasmid DNA. It is used extensively in the pharmaceutical field for destroying gram-positive bacteria, and can be used to support already-existing immune defenses to fight bacterial infections. This enzyme is particularly important for preventing bacterial diseases in infants. Because of its antibacterial properties, lysozyme can also be used in the food industry to help prevent spoilage of foods.<br />
<br />
= References =<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Sandbox_51&diff=1222736Sandbox 512011-03-31T01:00:59Z<p>John Ripollone: </p>
<hr />
<div><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
{{Template:Oberholser_Sandbox_Reservation}}<br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
= '''Lysozyme''' =<br />
<br />
=== Introduction ===<br />
<br />
Lysozyme - also known as muramidase, or glycoside hydrolase - is a powerful enzyme of biological significance found in abundance in tears, saliva, and human milk. In humans, it is encoded in the ''LYZ'' gene. Although it is responsible for the initial digestion of starches in the mouth, it is most widely identified as a non-specific defense in gram positive bacteria and in many species of fungi. Due to its antibacterial effects, it is a strong component of the innate immune system, and is an important part of an infant's diet to ward off diarrheal diseases. Since it is a small, easily available, and highly stable protein containing only 129 amino acid residues, it has been subject to extensive research regarding its function and structure. Hen Egg White (HEW) Lysozyme is shown below.<br />
<br />
=== History ===<br />
<br />
Lysozyme is an enzyme known for its unique ability to degrade the polysaccharide architecture of many kinds of cell walls, normally for the purpose of protection against bacterial infection<ref>Lysozyme. 2010. Citizendium.org. http://en.citizendium.org/wiki/Lysozyme</ref>. Its effects were first noticed by Laschtschenko in 1909. It was officially characterized and termed “lysozyme” by Alexander Fleming, the same person credited for the accidental discovery of penicillin. <br />
The characterization of lysozyme in 1922 by Alexander Fleming was providential in that the undertaken experiment related to the discovery of lysozyme was not geared toward any knowledge of such a protein as lysozyme <ref>Lysozyme. 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. During the unrelated experiment, nasal drippings were inadvertently introduced to a petri dish containing a bacterial culture, which culture consequently exhibited the results of an as yet unknown enzymatic reaction. The observation of this unknown reaction led to further research on the components of this reaction as well as to the corresponding identification of the newfound "lysozyme." Fleming's discovery was complemented by David C. Phillips' 1965 description of the three-dimensional structure of lysozyme via a 200 pm resolution model obtained from X-ray crystallography <ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. Phillips' work was especially groundbreaking since Phillips had managed to successfully elucidate the structure of an enzyme via X-ray crystallography - a feat that had never before been accomplished<ref>Bugg, T. 1997. An Introduction to Enzyme and Coenzyme Chemistry. Blackwell Science Ltd., Oxford </ref>. Phillips' research also led to the first sufficiently described enzymatic mechanism of catalytic action <ref>1967. Proc R Soc Lond B Bio 167 (1009): 389–401.</ref>. Thus, Phillips' elucidation of the function of lysozyme led Phillips to reach a more general conclusion on the diversity of enzymatic chemical action in relation to enzymatic structure. Clearly, the findings of Phillips as well as the more general historical development of the understanding of the structure and function of lysozyme have been paramount to the more general realm of enzyme chemistry.<br />
<br />
<br />
[[Image:nag-nam2.jpg|thumb|left|350px|Lysozyme Cleavage Site]]<br />
<ref>Image from: http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm</ref> <br />
<br />
=== Function===<br />
<br />
Lysozyme is known for damaging bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid (NAM) and N-acetyl-D-glucosamine (NAG) residues in peptidoglycan, and between N-acetyl-D-glucosamine residues in chitodextrins. In this way, lysozyme is efficient in lysing the cell walls of both bacteria and fungi. The location of cleavage for lysozyme on this architectural theme is the β(1-4) glycosidic linkage connecting the C1 carbon of NAM to the C4 carbon of NAG. <br />
<br />
The particular substrate of preference for this cleavage type is a (NAG-NAM)₃ hexasaccharide, within which substrate occurs the<br />
cleaving target glycosidic bond, NAM₄-β-O-NAG₅. The individual hexasaccharide binding units are designated A-F, with NAM₄-β-O-NAG₅ glycosidic bond cleavage preference corresponding to a D-E unit glycosidic bond cleavage preference. <br />
<br />
<br />
<br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='right' caption='' /><br />
<br />
= Enzymatic Activity of Lysozyme =<br />
<br />
Enzymes are designed to attract and to bind specific substrates. The active site of and lysozyme and its specific ligands are described in the following sections<br />
<br />
=== Active Site ===<br />
<br />
The <scene name='Sandbox_39/Active_site/1'>active site</scene> of lysozyme is formulated as a prominent cleft outlined by the two aforementioned catalytic amino acids, Glu 35 and Asp 52. The active site is geometrically bent to augment ligand binding, and the two amino acids interact with the ligand in the binding site. Asp52 is depicted in green, and Glu35 is depicted in purple. <br />
<br />
=== Ligands ===<br />
<br />
A <scene name='Sandbox_39/Ligands_1/1'>ligand</scene> is able to bind to the active site of an enzyme to form a biologically relevant complex. The model to the right shows a space-filling model of lysozyme with the protein distinguishable in brown and the ligand distinguishable in green. Another model of the ligand can be seen in this <br />
<scene name='Sandbox_39/Ribbon_ligand/1'>ribbon diagram</scene>, with the ligand protruding as a space-filling model from the active site. Here, it is clear that the ligand is a polysaccharide. <br />
<br />
The lysozyme reaction is characterized by hydrolysis of the beta (1-4) glycosidic bond between NAM and NAG. Lysozyme has a very specific active site, which can bind only six sugar rings from a polysaccharide chain. Once lysozyme binds to this chain, it hydrolyzes them. These six sugar rings represent the ligand of lysozyme. The lysozyme then distorts the fourth sugar in the six-membered complex, producing stress on the molecule and breaking the glycosidic bond.<br />
<br />
The amino acid side-chains Glu35 and Asp52 are critical to the activity of this enzyme. Glu35 acts as a proton donor to the glycosidic bond, cleaving the C-O bond in the substrate, and Asp52 acts as a nucleophile to generate a glycosyl enzyme intermediate. The glycosyl enzyme intermediate then reacts with a water molecule to give the product of hydrolysis. <br />
<br />
[[Image:jrip.jpg|thumb|left|350px|Mechanism of Lysozyme]]<br />
<ref>Image from: http://www.google.com/imgres?imgurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/pics-and-strucs/lysozyme-mech.gif&imgrefurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm&usg=__ormapG4XKg-tR5GrMSOdSMTV4vE=&h=603&w=801&sz=7&hl=en&start=17&zoom=1&tbnid=nvr9gvFrUILDkM:&tbnh=143&tbnw=189&prev=/images%3Fq%3DThe%2Blysozyme%2Breaction%2Bmechanism%26um%3D1%26hl%3Den%26sa%3DN%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C304&um=1&itbs=1&iact=hc&vpx=521&vpy=349&dur=448&hovh=191&hovw=254&tx=140&ty=48&ei=JQ_LTPKzLIjCsAPkzt2KDg&oei=IA_LTP74OsG78gapm-GFAQ&esq=2&page=2&ndsp=18&ved=1t:429,r:2,s:17&biw=1280&bih=647</ref><br />
<br />
=== Mechanism === <br />
<br />
The lysozyme mechanism of action results in the hydrolysis of a glycoside (hence the familial distinction of lysozyme as a glycosylase<ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>), which corresponds to the conversion of an acetal to a hemiacetal, which reaction (general degradation of glycosidic bond to units "capped" by newly formed hydroxyl groups) necessitates acid catalysis, since the conversion of acetal to hemiacetal involves the protonation of the reactant oxygen prior to actual bond cleavage. <ref>Pratt, C.W., Voet, D., Voet, J.G. Fundamentals of Biochemistry - Life at the Molecular Level - Third Edition. Voet, Voet and Pratt, 2008.</ref>. Furthermore, the transition state obtained from this protonation is a covalent, oxonium ion, intermediate that must obtain resonance stabilization. The need for some means of acid catalysis and covalent resonance stabilization is adequately provided by the Glu 35 and Asp 52 residues of lysozyme, respectively. The reaction mechanism of lysozyme is demonstrated below. In the following image, the reaction begins at the upper left-hand side, and proceeds according to reaction arrows.<br />
<br />
As seen to the left, lysozyme works by hydrolyzing the glycosidic bond, distorting the bond between the NAM and NAG. This produces a glycosyl enzyme intermediate, which reacts with a water molecule to produce the product and the unchanged enzyme.<br />
=== Inhibitors ===<br />
<br />
Lysozyme is best inhibited by small saccharides which act competitively with the natural substrate. The smaller saccharides will bind to the first three binding sites of the cleft (sites A-C), but will not reach sites D and E, where the enzyme cuts the glycosidic bond. So, the competitive inhibitor will stick in the cleft, not allowing the substrate to bind to the enzyme complex.<ref>http://mcdb-webarchive.mcdb.ucsb.edu/sears/biochemistry/tw-enz/lysozyme/HEWL/lysozyme-overview.htm</ref> Several known inhibitors of lysozyme are: SDS, N-acetyl-D-glucosamine, and various alcohols and oxidizing agents.<ref>http://www.worthington-biochem.com/ly/default.html</ref> <br />
<br />
=== Zymogen of Lysozyme: Enzymatic Precursor ===<br />
<br />
Zymogens are inactive enzyme precursors. Enzymes are developed in an inactive way to prevent the enzyme from digesting the cell that produced it. This process also prevents the enzyme from becoming active in the wrong portion of the body. Lysozyme's zymogen, simply titled “pre-lysozyme,” was sequenced in 1977 by R D Palmiter, J Gagnon, L H Ericsson and K A Walsh, and has since been sequenced much more extensively. <br />
<br />
<applet load='1hew' size='350' frame='true' align='right' caption='' /><br />
<br />
= Composition and Structure of Lysozyme =<br />
<br />
All proteins consist of carbon, hydrogen, nitrogen, oxygen, and sulfur, as do most organic molecules. Enzymes are composed in such a way as to maximize their reactivity with their desired substrate, increasing the efficiency of biological reactions. The <scene name='Sandbox_39/Elements/1'>composition of lysozyme</scene> can be seen on the left, with the carbon atoms outlined in gray, oxygen atoms in red, nitrogen atoms in blue, sulfur atoms in yellow, and the three-letter abbreviation for the <scene name='Sandbox_39/Amino_acid_residues/1'>amino acid residues</scene> in purple.<br />
<br />
Lysozyme, like all proteins, also contains a <scene name='Sandbox_39/C_and_n_terminal_residues/1'> 3'C and 5'N terminal </scene>, and these can be seen by following the colors of the rainbow across the molecule. Starting at the red end, the 3' C terminal end, one can work the entire way through to the 5' N terminal end, showing the folding pattern and chain of the protein.<br />
<br />
== Secondary Structure ==<br />
<br />
Lysozyme contains five <scene name='Sandbox_38/A/2'>alpha helical</scene> regions and five regions containing <scene name='Sandbox_38/B/1'>beta sheets</scene> as displayed in this <scene name='Sandbox_38/Alphab/1'>image</scene>. Linking these secondary structures, a number of beta turns and a large number of random coils make up the remainder of the polypeptide backbone. The polypeptide backbone of lysozyme involved in the 3 antiparallel beta sheets display the beta hairpin motif of supersecondary structure. This depiction of lysozyme contains an antiparallel beta-pleated sheet, which contributes greatly to the stability of the molecule by providing the correct alignment of hydrogen bonds. Lysozyme also contains a great deal of random coil, which is seen in the white regions of the molecule.<br />
<br />
==Amino Acid Residues==<br />
<br />
The amino acids present in the lysozyme polypeptide sequence have a direct influence not only on primary structure, but also on the secondary and tertiary structures, which can be influenced by polarity and charge of the sidechains. The various amino acid <scene name='Sandbox_38/Aminoi/1'>residues</scene> differ in their properties because of the great variety of side chains present on each amino acid. Polar and nonpolar (and charged and uncharged) side chains lead to various degrees of hydrophobicity and hydrophilicity, which affects protein folding. In lysozyme, these <scene name='Sandbox_38/Sc/1'>side chains</scene> are displayed for each amino acid residue.<br />
<br />
= Bonding Interactions =<br />
<br />
=== Disulfide Bonding in Lysozyme ===<br />
<br />
Lysozyme contains four <scene name='Sandbox_39/Disulfide_bonds/1'>disulfide bonds</scene> involving eight cysteine residues, which are highlighted in yellow on the left. Disulfide bonds are intramolecular forces that stabilize the tertiary structure of many proteins. Disulfide bonds are present in four locations in lysozyme: between Cys 6 and Cys 127, between Cys 30 and Cys 115, between Cys 64 and Cys 80 and between Cys 76 and Cys 94. <br />
<br />
=== Hydrogen Bonding ===<br />
<br />
In all proteins <scene name='Sandbox_39/Hydrogen_bonds/2'>hydrogen bonds</scene> are essential for stability. In this ribbon diagram, the hydrogen bonds can be seen between the secondary structures of lysozyme highlighted in orange. Since the double bonds of the alpha carbons in the main chain of lysozyme cause torsional strain, lysozyme is limited to very specific hydrogen bonding between the amino acid residues. This representation clearly shows how crucial hydrogen bonding is to help maintain the stability of the protein. <br />
<br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='left' caption='' /><br />
<br />
=== Hydrophobicity ===<br />
<br />
Lysozyme contains both hydrophobic and hydrophilic regions ( <scene name='Sandbox_39/Hydrophobicity/2'>Hydrophobicity</scene> ). The hydrophilic effect, or the desire for proteins to be at a specific position regarding water, is the single most important determinant of protein folding. These regions can be displayed with the hydrophobic regions in gray and the polar, hydrophillic regions in purple. This coloration highlights the location of these regions, showing that the majority of the hydrophobic regions are inside of the protein and that the majority of the hydrophillic regions are on the outside of the protein.<br />
<br />
Here, lysozyme can also be seen interacting with <scene name='Sandbox_39/Water/1'>water</scene>, demonstrating how water remains almost exclusively on the outside of the molecule where the polar residues reside. <br />
<br />
====Polarity====<br />
<br />
The nature of the amino acid sidechains in the lysozyme polypeptide sequence leads to regions of varying hydrophobicities and polarities of the enzyme structure. The presence of certain regions of hydrophilicity and hydrophobicity is a driving force in determining protein structure when folding. The varying polarities of the side chains influence the locations of residues in the enzyme structure. Nonpolar residues appear blue, and polar residues appear red in the following <scene name='Sandbox_38/Non_polar_blue/1'>polarity</scene> display of lysozyme. Nonpolar residues will display hydrophobic tendencies occurring mostly on the interior of the enzyme while polar residues will increase in abundance on the surface of the protein in order to increase contact with the aqueous solvent so as to satisfy their hydrophilic nature. By observing a space-filled structural depiction of <scene name='Sandbox_38/Non_polar_blu/1'>lysozyme polarity</scene> with polar molecules colored red and nonpolar molecules colored blue the influence of polarity on nucleotide arrangement and protein folding is evident, with the blue (nonpolar) regions inside the red (polar) regions. The presence of <scene name='Sandbox_38/Water/1'>water molecules</scene> interacting with the various hydrophilic residues is depicted to further display how polarity affects structure. Water is depicted as yellow, and the polar and nonpolar regions remain their respective color.<br />
<br />
<br />
====Charge====<br />
<br />
Charges of the various regions of the lysozyme structure display a hydrophilic nature and thus also affect the location of that region of polypeptides and the overall folding of the protein. Charged regions of the protein will display hydrophilic tendencies and therefore will most often be located on the surface of the lysozyme molecule where they can interact with the aqueous solvent. Non-charged portions will display hydrophobic tendencies and be located on the interior of the molecule. The effect of various <scene name='Sandbox_38/Rb/1'>charges</scene> on protein structure can be visualized with charged molecules represented by red anionic and blue cationic regions, and uncharged regions colored in grey. This depiction of lysozyme uses a spacefill representation of lysozyme to depict <scene name='Sandbox_38/Chargeddd/1'>charges</scene>.<br />
<br />
<br />
<br />
=== Hydrogen Bonding ===<br />
<br />
In all proteins <scene name='Sandbox_39/Hydrogen_bonds/2'>hydrogen bonds</scene> are essential for stability. In this ribbon diagram, the hydrogen bonds can be seen between the secondary structures of lysozyme highlighted in orange. Since the double bonds of the alpha carbons in the main chain of lysozyme cause torsional strain, lysozyme is limited to very specific hydrogen bonding between the amino acid residues. This representation clearly shows how crucial hydrogen bonding is to help maintain the stability of the protein. <br />
<br />
<br />
= Applications of Lysozyme =<br />
<br />
Since lysozyme has been widely recognized for its antibacterial and antifungal properties, it has a wide variety of uses both in biochemical and pharmaceutical applications. In molecular biology, lysozyme is often used in the alkaline-lysis procedure for extracting and isolating plasmid DNA. It is used extensively in the pharmaceutical field for destroying gram-positive bacteria, and can be used to support already-existing immune defenses to fight bacterial infections. This enzyme is particularly important for preventing bacterial diseases in infants. Because of its antibacterial properties, lysozyme can also be used in the food industry to help prevent spoilage of foods.<br />
<br />
= References =<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Sandbox_51&diff=1222726Sandbox 512011-03-31T00:50:18Z<p>John Ripollone: </p>
<hr />
<div><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
{{Template:Oberholser_Sandbox_Reservation}}<br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
= '''Lysozyme''' =<br />
<br />
=== Introduction ===<br />
<br />
Lysozyme - also known as muramidase, or glycoside hydrolase - is a powerful enzyme of biological significance found in abundance in tears, saliva, and human milk. In humans, it is encoded in the ''LYZ'' gene. Although it is responsible for the initial digestion of starches in the mouth, it is most widely identified as a non-specific defense in gram positive bacteria and in many species of fungi. Due to its antibacterial effects, it is a strong component of the innate immune system, and is an important part of an infant's diet to ward off diarrheal diseases. Since it is a small, easily available, and highly stable protein containing only 129 amino acid residues, it has been subject to extensive research regarding its function and structure. Hen Egg White (HEW) Lysozyme is shown below.<br />
<br />
<br />
=== History ===<br />
<br />
Lysozyme is an enzyme known for its unique ability to degrade the polysaccharide architecture of many kinds of cell walls, normally for the purpose of protection against bacterial infection<ref>Lysozyme. 2010. Citizendium.org. http://en.citizendium.org/wiki/Lysozyme</ref>. Its effects were first noticed by Laschtschenko in 1909. It was officially characterized and termed “lysozyme” by Alexander Fleming, the same person credited for the accidental discovery of penicillin. <br />
The characterization of lysozyme in 1922 by Alexander Fleming was providential in that the undertaken experiment related to the discovery of lysozyme was not geared toward any knowledge of such a protein as lysozyme <ref>Lysozyme. 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. During the unrelated experiment, nasal drippings were inadvertently introduced to a petri dish containing a bacterial culture, which culture consequently exhibited the results of an as yet unknown enzymatic reaction. The observation of this unknown reaction led to further research on the components of this reaction as well as to the corresponding identification of the newfound "lysozyme." Fleming's discovery was complemented by David C. Phillips' 1965 description of the three-dimensional structure of lysozyme via a 200 pm resolution model obtained from X-ray crystallography <ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>. Phillips' work was especially groundbreaking since Phillips had managed to successfully elucidate the structure of an enzyme via X-ray crystallography - a feat that had never before been accomplished<ref>Bugg, T. 1997. An Introduction to Enzyme and Coenzyme Chemistry. Blackwell Science Ltd., Oxford </ref>. Phillips' research also led to the first sufficiently described enzymatic mechanism of catalytic action <ref>1967. Proc R Soc Lond B Bio 167 (1009): 389–401.</ref>. Thus, Phillips' elucidation of the function of lysozyme led Phillips to reach a more general conclusion on the diversity of enzymatic chemical action in relation to enzymatic structure. Clearly, the findings of Phillips as well as the more general historical development of the understanding of the structure and function of lysozyme have been paramount to the more general realm of enzyme chemistry.<br />
<br />
<br />
=== Function===<br />
<br />
Lysozyme is known for damaging bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid (NAM) and N-acetyl-D-glucosamine (NAG) residues in peptidoglycan, and between N-acetyl-D-glucosamine residues in chitodextrins. In this way, lysozyme is efficient in lysing the cell walls of both bacteria and fungi. The location of cleavage for lysozyme on this architectural theme is the β(1-4) glycosidic linkage connecting the C1 carbon of NAM to the C4 carbon of NAG. <br />
<br />
[[Image:nag-nam2.jpg]]<br />
<ref>Image from: http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm</ref> <br />
<br />
The particular substrate of preference for this cleavage type is a (NAG-NAM)₃ hexasaccharide, within which substrate occurs the<br />
cleaving target glycosidic bond, NAM₄-β-O-NAG₅. The individual hexasaccharide binding units are designated A-F, with NAM₄-β-O-NAG₅ glycosidic bond cleavage preference corresponding to a D-E unit glycosidic bond cleavage preference. <br />
<br />
<br />
<br />
<br />
<br />
<applet load='1hew' size='350' frame='true' align='right' caption='' /><br />
<br />
= Composition and Structure of Lysozyme =<br />
<br />
All proteins consist of carbon, hydrogen, nitrogen, oxygen, and sulfur, as do most organic molecules. Enzymes are composed in such a way as to maximize their reactivity with their desired substrate, increasing the efficiency of biological reactions. The <scene name='Sandbox_39/Elements/1'>composition of lysozyme</scene> can be seen on the left, with the carbon atoms outlined in gray, oxygen atoms in red, nitrogen atoms in blue, sulfur atoms in yellow, and the three-letter abbreviation for the <scene name='Sandbox_39/Amino_acid_residues/1'>amino acid residues</scene> in purple.<br />
<br />
Lysozyme, like all proteins, also contains a <scene name='Sandbox_39/C_and_n_terminal_residues/1'> 3'C and 5'N terminal </scene>, and these can be seen by following the colors of the rainbow across the molecule. Starting at the red end, the 3' C terminal end, one can work the entire way through to the 5' N terminal end, showing the folding pattern and chain of the protein.<br />
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== Secondary Structure ==<br />
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Lysozyme contains five <scene name='Sandbox_38/A/2'>alpha helical</scene> regions and five regions containing <scene name='Sandbox_38/B/1'>beta sheets</scene> as displayed in this <scene name='Sandbox_38/Alphab/1'>image</scene>. Linking these secondary structures, a number of beta turns and a large number of random coils make up the remainder of the polypeptide backbone. The polypeptide backbone of lysozyme involved in the 3 antiparallel beta sheets display the beta hairpin motif of supersecondary structure. This depiction of lysozyme contains an antiparallel beta-pleated sheet, which contributes greatly to the stability of the molecule by providing the correct alignment of hydrogen bonds. Lysozyme also contains a great deal of random coil, which is seen in the white regions of the molecule.<br />
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==Amino Acid Residues==<br />
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The amino acids present in the lysozyme polypeptide sequence have a direct influence not only on primary structure, but also on the secondary and tertiary structures, which can be influenced by polarity and charge of the sidechains. The various amino acid <scene name='Sandbox_38/Aminoi/1'>residues</scene> differ in their properties because of the great variety of side chains present on each amino acid. Polar and nonpolar (and charged and uncharged) side chains lead to various degrees of hydrophobicity and hydrophilicity, which affects protein folding. In lysozyme, these <scene name='Sandbox_38/Sc/1'>side chains</scene> are displayed for each amino acid residue.<br />
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= Bonding Interactions =<br />
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=== Disulfide Bonding in Lysozyme ===<br />
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Lysozyme contains four <scene name='Sandbox_39/Disulfide_bonds/1'>disulfide bonds</scene> involving eight cysteine residues, which are highlighted in yellow on the left. Disulfide bonds are intramolecular forces that stabilize the tertiary structure of many proteins. Disulfide bonds are present in four locations in lysozyme: between Cys 6 and Cys 127, between Cys 30 and Cys 115, between Cys 64 and Cys 80 and between Cys 76 and Cys 94. <br />
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=== Hydrogen Bonding ===<br />
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In all proteins <scene name='Sandbox_39/Hydrogen_bonds/2'>hydrogen bonds</scene> are essential for stability. In this ribbon diagram, the hydrogen bonds can be seen between the secondary structures of lysozyme highlighted in orange. Since the double bonds of the alpha carbons in the main chain of lysozyme cause torsional strain, lysozyme is limited to very specific hydrogen bonding between the amino acid residues. This representation clearly shows how crucial hydrogen bonding is to help maintain the stability of the protein. <br />
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<applet load='1hew' size='350' frame='true' align='left' caption='' /><br />
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=== Hydrophobicity ===<br />
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Lysozyme contains both hydrophobic and hydrophilic regions ( <scene name='Sandbox_39/Hydrophobicity/2'>Hydrophobicity</scene> ). The hydrophilic effect, or the desire for proteins to be at a specific position regarding water, is the single most important determinant of protein folding. These regions can be displayed with the hydrophobic regions in gray and the polar, hydrophillic regions in purple. This coloration highlights the location of these regions, showing that the majority of the hydrophobic regions are inside of the protein and that the majority of the hydrophillic regions are on the outside of the protein.<br />
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Here, lysozyme can also be seen interacting with <scene name='Sandbox_39/Water/1'>water</scene>, demonstrating how water remains almost exclusively on the outside of the molecule where the polar residues reside. <br />
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====Polarity====<br />
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The nature of the amino acid sidechains in the lysozyme polypeptide sequence leads to regions of varying hydrophobicities and polarities of the enzyme structure. The presence of certain regions of hydrophilicity and hydrophobicity is a driving force in determining protein structure when folding. The varying polarities of the side chains influence the locations of residues in the enzyme structure. Nonpolar residues appear blue, and polar residues appear red in the following <scene name='Sandbox_38/Non_polar_blue/1'>polarity</scene> display of lysozyme. Nonpolar residues will display hydrophobic tendencies occurring mostly on the interior of the enzyme while polar residues will increase in abundance on the surface of the protein in order to increase contact with the aqueous solvent so as to satisfy their hydrophilic nature. By observing a space-filled structural depiction of <scene name='Sandbox_38/Non_polar_blu/1'>lysozyme polarity</scene> with polar molecules colored red and nonpolar molecules colored blue the influence of polarity on nucleotide arrangement and protein folding is evident, with the blue (nonpolar) regions inside the red (polar) regions. The presence of <scene name='Sandbox_38/Water/1'>water molecules</scene> interacting with the various hydrophilic residues is depicted to further display how polarity affects structure. Water is depicted as yellow, and the polar and nonpolar regions remain their respective color.<br />
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====Charge====<br />
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Charges of the various regions of the lysozyme structure display a hydrophilic nature and thus also affect the location of that region of polypeptides and the overall folding of the protein. Charged regions of the protein will display hydrophilic tendencies and therefore will most often be located on the surface of the lysozyme molecule where they can interact with the aqueous solvent. Non-charged portions will display hydrophobic tendencies and be located on the interior of the molecule. The effect of various <scene name='Sandbox_38/Rb/1'>charges</scene> on protein structure can be visualized with charged molecules represented by red anionic and blue cationic regions, and uncharged regions colored in grey. This depiction of lysozyme uses a spacefill representation of lysozyme to depict <scene name='Sandbox_38/Chargeddd/1'>charges</scene>.<br />
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=== Hydrogen Bonding ===<br />
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In all proteins <scene name='Sandbox_39/Hydrogen_bonds/2'>hydrogen bonds</scene> are essential for stability. In this ribbon diagram, the hydrogen bonds can be seen between the secondary structures of lysozyme highlighted in orange. Since the double bonds of the alpha carbons in the main chain of lysozyme cause torsional strain, lysozyme is limited to very specific hydrogen bonding between the amino acid residues. This representation clearly shows how crucial hydrogen bonding is to help maintain the stability of the protein. <br />
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<applet load='1hew' size='350' frame='true' align='right' caption='' /><br />
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= Enzymatic Activity of Lysozyme =<br />
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Enzymes are designed to attract and to bind specific substrates. The active site of and lysozyme and its specific ligands are described in the following sections<br />
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=== Active Site ===<br />
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The <scene name='Sandbox_39/Active_site/1'>active site</scene> of lysozyme is formulated as a prominent cleft outlined by the two aforementioned catalytic amino acids, Glu 35 and Asp 52. The active site is geometrically bent to augment ligand binding, and the two amino acids interact with the ligand in the binding site. Asp52 is depicted in green, and Glu35 is depicted in purple. <br />
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=== Ligands ===<br />
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A <scene name='Sandbox_39/Ligands_1/1'>ligand</scene> is able to bind to the active site of an enzyme to form a biologically relevant complex. The model to the right shows a space-filling model of lysozyme with the protein distinguishable in brown and the ligand distinguishable in green. Another model of the ligand can be seen in this <br />
<scene name='Sandbox_39/Ribbon_ligand/1'>ribbon diagram</scene>, with the ligand protruding as a space-filling model from the active site. Here, it is clear that the ligand is a polysaccharide. <br />
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The lysozyme reaction is characterized by hydrolysis of the beta (1-4) glycosidic bond between NAM and NAG. Lysozyme has a very specific active site, which can bind only six sugar rings from a polysaccharide chain. Once lysozyme binds to this chain, it hydrolyzes them. These six sugar rings represent the ligand of lysozyme. The lysozyme then distorts the fourth sugar in the six-membered complex, producing stress on the molecule and breaking the glycosidic bond.<br />
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The amino acid side-chains Glu35 and Asp52 are critical to the activity of this enzyme. Glu35 acts as a proton donor to the glycosidic bond, cleaving the C-O bond in the substrate, and Asp52 acts as a nucleophile to generate a glycosyl enzyme intermediate. The glycosyl enzyme intermediate then reacts with a water molecule to give the product of hydrolysis. <br />
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=== Mechanism === <br />
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The lysozyme mechanism of action results in the hydrolysis of a glycoside (hence the familial distinction of lysozyme as a glycosylase<ref>Lysozyme, 2008. Lysozyme.co.uk. http://lysozyme.co.uk/</ref>), which corresponds to the conversion of an acetal to a hemiacetal, which reaction (general degradation of glycosidic bond to units "capped" by newly formed hydroxyl groups) necessitates acid catalysis, since the conversion of acetal to hemiacetal involves the protonation of the reactant oxygen prior to actual bond cleavage. <ref>Pratt, C.W., Voet, D., Voet, J.G. Fundamentals of Biochemistry - Life at the Molecular Level - Third Edition. Voet, Voet and Pratt, 2008.</ref>. Furthermore, the transition state obtained from this protonation is a covalent, oxonium ion, intermediate that must obtain resonance stabilization. The need for some means of acid catalysis and covalent resonance stabilization is adequately provided by the Glu 35 and Asp 52 residues of lysozyme, respectively. The reaction mechanism of lysozyme is demonstrated below. In the following image, the reaction begins at the upper left-hand side, and proceeds according to reaction arrows.<br />
[[Image:jrip.jpg]]<br />
<ref>Image from: http://www.google.com/imgres?imgurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/pics-and-strucs/lysozyme-mech.gif&imgrefurl=http://www.vuw.ac.nz/staff/paul_teesdale-spittle/essentials/chapter-6/proteins/lysozyme.htm&usg=__ormapG4XKg-tR5GrMSOdSMTV4vE=&h=603&w=801&sz=7&hl=en&start=17&zoom=1&tbnid=nvr9gvFrUILDkM:&tbnh=143&tbnw=189&prev=/images%3Fq%3DThe%2Blysozyme%2Breaction%2Bmechanism%26um%3D1%26hl%3Den%26sa%3DN%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C304&um=1&itbs=1&iact=hc&vpx=521&vpy=349&dur=448&hovh=191&hovw=254&tx=140&ty=48&ei=JQ_LTPKzLIjCsAPkzt2KDg&oei=IA_LTP74OsG78gapm-GFAQ&esq=2&page=2&ndsp=18&ved=1t:429,r:2,s:17&biw=1280&bih=647</ref><br />
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As seen above, lysozyme works by hydrolyzing the glycosidic bond, distorting the bond between the NAM and NAG. This produces a glycosyl enzyme intermediate, which reacts with a water molecule to produce the product and the unchanged enzyme.<br />
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=== Inhibitors ===<br />
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Lysozyme is best inhibited by small saccharides which act competitively with the natural substrate. The smaller saccharides will bind to the first three binding sites of the cleft (sites A-C), but will not reach sites D and E, where the enzyme cuts the glycosidic bond. So, the competitive inhibitor will stick in the cleft, not allowing the substrate to bind to the enzyme complex.<ref>http://mcdb-webarchive.mcdb.ucsb.edu/sears/biochemistry/tw-enz/lysozyme/HEWL/lysozyme-overview.htm</ref> Several known inhibitors of lysozyme are: SDS, N-acetyl-D-glucosamine, and various alcohols and oxidizing agents.<ref>http://www.worthington-biochem.com/ly/default.html</ref> <br />
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=== Zymogen of Lysozyme: Enzymatic Precursor ===<br />
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Zymogens are inactive enzyme precursors. Enzymes are developed in an inactive way to prevent the enzyme from digesting the cell that produced it. This process also prevents the enzyme from becoming active in the wrong portion of the body. Lysozyme's zymogen, simply titled “pre-lysozyme,” was sequenced in 1977 by R D Palmiter, J Gagnon, L H Ericsson and K A Walsh, and has since been sequenced much more extensively. <br />
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= Applications of Lysozyme =<br />
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Since lysozyme has been widely recognized for its antibacterial and antifungal properties, it has a wide variety of uses both in biochemical and pharmaceutical applications. In molecular biology, lysozyme is often used in the alkaline-lysis procedure for extracting and isolating plasmid DNA. It is used extensively in the pharmaceutical field for destroying gram-positive bacteria, and can be used to support already-existing immune defenses to fight bacterial infections. This enzyme is particularly important for preventing bacterial diseases in infants. Because of its antibacterial properties, lysozyme can also be used in the food industry to help prevent spoilage of foods.<br />
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= References =<br />
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<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1216299Ciprofloxacin2011-03-18T00:34:38Z<p>John Ripollone: </p>
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<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
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= Ciprofloxacin =<br />
Page constructed: 10 March, 2011 - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
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== General Information ==<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
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'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
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Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
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'''Aerobic Gram-Negative Bacteria''':<br />
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''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
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Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
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The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
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== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
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== Structure and Administration ==<br />
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=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
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[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
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=== Atomic Structure ===<br />
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<Structure load='CPF' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /><br />
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The specific atomic structure of Ciprofloxacin is shown <scene name='Sandbox_100/Labeled_cpf_final/1'>here</scene> (all atoms are labeled and numbered). <br />
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=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
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CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
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[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
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[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
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== Characteristic Protein Targets and Interactions ==<br />
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Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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<br />
=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
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=== Topoisomerase IV Target ===<br />
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<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
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=== Efflux Pump Interaction ===<br />
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<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Certain bacteria (''Escherichia coli'', for example) contain a proton motive force-dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). It has also been shown that, after ligand binding, a proton may bind to acidic residue in the transmembrane domain, which contains an as yet putative network of electrostatically interacting residues, the perturbation of which interacting residues leads to a series of conformational changes that result in drug expulsion. Residues involved in this chain of events include <scene name='Sandbox_100/Asp_407_408_efflux/1'>Asp 407, Asp 408</scene>, <scene name='Sandbox_100/Lys_940_efflux/1'>Lys 940</scene> and <scene name='Sandbox_100/Thr_178_efflux/1'>Thr 978</scene> (red, purple, green, respectively). The precise mechanism of the action of the AcrB efflux subunit (and of the tripartite AcrAB-TolC in general) is still under scrutiny. <br />
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== Conclusion ==<br />
As indicated in the explanation of the interaction between Ciprofloxacin and DNA Gyrase, the precise mechanisms of all Ciprofloxacin interactions and transport systems have not been fully elaborated. Relevant research, particularly for insight on the precise mechanism for AcrB drug efflux, are currently underway. Regardless of these gaps, it is clear that the action of Ciprofloxacin in vivo is important with respect to the treatment of bacterial infections. Taken from a more global perspective, the action of Ciprofloxacin on protein function seems to indicate a specific field of study that could provide insight into more precise mechanisms for protein function in general. Thus, Ciprofloxacin is indeed a compound of interest in anticipation of a greater understanding of biological functions. <br />
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== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203544Ciprofloxacin2011-03-11T12:27:29Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
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<br />
= Ciprofloxacin =<br />
Page constructed: 10 March, 2011 - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
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== General Information ==<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
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'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
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Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
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'''Aerobic Gram-Negative Bacteria''':<br />
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''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
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Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
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The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
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== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
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== Structure and Administration ==<br />
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=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
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[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
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=== Atomic Structure ===<br />
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<Structure load='CPF' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /><br />
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The specific atomic structure of Ciprofloxacin is shown <scene name='Sandbox_100/Labeled_cpf_final/1'>here</scene> (all atoms are labeled and numbered). <br />
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=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
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CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
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[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
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[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
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== Characteristic Protein Targets and Interactions ==<br />
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Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
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=== Topoisomerase IV Target ===<br />
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<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
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The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
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<br />
=== Efflux Pump Interaction ===<br />
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<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). It has also been shown that, after ligand binding, a proton may bind to acidic residue in the transmembrane domain, which contains an as yet putative network of electrostatically interacting residues, the perturbation of which interacting residues leads to a series of conformational changes that result in drug expulsion. Residues involved in this chain of events include <scene name='Sandbox_100/Asp_407_408_efflux/1'>Asp 407, Asp 408</scene>, <scene name='Sandbox_100/Lys_940_efflux/1'>Lys 940</scene> and <scene name='Sandbox_100/Thr_178_efflux/1'>Thr 978</scene> (red, purple, green, respectively). The precise mechanism of the action of the AcrB efflux subunit (and of the tripartite AcrAB-TolC in general) is still under scrutiny. <br />
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== Conclusion ==<br />
As indicated in the explanation of the interaction between Ciprofloxacin and DNA Gyrase, the precise mechanisms of all Ciprofloxacin interactions and transport systems have not been fully elaborated. Relevant research, particularly for insight on the precise mechanism for AcrB drug efflux, are currently underway. Regardless of these gaps, it is clear that the action of Ciprofloxacin in vivo is important with respect to the treatment of bacterial infections. Taken from a more global perspective, the action of Ciprofloxacin on protein function seems to indicate a specific field of study that could provide insight into more precise mechanisms for protein function in general. Thus, Ciprofloxacin is indeed a compound of interest in anticipation of a greater understanding of biological functions. <br />
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== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203543Ciprofloxacin2011-03-11T12:26:11Z<p>John Ripollone: </p>
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<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
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<br />
= Ciprofloxacin =<br />
Page constructed: 10 March, 2011 - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
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== General Information ==<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
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'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
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Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
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'''Aerobic Gram-Negative Bacteria''':<br />
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''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
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Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
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The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
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== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
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== Structure and Administration ==<br />
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=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
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[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
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=== Atomic Structure ===<br />
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<Structure load='CPF' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /><br />
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The specific atomic structure of Ciprofloxacin is shown <scene name='Sandbox_100/Labeled_cpf_final/1'>here</scene> (all atoms are labeled and numbered). <br />
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=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
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CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
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[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
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[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
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== Characteristic Protein Targets and Interactions ==<br />
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Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
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=== Topoisomerase IV Target ===<br />
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<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
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The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
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=== Efflux Pump Interaction ===<br />
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<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). It has also been shown that, after ligand binding, a proton may bind to acidic residue in the transmembrane domain, which contains an as yet putative network of electrostatically interacting residues, the perturbation of which interacting residues leads to a series of conformational changes that result in drug expulsion. Residues involved in this chain of events include <scene name='Sandbox_100/Asp_407_408_efflux/1'>Asp 407, Asp 408</scene>, <scene name='Sandbox_100/Lys_940_efflux/1'>Lys 940</scene> and <scene name='Sandbox_100/Thr_178_efflux/1'>Thr 978</scene> (red, purple, green, respectively). The precise mechanism of the action of the AcrB efflux subunit (and of the tripartite AcrAB-TolC in general) is still under scrutiny. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Conclusion ==<br />
As indicated in the explanation of the interaction between Ciprofloxacin and DNA Gyrase, the precise mechanisms of all Ciprofloxacin interactions and transport systems have not been fully elaborated. Relevant research, particularly for insight on the precise mechanism for AcrB drug efflux, are currently underway. Regardless of these gaps, it is clear that the action of Ciprofloxacin in vivo is important with respect to the treatment of bacterial infections. Taken from a more global perspective, the action of Ciprofloxacin on protein function seems to indicate a specific field of study that could provide insight into more precise mechanisms for protein function in general. Thus, Ciprofloxacin is indeed a compound of interest in anticipation of a greater understanding of biological functions. <br />
<br />
<br />
== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203542Ciprofloxacin2011-03-11T12:24:29Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page constructed: 10 March, 2011 - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
<br />
'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
<br />
Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
<br />
'''Aerobic Gram-Negative Bacteria''':<br />
<br />
''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
<br />
Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
<br />
The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
<br />
[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
<br />
<br />
=== Atomic Structure ===<br />
<br />
<Structure load='CPF' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /><br />
<br />
The specific atomic structure of Ciprofloxacin is shown here (all atoms are labeled and numbered). <br />
<br />
=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
<br />
[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
<br />
CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
<br />
<br />
[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
<br />
Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
<br />
<br />
<br />
== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
<br />
[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
<br />
== Characteristic Protein Targets and Interactions ==<br />
<br />
Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
<br />
<br />
<br />
=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
<br />
A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
<br />
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<br />
<br />
=== Topoisomerase IV Target ===<br />
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<br />
<br />
<br />
<br />
<br />
<br />
<br />
<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
<br />
<br />
<br />
<br />
<br />
<br />
=== Efflux Pump Interaction ===<br />
<br />
<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). It has also been shown that, after ligand binding, a proton may bind to acidic residue in the transmembrane domain, which contains an as yet putative network of electrostatically interacting residues, the perturbation of which interacting residues leads to a series of conformational changes that result in drug expulsion. Residues involved in this chain of events include <scene name='Sandbox_100/Asp_407_408_efflux/1'>Asp 407, Asp 408</scene>, <scene name='Sandbox_100/Lys_940_efflux/1'>Lys 940</scene> and <scene name='Sandbox_100/Thr_178_efflux/1'>Thr 978</scene> (red, purple, green, respectively). The precise mechanism of the action of the AcrB efflux subunit (and of the tripartite AcrAB-TolC in general) is still under scrutiny. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Conclusion ==<br />
As indicated in the explanation of the interaction between Ciprofloxacin and DNA Gyrase, the precise mechanisms of all Ciprofloxacin interactions and transport systems have not been fully elaborated. Relevant research, particularly for insight on the precise mechanism for AcrB drug efflux, are currently underway. Regardless of these gaps, it is clear that the action of Ciprofloxacin in vivo is important with respect to the treatment of bacterial infections. Taken from a more global perspective, the action of Ciprofloxacin on protein function seems to indicate a specific field of study that could provide insight into more precise mechanisms for protein function in general. Thus, Ciprofloxacin is indeed a compound of interest in anticipation of a greater understanding of biological functions. <br />
<br />
<br />
== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203541Ciprofloxacin2011-03-11T12:23:27Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page constructed: 10 March, 2011 - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
<br />
'''Aerobic Gram-Negative Bacteria''': <br />
<br />
''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
<br />
Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
<br />
'''Aerobic Gram-Negative Bacteria''':<br />
<br />
''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
<br />
Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
<br />
The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
<br />
[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
<br />
<br />
=== Atomic Structure ===<br />
The specific atomic structure of Ciprofloxacin is shown here (all atoms are labeled and numbered). <br />
<Structure load='CPF' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /><br />
<br />
<br />
=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
<br />
[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
<br />
CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
<br />
<br />
[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
<br />
Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
<br />
<br />
<br />
== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
<br />
[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
<br />
== Characteristic Protein Targets and Interactions ==<br />
<br />
Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
<br />
<br />
<br />
=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
<br />
A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
<br />
<br />
<br />
<br />
=== Topoisomerase IV Target ===<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
<br />
<br />
<br />
<br />
<br />
<br />
=== Efflux Pump Interaction ===<br />
<br />
<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). It has also been shown that, after ligand binding, a proton may bind to acidic residue in the transmembrane domain, which contains an as yet putative network of electrostatically interacting residues, the perturbation of which interacting residues leads to a series of conformational changes that result in drug expulsion. Residues involved in this chain of events include <scene name='Sandbox_100/Asp_407_408_efflux/1'>Asp 407, Asp 408</scene>, <scene name='Sandbox_100/Lys_940_efflux/1'>Lys 940</scene> and <scene name='Sandbox_100/Thr_178_efflux/1'>Thr 978</scene> (red, purple, green, respectively). The precise mechanism of the action of the AcrB efflux subunit (and of the tripartite AcrAB-TolC in general) is still under scrutiny. <br />
<br />
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<br />
<br />
<br />
<br />
== Conclusion ==<br />
As indicated in the explanation of the interaction between Ciprofloxacin and DNA Gyrase, the precise mechanisms of all Ciprofloxacin interactions and transport systems have not been fully elaborated. Relevant research, particularly for insight on the precise mechanism for AcrB drug efflux, are currently underway. Regardless of these gaps, it is clear that the action of Ciprofloxacin in vivo is important with respect to the treatment of bacterial infections. Taken from a more global perspective, the action of Ciprofloxacin on protein function seems to indicate a specific field of study that could provide insight into more precise mechanisms for protein function in general. Thus, Ciprofloxacin is indeed a compound of interest in anticipation of a greater understanding of biological functions. <br />
<br />
<br />
== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203453Ciprofloxacin2011-03-11T04:21:03Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page constructed: 10 March, 2011 - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
<br />
'''Aerobic Gram-Negative Bacteria''': <br />
<br />
''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
<br />
Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
<br />
'''Aerobic Gram-Negative Bacteria''':<br />
<br />
''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
<br />
Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
<br />
The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
<br />
[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
<br />
<br />
=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
<br />
[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
<br />
CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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<br />
[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
<br />
Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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<br />
<br />
== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
<br />
[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
<br />
== Characteristic Protein Targets and Interactions ==<br />
<br />
Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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<br />
<br />
=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
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<br />
=== Topoisomerase IV Target ===<br />
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<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
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<br />
=== Efflux Pump Interaction ===<br />
<br />
<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). It has also been shown that, after ligand binding, a proton may bind to acidic residue in the transmembrane domain, which contains an as yet putative network of electrostatically interacting residues, the perturbation of which interacting residues leads to a series of conformational changes that result in drug expulsion. Residues involved in this chain of events include <scene name='Sandbox_100/Asp_407_408_efflux/1'>Asp 407, Asp 408</scene>, <scene name='Sandbox_100/Lys_940_efflux/1'>Lys 940</scene> and <scene name='Sandbox_100/Thr_178_efflux/1'>Thr 978</scene> (red, purple, green, respectively). The precise mechanism of the action of the AcrB efflux subunit (and of the tripartite AcrAB-TolC in general) is still under scrutiny. <br />
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== Conclusion ==<br />
As indicated in the explanation of the interaction between Ciprofloxacin and DNA Gyrase, the precise mechanisms of all Ciprofloxacin interactions and transport systems have not been fully elaborated. Relevant research, particularly for insight on the precise mechanism for AcrB drug efflux, are currently underway. Regardless of these gaps, it is clear that the action of Ciprofloxacin in vivo is important with respect to the treatment of bacterial infections. Taken from a more global perspective, the action of Ciprofloxacin on protein function seems to indicate a specific field of study that could provide insight into more precise mechanisms for protein function in general. Thus, Ciprofloxacin is indeed a compound of interest in anticipation of a greater understanding of biological functions. <br />
<br />
<br />
== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203450Ciprofloxacin2011-03-11T04:18:53Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
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<br />
= Ciprofloxacin =<br />
Page constructed: 10 March, 2011 - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
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<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
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'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
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Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
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'''Aerobic Gram-Negative Bacteria''':<br />
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''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
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Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
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The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
<br />
[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
<br />
<br />
=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
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[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
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[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
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== Characteristic Protein Targets and Interactions ==<br />
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Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
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=== Topoisomerase IV Target ===<br />
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<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
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The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
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=== Efflux Pump Interaction ===<br />
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<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). It has also been shown that, after ligand binding, a proton may bind to acidic residue in the transmembrane domain, which contains an as yet putative network of electrostatically interacting residues, the perturbation of which interacting residues leads to a series of conformational changes that result in drug expulsion. Residues involved in this chain of events include <scene name='Sandbox_100/Asp_407_408_efflux/1'>Asp 407, Asp 408</scene>, <scene name='Sandbox_100/Lys_940_efflux/1'>Lys 940</scene> and <scene name='Sandbox_100/Thr_178_efflux/1'>Thr 978</scene> (red, purple, green, respectively). The precise mechanism of the action of the AcrB efflux subunit (and of the tripartite AcrAB-TolC in general) is still under scrutiny. <br />
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== Conclusion ==<br />
As indicated in the explanation of the interaction between Ciprofloxacin and DNA Gyrase, the precise mechanisms of all Ciprofloxacin interactions and transport systems have not been fully elaborated. Relevant research, particularly for insight on the precise mechanism for AcrB drug efflux, are currently underway. Regardless of these gaps, it is clear that the action of Ciprofloxacin in vivo is important with respect to the treatment of bacterial infections. Taken from a more global perspective, the action of Ciprofloxacin on protein function seems to indicate a specific field of study that could provide insight into more precise mechanisms for protein function in general. Thus, Ciprofloxacin is indeed a compound of interest in anticipation of a greater understanding of biological functions. <br />
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== References ==<br />
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<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203448Ciprofloxacin2011-03-11T04:18:17Z<p>John Ripollone: </p>
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<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
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= Ciprofloxacin =<br />
Page constructed: 10 March, 2011 - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
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== General Information ==<br />
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<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
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'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
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Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
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'''Aerobic Gram-Negative Bacteria''':<br />
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''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
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Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
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The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
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== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
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== Structure and Administration ==<br />
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=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
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[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
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=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
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CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
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[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
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[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
<br />
== Characteristic Protein Targets and Interactions ==<br />
<br />
Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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<br />
<br />
=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
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=== Topoisomerase IV Target ===<br />
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<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
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<br />
=== Efflux Pump Interaction ===<br />
<br />
<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). It has also been shown that, after ligand binding, a proton may bind to acidic residue in the transmembrane domain, which contains an as yet putative network of electrostatically interacting residues, the perturbation of which interacting residues leads to a series of conformational changes that result in drug expulsion. Residues involved in this chain of events include <scene name='Sandbox_100/Asp_407_408_efflux/1'>Asp 407, Asp 408</scene>, <scene name='Sandbox_100/Lys_940_efflux/1'>Lys 940</scene> and <scene name='Sandbox_100/Thr_178_efflux/1'>Thr 978</scene> (red, purple, green, respectively). The precise mechanism of the action of the AcrB efflux subunit (and of the tripartite AcrAB-TolC in general) is still under scrutiny. <br />
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== Conclusion ==<br />
As indicated in the explanation of the interaction between Ciprofloxacin and DNA Gyrase, the precise mechanisms of all Ciprofloxacin interactions and transport systems have not been fully elaborated. Relevant research, particularly for insight on the precise mechanism for AcrB drug efflux, are currently underway. Regardless of these gaps, it is clear that the action of Ciprofloxacin in vivo is important with respect to the treatment of bacterial infections. Taken from a more global perspective, the action of Ciprofloxacin on protein function seems to indicate a specific field of study that could provide insight into more precise mechanisms for protein function in general. Thus, Ciprofloxacin is indeed a compound of interest in anticipation of a greater understanding of biological functions. <br />
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<br />
== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203447Ciprofloxacin2011-03-11T04:16:37Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page constructed: 10 March, 2011 - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
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== General Information ==<br />
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<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
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'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
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Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
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'''Aerobic Gram-Negative Bacteria''':<br />
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''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
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Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
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The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
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== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
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== Structure and Administration ==<br />
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=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
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[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
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=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
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CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
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[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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<br />
== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
<br />
[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
<br />
== Characteristic Protein Targets and Interactions ==<br />
<br />
Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
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=== Topoisomerase IV Target ===<br />
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<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
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<br />
=== Efflux Pump Interaction ===<br />
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<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). It has also been shown that, after ligand binding, a proton may bind to acidic residue in the transmembrane domain, which contains an as yet putative network of electrostatically interacting residues, the perturbation of which interacting residues leads to a series of conformational changes that result in drug expulsion. Residues involved in this chain of events include <scene name='Sandbox_100/Asp_407_408_efflux/1'>Asp 407, Asp 408</scene>, <scene name='Sandbox_100/Lys_940_efflux/1'>Lys 940</scene> and <scene name='Sandbox_100/Thr_178_efflux/1'>Thr 978</scene> (red, purple, green, respectively). The precise mechanism of the action of the AcrB efflux subunit (and of the tripartite AcrAB-TolC in general) is still under scrutiny. <br />
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== Conclusion ==<br />
As indicated in the explanation of the interaction between Ciprofloxacin and DNA Gyrase, the precise mechanisms of all Ciprofloxacin interactions and transport systems have not been fully elaborated. Relevant research, particularly for insight on the precise mechanism for AcrB drug efflux, are currently underway. Regardless of these gaps, it is clear that the action of Ciprofloxacin in vivo is important with respect to the treatment of bacterial infections. Taken from a more global perspective, the action of Ciprofloxacin on protein function seems to indicate a specific field of study that could provide insight into more precise mechanisms for protein function in general. Thus, Ciprofloxacin is indeed a compound of interest in anticipation of a greater understanding of biological functions. <br />
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== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203446Ciprofloxacin2011-03-11T04:16:11Z<p>John Ripollone: </p>
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<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page constructed: 10 March, 2011 - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
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== General Information ==<br />
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<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
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'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
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Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
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'''Aerobic Gram-Negative Bacteria''':<br />
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''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
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Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
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The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
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== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
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== Structure and Administration ==<br />
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=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
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[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
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=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
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CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
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[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
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[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
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== Characteristic Protein Targets and Interactions ==<br />
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Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
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=== Topoisomerase IV Target ===<br />
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<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
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The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
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=== Efflux Pump Interaction ===<br />
<br />
<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). It has also been shown that, after ligand binding, a proton may bind to acidic residue in the transmembrane domain, which contains an as yet putative network of electrostatically interacting residues, the perturbation of which interacting residues leads to a series of conformational changes that result in drug expulsion. Residues involved in this chain of events include <scene name='Sandbox_100/Asp_407_408_efflux/1'>Asp 407, Asp 408</scene>, <scene name='Sandbox_100/Lys_940_efflux/1'>Lys 940</scene> and <scene name='Sandbox_100/Thr_178_efflux/1'>Thr 978</scene> (red, purple, green, respectively). The precise mechanism of the action of the AcrB efflux subunit (and of the tripartite AcrAB-TolC in general) is still under scrutiny. <br />
<br />
<br />
<br />
== Conclusion ==<br />
As indicated in the explanation of the interaction between Ciprofloxacin and DNA Gyrase, the precise mechanisms of all Ciprofloxacin interactions and transport systems have not been fully elaborated. Relevant research, particularly for insight on the precise mechanism for AcrB drug efflux, are currently underway. Regardless of these gaps, it is clear that the action of Ciprofloxacin in vivo is important with respect to the treatment of bacterial infections. Taken from a more global perspective, the action of Ciprofloxacin on protein function seems to indicate a specific field of study that could provide insight into more precise mechanisms for protein function in general. Thus, Ciprofloxacin is indeed a compound of interest in anticipation of a greater understanding of biological functions. <br />
<br />
<br />
== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203445Ciprofloxacin2011-03-11T04:15:42Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page constructed: 10 March, 2011 - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
<br />
Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
<br />
'''Aerobic Gram-Negative Bacteria''': <br />
<br />
''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
<br />
Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
<br />
'''Aerobic Gram-Negative Bacteria''':<br />
<br />
''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
<br />
Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
<br />
The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
<br />
[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
<br />
<br />
=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
<br />
[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
<br />
CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
<br />
<br />
[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
<br />
Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
<br />
<br />
<br />
== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
<br />
[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
<br />
== Characteristic Protein Targets and Interactions ==<br />
<br />
Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
<br />
<br />
<br />
=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
<br />
A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
<br />
<br />
<br />
<br />
=== Topoisomerase IV Target ===<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
<br />
<br />
<br />
<br />
<br />
=== Efflux Pump Interaction ===<br />
<br />
<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). It has also been shown that, after ligand binding, a proton may bind to acidic residue in the transmembrane domain, which contains an as yet putative network of electrostatically interacting residues, the perturbation of which interacting residues leads to a series of conformational changes that result in drug expulsion. Residues involved in this chain of events include <scene name='Sandbox_100/Asp_407_408_efflux/1'>Asp 407, Asp 408</scene>, <scene name='Sandbox_100/Lys_940_efflux/1'>Lys 940</scene> and <scene name='Sandbox_100/Thr_178_efflux/1'>Thr 978</scene> (red, purple, green, respectively). The precise mechanism of the action of the AcrB efflux subunit (and of the tripartite AcrAB-TolC in general) is still under scrutiny. <br />
<br />
<br />
<br />
== Conclusion ==<br />
As indicated in the explanation of the interaction between Ciprofloxacin and DNA Gyrase, the precise mechanisms of all Ciprofloxacin interactions and transport systems have not been fully elaborated. Relevant research, particularly for insight on the precise mechanism for AcrB drug efflux, are currently underway. Regardless of these gaps, it is clear that the action of Ciprofloxacin in vivo is important with respect to the treatment of bacterial infections. Taken from a more global perspective, the action of Ciprofloxacin on protein function seems to indicate a specific field of study that could provide insight into more precise mechanisms for protein function in general. Thus, Ciprofloxacin is indeed a compound of interest in anticipation of a greater understanding of biological functions. <br />
<br />
<br />
== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203444Ciprofloxacin2011-03-11T04:15:03Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page constructed: 10 March, 2011 - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
<br />
Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
<br />
'''Aerobic Gram-Negative Bacteria''': <br />
<br />
''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
<br />
Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
<br />
'''Aerobic Gram-Negative Bacteria''':<br />
<br />
''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
<br />
Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
<br />
The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
<br />
[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
<br />
<br />
=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
<br />
[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
<br />
CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
<br />
<br />
[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
<br />
Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
<br />
<br />
<br />
== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
<br />
[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
<br />
== Characteristic Protein Targets and Interactions ==<br />
<br />
Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
<br />
<br />
<br />
=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
<br />
A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
<br />
<br />
<br />
<br />
=== Topoisomerase IV Target ===<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
<br />
<br />
<br />
<br />
=== Efflux Pump Interaction ===<br />
<br />
<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). It has also been shown that, after ligand binding, a proton may bind to acidic residue in the transmembrane domain, which contains an as yet putative network of electrostatically interacting residues, the perturbation of which interacting residues leads to a series of conformational changes that result in drug expulsion. Residues involved in this chain of events include <scene name='Sandbox_100/Asp_407_408_efflux/1'>Asp 407, Asp 408</scene>, <scene name='Sandbox_100/Lys_940_efflux/1'>Lys 940</scene> and <scene name='Sandbox_100/Thr_178_efflux/1'>Thr 978</scene> (red, purple, green, respectively). The precise mechanism of the action of the AcrB efflux subunit (and of the tripartite AcrAB-TolC in general) is still under scrutiny. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Conclusion ==<br />
As indicated in the explanation of the interaction between Ciprofloxacin and DNA Gyrase, the precise mechanisms of all Ciprofloxacin interactions and transport systems have not been fully elaborated. Relevant research, particularly for insight on the precise mechanism for AcrB drug efflux, are currently underway. Regardless of these gaps, it is clear that the action of Ciprofloxacin in vivo is important with respect to the treatment of bacterial infections. Taken from a more global perspective, the action of Ciprofloxacin on protein function seems to indicate a specific field of study that could provide insight into more precise mechanisms for protein function in general. Thus, Ciprofloxacin is indeed a compound of interest in anticipation of a greater understanding of biological functions. <br />
<br />
<br />
== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203443Ciprofloxacin2011-03-11T04:14:21Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page constructed: 10 March, 2011 - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
<br />
Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
<br />
'''Aerobic Gram-Negative Bacteria''': <br />
<br />
''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
<br />
Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
<br />
'''Aerobic Gram-Negative Bacteria''':<br />
<br />
''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
<br />
Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
<br />
The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
<br />
[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
<br />
<br />
=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
<br />
[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
<br />
CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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<br />
[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
<br />
Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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<br />
<br />
== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
<br />
[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
<br />
== Characteristic Protein Targets and Interactions ==<br />
<br />
Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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<br />
=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
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<br />
=== Topoisomerase IV Target ===<br />
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<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
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<br />
=== Efflux Pump Interaction ===<br />
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<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). It has also been shown that, after ligand binding, a proton may bind to acidic residue in the transmembrane domain, which contains an as yet putative network of electrostatically interacting residues, the perturbation of which interacting residues leads to a series of conformational changes that result in drug expulsion. Residues involved in this chain of events include <scene name='Sandbox_100/Asp_407_408_efflux/1'>Asp 407, Asp 408</scene>, <scene name='Sandbox_100/Lys_940_efflux/1'>Lys 940</scene> and <scene name='Sandbox_100/Thr_178_efflux/1'>Thr 978</scene> (red, purple, green, respectively). The precise mechanism of the action of the AcrB efflux subunit (and of the tripartite AcrAB-TolC in general) is still under scrutiny. <br />
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== Conclusion ==<br />
As indicated in the explanation of the interaction between Ciprofloxacin and DNA Gyrase, the precise mechanisms of all Ciprofloxacin interactions and transport systems have not been fully elaborated. Relevant research, particularly for insight on the precise mechanism for AcrB drug efflux, are currently underway. Regardless of these gaps, it is clear that the action of Ciprofloxacin in vivo is important with respect to the treatment of bacterial infections. Taken from a more global perspective, the action of Ciprofloxacin on protein function seems to indicate a specific field of study that could provide insight into more precise mechanisms for protein function in general. Thus, Ciprofloxacin is indeed a compound of interest in anticipation of a greater understanding of biological functions. <br />
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<br />
== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203441Ciprofloxacin2011-03-11T04:13:36Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
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<br />
= Ciprofloxacin =<br />
Page constructed: 10 March, 2011 - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
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<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
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'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
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Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
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'''Aerobic Gram-Negative Bacteria''':<br />
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''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
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Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
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The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
<br />
[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
<br />
<br />
=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
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[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
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[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
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== Characteristic Protein Targets and Interactions ==<br />
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Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
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=== Topoisomerase IV Target ===<br />
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<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
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The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
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=== Efflux Pump Interaction ===<br />
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<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). It has also been shown that, after ligand binding, a proton may bind to acidic residue in the transmembrane domain, which contains an as yet putative network of electrostatically interacting residues, the perturbation of which interacting residues leads to a series of conformational changes that result in drug expulsion. Residues involved in this chain of events include <scene name='Sandbox_100/Asp_407_408_efflux/1'>Asp 407, Asp 408</scene>, <scene name='Sandbox_100/Lys_940_efflux/1'>Lys 940</scene> and <scene name='Sandbox_100/Thr_178_efflux/1'>Thr 978</scene> (red, purple, green, respectively). The precise mechanism of the action of the AcrB efflux subunit (and of the tripartite AcrAB-TolC in general) is still under scrutiny. <br />
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== Conclusion ==<br />
As indicated in the explanation of the interaction between Ciprofloxacin and DNA Gyrase, the precise mechanisms of all Ciprofloxacin interactions and transport systems have not been fully elaborated. Relevant research, particularly for insight on the precise mechanism for AcrB drug efflux, are currently underway. Regardless of these gaps, it is clear that the action of Ciprofloxacin in vivo is important with respect to the treatment of bacterial infections. Taken from a more global perspective, the action of Ciprofloxacin on protein function seems to indicate a specific field of study that could provide insight into more precise mechanisms for protein function in general. Thus, Ciprofloxacin is indeed a compound of interest in anticipation of a greater understanding of biological functions. <br />
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== References ==<br />
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<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203440Ciprofloxacin2011-03-11T04:12:50Z<p>John Ripollone: </p>
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<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
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= Ciprofloxacin =<br />
Page constructed: 10 March, 2011 - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
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== General Information ==<br />
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<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
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'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
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Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
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'''Aerobic Gram-Negative Bacteria''':<br />
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''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
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Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
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The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
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== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
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== Structure and Administration ==<br />
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=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
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[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
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=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
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CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
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[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
<br />
[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
<br />
== Characteristic Protein Targets and Interactions ==<br />
<br />
Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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<br />
<br />
=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
<br />
<br />
=== Topoisomerase IV Target ===<br />
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<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
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<br />
=== Efflux Pump Interaction ===<br />
<br />
<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). It has also been shown that, after ligand binding, a proton may bind to acidic residue in the transmembrane domain, which contains an as yet putative network of electrostatically interacting residues, the perturbation of which interacting residues leads to a series of conformational changes that result in drug expulsion. Residues involved in this chain of events include <scene name='Sandbox_100/Asp_407_408_efflux/1'>Asp 407, Asp 408</scene>, <scene name='Sandbox_100/Lys_940_efflux/1'>Lys 940</scene> and <scene name='Sandbox_100/Thr_178_efflux/1'>Thr 978</scene> (red, purple, green, respectively). The precise mechanism of the action of the AcrB efflux subunit (and of the tripartite AcrAB-TolC in general) is still under scrutiny. <br />
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== Conclusion ==<br />
As indicated in the explanation of the interaction between Ciprofloxacin and DNA Gyrase, the precise mechanisms of all Ciprofloxacin interactions and transport systems have not been fully elaborated. Relevant research, particularly for insight on the precise mechanism for AcrB drug efflux, are currently underway. Regardless of these gaps, it is clear that the action of Ciprofloxacin in vivo is important with respect to the treatment of bacterial infections. Taken from a more global perspective, the action of Ciprofloxacin on protein function seems to indicate a specific field of study that could provide insight into more precise mechanisms for protein function in general. Thus, Ciprofloxacin is indeed a compound of interest in anticipation of a greater understanding of biological functions. <br />
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<br />
== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203439Ciprofloxacin2011-03-11T04:11:25Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page constructed: 10 March, 2011 - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
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== General Information ==<br />
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<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
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'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
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Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
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'''Aerobic Gram-Negative Bacteria''':<br />
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''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
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Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
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The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
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== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
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== Structure and Administration ==<br />
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=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
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[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
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=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
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CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
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[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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<br />
== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
<br />
[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
<br />
== Characteristic Protein Targets and Interactions ==<br />
<br />
Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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<br />
=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
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<br />
=== Topoisomerase IV Target ===<br />
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<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
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<br />
=== Efflux Pump Interaction ===<br />
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<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). It has also been shown that, after ligand binding, a proton may bind to acidic residue in the transmembrane domain, which contains an as yet putative network of electrostatically interacting residues, the perturbation of which interacting residues leads to a series of conformational changes that result in drug expulsion. Residues involved in this chain of events include <scene name='Sandbox_100/Asp_407_408_efflux/1'>Asp 407, Asp 408</scene>, <scene name='Sandbox_100/Lys_940_efflux/1'>Lys 940</scene> and <scene name='Sandbox_100/Thr_178_efflux/1'>Thr 978</scene> (red, purple, green, respectively). The precise mechanism of the action of the AcrB efflux subunit (and of the tripartite AcrAB-TolC in general) is still under scrutiny. <br />
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== Conclusion ==<br />
As indicated in the explanation of the interaction between Ciprofloxacin and DNA Gyrase, the precise mechanisms of all Ciprofloxacin interactions and transport systems have not been fully elaborated. Relevant research, particularly for insight on the precise mechanism for AcrB drug efflux, are currently underway. Regardless of these gaps, it is clear that the action of Ciprofloxacin in vivo is important with respect to the treatment of bacterial infections. Taken from a more global perspective, the action of Ciprofloxacin on protein function seems to indicate a specific field of study that could provide insight into more precise mechanisms for protein function in general. Thus, Ciprofloxacin is indeed a compound of interest in anticipation of a greater understanding of biological functions. <br />
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== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203438Ciprofloxacin2011-03-11T04:10:04Z<p>John Ripollone: </p>
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<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page constructed: 10 March, 2011 - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
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== General Information ==<br />
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<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
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'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
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Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
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'''Aerobic Gram-Negative Bacteria''':<br />
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''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
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Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
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The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
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== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
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== Structure and Administration ==<br />
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=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
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[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
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=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
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CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
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[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
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[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
<br />
== Characteristic Protein Targets and Interactions ==<br />
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Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
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=== Topoisomerase IV Target ===<br />
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<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
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The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
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=== Efflux Pump Interaction ===<br />
<br />
<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). It has also been shown that, after ligand binding, a proton may bind to acidic residue in the transmembrane domain, which contains an as yet putative network of electrostatically interacting residues, the perturbation of which interacting residues leads to a series of conformational changes that result in drug expulsion. Residues involved in this chain of events include <scene name='Sandbox_100/Asp_407_408_efflux/1'>Asp 407, Asp 408</scene>, <scene name='Sandbox_100/Lys_940_efflux/1'>Lys 940</scene> and <scene name='Sandbox_100/Thr_178_efflux/1'>Thr 978</scene> (red, purple, green, respectively). <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Conclusion ==<br />
As indicated in the explanation of the interaction between Ciprofloxacin and DNA Gyrase, the precise mechanisms of all Ciprofloxacin interactions and transport systems have not been fully elaborated. Relevant research, particularly for insight on the precise mechanism for AcrB drug efflux, are currently underway. Regardless of these gaps, it is clear that the action of Ciprofloxacin in vivo is important with respect to the treatment of bacterial infections. Taken from a more global perspective, the action of Ciprofloxacin on protein function seems to indicate a specific field of study that could provide insight into more precise mechanisms for protein function in general. Thus, Ciprofloxacin is indeed a compound of interest in anticipation of a greater understanding of biological functions. <br />
<br />
<br />
== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203437Ciprofloxacin2011-03-11T04:09:34Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page constructed: 10 March, 2011 - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
<br />
Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
<br />
'''Aerobic Gram-Negative Bacteria''': <br />
<br />
''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
<br />
Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
<br />
'''Aerobic Gram-Negative Bacteria''':<br />
<br />
''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
<br />
Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
<br />
The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
<br />
[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
<br />
<br />
=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
<br />
[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
<br />
CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
<br />
<br />
[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
<br />
Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
<br />
<br />
<br />
== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
<br />
[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
<br />
== Characteristic Protein Targets and Interactions ==<br />
<br />
Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
<br />
<br />
<br />
=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
<br />
A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
<br />
<br />
=== Topoisomerase IV Target ===<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
<br />
<br />
=== Efflux Pump Interaction ===<br />
<br />
<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). It has also been shown that, after ligand binding, a proton may bind to acidic residue in the transmembrane domain, which contains an as yet putative network of electrostatically interacting residues, the perturbation of which interacting residues leads to a series of conformational changes that result in drug expulsion. Residues involved in this chain of events include <scene name='Sandbox_100/Asp_407_408_efflux/1'>Asp 407, Asp 408</scene>, <scene name='Sandbox_100/Lys_940_efflux/1'>Lys 940</scene> and <scene name='Sandbox_100/Thr_178_efflux/1'>Thr 978</scene> (red, purple, green, respectively). <br />
<br />
<br />
<br />
<br />
<br />
<br />
== Conclusion ==<br />
As indicated in the explanation of the interaction between Ciprofloxacin and DNA Gyrase, the precise mechanisms of all Ciprofloxacin interactions and transport systems have not been fully elaborated. Relevant research, particularly for insight on the precise mechanism for AcrB drug efflux, are currently underway. Regardless of these gaps, it is clear that the action of Ciprofloxacin in vivo is important with respect to the treatment of bacterial infections. Taken from a more global perspective, the action of Ciprofloxacin on protein function seems to indicate a specific field of study that could provide insight into more precise mechanisms for protein function in general. Thus, Ciprofloxacin is indeed a compound of interest in anticipation of a greater understanding of biological functions. <br />
<br />
<br />
== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203436Ciprofloxacin2011-03-11T04:08:52Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page constructed: 10 March, 2011 - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
<br />
Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
<br />
'''Aerobic Gram-Negative Bacteria''': <br />
<br />
''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
<br />
Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
<br />
'''Aerobic Gram-Negative Bacteria''':<br />
<br />
''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
<br />
Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
<br />
The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
<br />
[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
<br />
<br />
=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
<br />
[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
<br />
CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
<br />
<br />
[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
<br />
Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
<br />
<br />
<br />
== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
<br />
[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
<br />
== Characteristic Protein Targets and Interactions ==<br />
<br />
Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
<br />
<br />
<br />
=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
<br />
A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
<br />
<br />
=== Topoisomerase IV Target ===<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
<br />
<br />
=== Efflux Pump Interaction ===<br />
<br />
<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). It has also been shown that, after ligand binding, a proton may bind to acidic residue in the transmembrane domain, which contains an as yet putative network of electrostatically interacting residues, the perturbation of which interacting residues leads to a series of conformational changes that result in drug expulsion. Residues involved in this chain of events include <scene name='Sandbox_100/Asp_407_408_efflux/1'>Asp 407, Asp 408</scene>, <scene name='Sandbox_100/Lys_940_efflux/1'>Lys 940</scene> and <scene name='Sandbox_100/Thr_178_efflux/1'>Thr 978</scene> (red, purple, green, respectively). <br />
<br />
<br />
== Conclusion ==<br />
As indicated in the explanation of the interaction between Ciprofloxacin and DNA Gyrase, the precise mechanisms of all Ciprofloxacin interactions and transport systems have not been fully elaborated. Relevant research, particularly for insight on the precise mechanism for AcrB drug efflux, are currently underway. Regardless of these gaps, it is clear that the action of Ciprofloxacin in vivo is important with respect to the treatment of bacterial infections. Taken from a more global perspective, the action of Ciprofloxacin on protein function seems to indicate a specific field of study that could provide insight into more precise mechanisms for protein function in general. Thus, Ciprofloxacin is indeed a compound of interest in anticipation of a greater understanding of biological functions. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203425Ciprofloxacin2011-03-11T04:00:53Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page under construction - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
<br />
Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
<br />
'''Aerobic Gram-Negative Bacteria''': <br />
<br />
''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
<br />
Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
<br />
'''Aerobic Gram-Negative Bacteria''':<br />
<br />
''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
<br />
Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
<br />
The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
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[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
<br />
<br />
=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
<br />
[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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<br />
[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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<br />
== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
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[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
<br />
== Characteristic Protein Targets and Interactions ==<br />
<br />
Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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<br />
=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
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=== Topoisomerase IV Target ===<br />
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<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
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=== Efflux Pump Interaction ===<br />
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<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). It has also been shown that, after ligand binding, a proton may bind to acidic residue in the transmembrane domain, which contains an as yet putative network of electrostatically interacting residues, the perturbation of which interacting residues leads to a series of conformational changes that result in drug expulsion. Residues involved in this chain of events include <scene name='Sandbox_100/Asp_407_408_efflux/1'>Asp 407, Asp 408</scene>, <scene name='Sandbox_100/Lys_940_efflux/1'>Lys 940</scene> and <scene name='Sandbox_100/Thr_178_efflux/1'>Thr 978</scene> (red, purple, green, respectively). <br />
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== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203423Ciprofloxacin2011-03-11T03:59:24Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page under construction - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
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'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
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Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
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'''Aerobic Gram-Negative Bacteria''':<br />
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''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
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Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
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The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
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== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
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[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
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<br />
=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
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[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
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[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
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== Characteristic Protein Targets and Interactions ==<br />
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Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
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=== Topoisomerase IV Target ===<br />
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<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
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The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
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=== Efflux Pump Interaction ===<br />
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<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). It has also been shown that, after ligand binding, a proton may bind to acidic residue in the transmembrane domain, which contains an as yet putative network of electrostatically interacting residues, the perturbation of which interacting residues leads to a series of conformational changes that result in drug expulsion. Residues involved in this chain of events include <scene name='Sandbox_100/Asp_407_408_efflux/1'>Asp 407, Asp 408</scene>, <scene name='Sandbox_100/Lys_940_efflux/1'>Lys 940</scene> and <scene name='Sandbox_100/Thr_178_efflux/1'>Thr 978</scene>. <br />
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== References ==<br />
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<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203416Ciprofloxacin2011-03-11T03:48:06Z<p>John Ripollone: </p>
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<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
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= Ciprofloxacin =<br />
Page under construction - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
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== General Information ==<br />
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<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
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'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
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Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
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'''Aerobic Gram-Negative Bacteria''':<br />
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''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
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Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
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The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
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== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
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== Structure and Administration ==<br />
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=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
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[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
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=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
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CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
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[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
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[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
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== Characteristic Protein Targets and Interactions ==<br />
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Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
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=== Topoisomerase IV Target ===<br />
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<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
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=== Efflux Pump Interaction ===<br />
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<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). It has been shown that <scene name='Sandbox_100/Phe_residues/1'> Phe 386 and Phe 388</scene> contribute to the effectiveness of the initial affinity of AcrB for all targets <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref> (in this scene, both Phe residues are magenta). <br />
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== References ==<br />
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<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203406Ciprofloxacin2011-03-11T03:35:06Z<p>John Ripollone: </p>
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<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
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<br />
= Ciprofloxacin =<br />
Page under construction - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
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== General Information ==<br />
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<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
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'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
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Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
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'''Aerobic Gram-Negative Bacteria''':<br />
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''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
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Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
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The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
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== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
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== Structure and Administration ==<br />
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=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
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[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
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=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
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CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
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[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
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[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
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== Characteristic Protein Targets and Interactions ==<br />
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Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene> (in this scene DNA is in mesh formation). The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
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=== Topoisomerase IV Target ===<br />
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<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
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The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
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=== Efflux Pump Interaction ===<br />
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<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). <br />
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== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203404Ciprofloxacin2011-03-11T03:33:18Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page under construction - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
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<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
<br />
Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
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'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
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Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
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'''Aerobic Gram-Negative Bacteria''':<br />
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''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
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Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
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The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
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== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
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== Structure and Administration ==<br />
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=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
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[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
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=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
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CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
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[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
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[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
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== Characteristic Protein Targets and Interactions ==<br />
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Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene>. The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
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=== Topoisomerase IV Target ===<br />
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<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
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The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). The ligand depicted here intercalates within the DNA structure slightly more aggressively than Ciprofloxacin intercalates within DNA Gyrase (see above), since the DNA structure in this case is <scene name='Sandbox_100/Topo_intercalation/1'>slightly more agitated</scene>(in this scene, DNA is in mesh formation). Yet the concept of obstruction of DNA motility via intercalation applies equivalently in this case and, thus, this model is sufficient for a replication of the action of Ciprofloxacin on DNA within DNA Topoisomerase IV. As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
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=== Efflux Pump Interaction ===<br />
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<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). <br />
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== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203387Ciprofloxacin2011-03-11T03:02:51Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page under construction - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
<br />
Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
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'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
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Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
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'''Aerobic Gram-Negative Bacteria''':<br />
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''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
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Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
<br />
The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
<br />
[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
<br />
<br />
=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
<br />
[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
<br />
CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
<br />
<br />
[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
<br />
Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
<br />
<br />
<br />
== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
<br />
[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
<br />
== Characteristic Protein Targets and Interactions ==<br />
<br />
Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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<br />
<br />
=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
<br />
A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene>. The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
<br />
<br />
=== Topoisomerase IV Target ===<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels). As expected, based on the aforementioned structural similarities, the interactions between the intercalating ligand (or, Ciprofloxacin) and the active site of DNA Topoisomerase IV are similar to those witnessed between Ciprofloxacin and DNA Gyrase. The active site of the protein is composed, primarily, of <scene name='Sandbox_100/Active_site_topo_iv_ligand/1'>alpha helices, with polar amino acid residues facing characteristically polar atoms within the structure of the intercalating ligand</scene> (in this scene, alpha helices are purple and polar amino acids on these alpha helices are blue).<br />
<br />
<br />
=== Efflux Pump Interaction ===<br />
<br />
<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). <br />
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<br />
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<br />
<br />
<br />
== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203384Ciprofloxacin2011-03-11T02:53:59Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page under construction - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
<br />
Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
<br />
'''Aerobic Gram-Negative Bacteria''': <br />
<br />
''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
<br />
Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
<br />
'''Aerobic Gram-Negative Bacteria''':<br />
<br />
''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
<br />
Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
<br />
The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
<br />
[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
<br />
<br />
=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
<br />
[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
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[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
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== Characteristic Protein Targets and Interactions ==<br />
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Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene>. The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein in general, is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
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=== Topoisomerase IV Target ===<br />
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<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
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The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels).<br />
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=== Efflux Pump Interaction ===<br />
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<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). <br />
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== References ==<br />
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<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203383Ciprofloxacin2011-03-11T02:53:08Z<p>John Ripollone: </p>
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<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
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= Ciprofloxacin =<br />
Page under construction - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
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== General Information ==<br />
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<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
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Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
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'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
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Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
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'''Aerobic Gram-Negative Bacteria''':<br />
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''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
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Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
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The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
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== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
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== Structure and Administration ==<br />
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=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
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[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
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=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
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CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
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[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
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[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
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== Characteristic Protein Targets and Interactions ==<br />
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Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene>. The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein in general, is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
<br />
<br />
=== Topoisomerase IV Target ===<br />
<br />
<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels).<br />
<br />
<br />
=== Efflux Pump Interaction ===<br />
<br />
<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain drugs <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>. The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is <scene name='Sandbox_100/Orientation_of_cipro_on_acrb/1'>captured by the AcrB subunit</scene> for exclusion from the bacterial cell (in this scene, AcrB is in the proposed transmembrane orientation assuming lower cytosolic face and upper exoplasmic face). <br />
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== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203381Ciprofloxacin2011-03-11T02:44:42Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page under construction - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
<br />
Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
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'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
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Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
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'''Aerobic Gram-Negative Bacteria''':<br />
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''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
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Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
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The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
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== Structure and Administration ==<br />
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=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
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[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
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=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
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CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
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[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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<br />
== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
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[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
<br />
== Characteristic Protein Targets and Interactions ==<br />
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Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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=== DNA Gyrase Target ===<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene>. The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein in general, is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
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<br />
=== Topoisomerase IV Target ===<br />
<br />
<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels).<br />
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<br />
=== Efflux Pump Interaction ===<br />
<br />
<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain foreign substances <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is captured by the AcrB subunit for exclusion from the bacterial cell. <br />
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== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203380Ciprofloxacin2011-03-11T02:43:50Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page under construction - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
<br />
Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
<br />
'''Aerobic Gram-Negative Bacteria''': <br />
<br />
''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
<br />
Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
<br />
'''Aerobic Gram-Negative Bacteria''':<br />
<br />
''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
<br />
Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
<br />
The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
<br />
[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
<br />
<br />
=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
<br />
[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
<br />
CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
<br />
<br />
[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
<br />
Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
<br />
<br />
<br />
== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
<br />
[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
<br />
== Characteristic Protein Targets and Interactions ==<br />
<br />
Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
<br />
<br />
<br />
=== DNA Gyrase Target ===<br />
<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
<br />
A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene>. The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein in general, is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
<br />
<br />
=== Topoisomerase IV Target ===<br />
<br />
<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels).<br />
<br />
<br />
=== Efflux Pump Interaction ===<br />
<br />
<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain foreign substances <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is captured by the AcrB subunit for exclusion from the bacterial cell. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203347Ciprofloxacin2011-03-11T01:20:29Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page under construction - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
<br />
Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
<br />
'''Aerobic Gram-Negative Bacteria''': <br />
<br />
''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
<br />
Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
<br />
'''Aerobic Gram-Negative Bacteria''':<br />
<br />
''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
<br />
Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
<br />
The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
<br />
[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
<br />
<br />
=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
<br />
[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
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[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
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== Characteristic Protein Targets and Interactions ==<br />
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Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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=== DNA Gyrase Target ===<br />
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<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene>. The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein in general, is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
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=== Topoisomerase IV Target ===<br />
<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
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The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels).<br />
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=== Efflux Pump Interaction ===<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain foreign substances <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is captured by the AcrB subunit for exclusion from the bacterial cell. <br />
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<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
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== References ==<br />
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<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203274Ciprofloxacin2011-03-10T16:53:07Z<p>John Ripollone: </p>
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<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
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<br />
= Ciprofloxacin =<br />
Page under construction - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
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== General Information ==<br />
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<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
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<scene name='Sandbox_100/Cpf_with_atomic_labels/1'>Labeled CPF</scene><br />
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Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
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'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
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Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
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'''Aerobic Gram-Negative Bacteria''':<br />
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''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
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Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
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The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
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== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
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== Structure and Administration ==<br />
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=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
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[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
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=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
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CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
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[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
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[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
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== Characteristic Protein Targets and Interactions ==<br />
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Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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=== DNA Gyrase Target ===<br />
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<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene>. The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein in general, is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
<br />
<br />
=== Topoisomerase IV Target ===<br />
<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels).<br />
<br />
<br />
=== Efflux Pump Interaction ===<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain foreign substances <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is captured by the AcrB subunit for exclusion from the bacterial cell. <br />
<br />
<br />
<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203242Ciprofloxacin2011-03-10T06:35:40Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page under construction - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
<scene name='Sandbox_100/Cpf_with_atomic_labels/1'>Labeled CPF</scene><br />
<br />
Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
<br />
'''Aerobic Gram-Negative Bacteria''': <br />
<br />
''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
<br />
Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
<br />
'''Aerobic Gram-Negative Bacteria''':<br />
<br />
''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
<br />
Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
<br />
The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
<br />
[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
<br />
<br />
=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
<br />
[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
<br />
CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
<br />
<br />
[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
<br />
Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
<br />
<br />
<br />
== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
<br />
== Characteristic Protein Targets and Interactions ==<br />
<br />
Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
<br />
<br />
<br />
=== DNA Gyrase Target ===<br />
<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
<br />
A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene>. The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein in general, is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown). <br />
<br />
<br />
<br />
<br />
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<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
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<br />
<br />
<br />
=== Topoisomerase IV Target ===<br />
<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels).<br />
<br />
<br />
=== Efflux Pump Interaction ===<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain foreign substances <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is captured by the AcrB subunit for exclusion from the bacterial cell. <br />
<br />
<br />
<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203239Ciprofloxacin2011-03-10T06:25:56Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page under construction - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
<scene name='Sandbox_100/Cpf_with_atomic_labels/1'>Labeled CPF</scene><br />
<br />
Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
<br />
'''Aerobic Gram-Negative Bacteria''': <br />
<br />
''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
<br />
Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
<br />
'''Aerobic Gram-Negative Bacteria''':<br />
<br />
''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
<br />
Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
<br />
The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
<br />
[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
<br />
<br />
=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
<br />
[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
<br />
CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
<br />
<br />
[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
<br />
Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
<br />
<br />
<br />
== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
<br />
== Characteristic Protein Targets and Interactions ==<br />
<br />
Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
<br />
<br />
<br />
=== DNA Gyrase Target ===<br />
<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
<br />
A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene>. The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue).<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
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<br />
<br />
<br />
=== Topoisomerase IV Target ===<br />
<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of <scene name='Sandbox_100/Example_topoisomerase_iv/1'>Streptococcus pneumoniae Topoisomerase IV in complex with DNA and attached ligand</scene> is shown (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in an "ironing device" shape with a <scene name='Sandbox_100/Topoisomerase_base_cleft_eg/1'>base cleft forming the active site for interaction with DNA </scene> (in this scene, DNA Topoisomerase IV is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and the example Ciprofloxacin structural analog, as in all scenes under this heading, maintains its atomic color labels).<br />
<br />
<br />
=== Efflux Pump Interaction ===<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain foreign substances <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is captured by the AcrB subunit for exclusion from the bacterial cell. <br />
<br />
<br />
<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203238Ciprofloxacin2011-03-10T06:19:12Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page under construction - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
<scene name='Sandbox_100/Cpf_with_atomic_labels/1'>Labeled CPF</scene><br />
<br />
Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
<br />
'''Aerobic Gram-Negative Bacteria''': <br />
<br />
''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
<br />
Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
<br />
'''Aerobic Gram-Negative Bacteria''':<br />
<br />
''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
<br />
Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
<br />
The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
<br />
[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
<br />
<br />
=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
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[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
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== Characteristic Protein Targets and Interactions ==<br />
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Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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=== DNA Gyrase Target ===<br />
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<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene>. The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue).<br />
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=== Topoisomerase IV Target ===<br />
<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
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The structural characterization of the inhibition of DNA replication via inhibition of the action of DNA Topoisomerase IV by Ciprofloxacin is similar to that via inhibition of the action of DNA Gyrase by Ciprofloxacin. An example structure of Topoisomerase IV with attached ligand is shown <scene name='Sandbox_100/Example_topoisomerase_iv/1'>here</scene> (note that this ligand is not Ciprofloxacin, but represents a structure that is analogous to that of Ciprofloxacin). The overall structure of DNA Topoisomerase IV is clearly analogous to that of DNA Gyrase since DNA Topoisomerase IV also appears in a "ironing device" shape with a base cleft forming the active site for interaction with DNA. <br />
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=== Efflux Pump Interaction ===<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain foreign substances <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is captured by the AcrB subunit for exclusion from the bacterial cell. <br />
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<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
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== References ==<br />
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<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203237Ciprofloxacin2011-03-10T06:10:19Z<p>John Ripollone: </p>
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<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
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= Ciprofloxacin =<br />
Page under construction - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
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== General Information ==<br />
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<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
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<scene name='Sandbox_100/Cpf_with_atomic_labels/1'>Labeled CPF</scene><br />
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Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
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'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
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Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
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'''Aerobic Gram-Negative Bacteria''':<br />
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''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
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Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
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The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
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== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
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== Structure and Administration ==<br />
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=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
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[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
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=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
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CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
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[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
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CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
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== Characteristic Protein Targets and Interactions ==<br />
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Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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=== DNA Gyrase Target ===<br />
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<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene>. The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue).<br />
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<br />
=== Topoisomerase IV Target ===<br />
<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
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<br />
=== Efflux Pump Interaction ===<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain foreign substances <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is captured by the AcrB subunit for exclusion from the bacterial cell. <br />
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<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
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== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203236Ciprofloxacin2011-03-10T06:08:18Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page under construction - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
<scene name='Sandbox_100/Cpf_with_atomic_labels/1'>Labeled CPF</scene><br />
<br />
Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
<br />
'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
<br />
Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
<br />
'''Aerobic Gram-Negative Bacteria''':<br />
<br />
''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
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Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
<br />
The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
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[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
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=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
<br />
[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
<br />
CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
<br />
Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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<br />
<br />
== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
<br />
== Characteristic Protein Targets and Interactions ==<br />
<br />
Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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<br />
=== DNA Gyrase Target ===<br />
<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
<br />
A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from ''Staphylococcus aureus'' in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene>. The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue).<br />
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=== Topoisomerase IV Target ===<br />
<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
<br />
<br />
<br />
<br />
=== Efflux Pump Interaction ===<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain foreign substances <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'', the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is captured by the AcrB subunit for exclusion from the bacterial cell. <br />
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<br />
<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
<br />
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<br />
<br />
<br />
== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203235Ciprofloxacin2011-03-10T06:04:54Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
<br />
<br />
= Ciprofloxacin =<br />
Page under construction - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
<br />
== General Information ==<br />
<br />
<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
<br />
<scene name='Sandbox_100/Cpf_with_atomic_labels/1'>Labeled CPF</scene><br />
<br />
Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
<br />
'''Aerobic Gram-Negative Bacteria''': <br />
<br />
''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
<br />
Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
<br />
'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
<br />
'''Aerobic Gram-Negative Bacteria''':<br />
<br />
''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
<br />
Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
<br />
The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
<br />
[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
<br />
<br />
=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
<br />
[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
<br />
CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
<br />
Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
<br />
<br />
<br />
== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
<br />
== Characteristic Protein Targets and Interactions ==<br />
<br />
Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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<br />
=== DNA Gyrase Target ===<br />
<br />
<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
<br />
A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from ''Staphylococcus aureus'' in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene>. The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue).<br />
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=== Topoisomerase IV Target ===<br />
<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
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=== Efflux Pump Interaction ===<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain foreign substances <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'' the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is captured by the AcrB subunit for exclusion from the bacterial cell. <br />
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<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
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== References ==<br />
<br />
<references/></div>John Ripollonehttps://proteopedia.org/index.php?title=Ciprofloxacin&diff=1203230Ciprofloxacin2011-03-10T05:31:47Z<p>John Ripollone: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after May 10, 2011. Sandbox 100 is reserved until then for use by John Ripollone - Messiah College, Grantham, PA (under the supervision of Dr. Hannah Tims).</td></tr><br />
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<br />
= Ciprofloxacin =<br />
Page under construction - by: John Ripollone, Department of Biological Sciences (in conjunction with the Department of Chemistry and Biochemistry) - Messiah College, Grantham, PA 17027.<br />
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== General Information ==<br />
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<Structure load='CPF' size='350' frame='true' align='right' caption='Molecular Structure of Ciprofloxacin' scene='Insert optional scene name here' /><br />
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<scene name='Sandbox_100/Cpf_with_atomic_labels/1'>Labeled CPF</scene><br />
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Ciprofloxacin is a broad-spectrum synthetic fluoroquinolone antibiotic that is generally effective against both aerobic gram-positive and aerobic gram-negative bacteria<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Bacterial organisms that have been shown to be efficiently targeted by ciprofloxacin are: <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
<br />
''Enterococcus faecalis'' (many strains are only moderately susceptible)'','' ''Staphylococcus aureus'' (methicillin-susceptible strains only)'','' ''Staphylococcus epidermidis'' (methicillin-susceptible strains only)'','' ''Staphylococcus saprophyticus,'' ''Streptococcus pneumoniae'' (penicillin-susceptible strains only)'','' ''Streptococcus pyogenes''.<br />
<br />
'''Aerobic Gram-Negative Bacteria''': <br />
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''Campylobacter jejuni, Citrobacter diversus, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei''.<br />
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Ciprofloxacin also exhibits ''in vitro'' minimum inhibitory concentrations of 1 μg/mL or less against strains of the following bacteria (with less adequate characterizations of the effects of treatment against these bacteria in terms of efficiency and general safety): <br />
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'''Aerobic Gram-Positive Bacteria (With Certain Strain Particularities)''':<br />
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''Staphylococcus haemolyticus,'' ''Staphylococcus hominis,'' ''Streptococcus pneumoniae'' (penicillin-resistant strains only).<br />
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'''Aerobic Gram-Negative Bacteria''':<br />
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''Acinetobacter Iwoffi, Aeromonas hydrophila, Edwardsiella tarda, Enterobacter aerogenes, Klebsiella oxytoca, Vibrio cholerae, Legionella pneumophila, Vibrio parahaemolyticus, Pasteurella multocida, Vibrio vulnificus, Salmonella enteritidis, Yersinia enterocolitica''.<br />
<br />
Most anaerobic bacteria exhibit Ciprofloxacin-resistance. <br />
<br />
The effectiveness of Ciprofloxacin against the anthrax-causing bacteria, ''Bacillus anthracis'' - both ''in vitro'' and by use of surrogate marker serum levels - has also been demonstrated<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref><ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin is currently a Federal Drug Administration (FDA)-approved treatment for patients who have been exposed to anthrax via inhalation<ref>2001. Information on Cipro (Ciprofloxacin Hydrochloride) for Inhalation Anthrax for Consumers: Questions and Answers. Fda.gov. http://www.fda.gov/Drugs/EmergencyPreparedness/BioterrorismandDrugPreparedness/ucm130711.htm. Last updated, 2009.</ref>. Likewise, Ciprofloxacin may be used to treat plague (from the bacteria, ''Yersinia pestis'') and tularemia (from the bacteria, ''Francisella tularensis''<ref>2011. Ciprofloxacin. Medicine Plus. American Society of Health-System Pharmacists Inc. 2011. http://www.nlm.nih.gov/medlineplus/druginfo/meds/a688016.html.</ref>. Thus, Ciprofloxacin demonstrates usefulness in the field of counter-bioterrorism given its action against bacteria that could potentially be implemented in biological warfare. Furthermore, in its extended-release tablet form, Ciprofloxacin tends to target, specifically, certain types of urological infections (e.g. epididymitis). The nature of Ciprofloxacin, then, as a powerful, broad-range antibiotic is crucial for broad-range bacterial infection treatment. An understanding of the action of Ciprofloxacin at the molecular level is, no doubt, necessary for an appreciation of the potency of Ciprofloxacin as witnessed at the macro level. <br />
<br />
== Historical Information ==<br />
The patented introduction of Ciprofloxacin in the United States occurred in 1987 as a result of the research efforts of Bayer Pharmaceuticals, although there have been reports that at least two European patents had pre-dated the Bayer patent by at least five years<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>. On October 27, 1987, the Federal Drug Administration (FDA) had approved the drug for use in the United States for the treatment of certain bacterial infections. The effectiveness of Ciprofloxacin as an antibiotic went unchallenged by all alternative antibiotics<ref>Ciprofloxacin - Activity, Business Aspects/Bayer Pharmaceutical. Encyclopedia.jrank.org. http://encyclopedia.jrank.org/articles/pages/1398940/Ciprofloxacin.html</ref>. Thus, other pharmaceutical companies were forced to offer their alternative antibiotics at lower costs (compared to the cost of Ciprofloxacin) so as to engage any sort of competition with Ciprofloxacin. Because of the tendency of doctors to prescribe lower-cost medication, Bayer Pharmaceuticals could not expand into the international pharmaceutical industry (which, as a whole, was steadily declining) and, consequently, was forced to downsize at the turn of the century. Indeed, the competitive effectiveness of Ciprofloxacin did not overcome the competitive pricing of drugs released by alternative pharmaceutical companies. Faced with the impending expiration of its patent for Ciprofloxacin in the early years of the millennium, Bayer Pharmaceuticals attempted to release variations of Ciprofloxacin. The release of Ciprofloxacin variations such as Pediatric Ciprofloxacin and Once-daily Ciprofloxacin allowed for the extension of the Bayer Pharmaceutical Ciprofloxacin patent. The popularity of Ciprofloxacin rose sharply after September 11, 2001 due its characteristic targeting of anthrax, which was projected as a possible tool for bioterrorism. The prescription of Ciprofloxacin for treatment of bacterial infections continues to this day. <br />
<br />
== Structure and Administration ==<br />
<br />
=== General Quinolone-Fluoroquinolone Structure ===<br />
The identification of Ciprofloxacin as a "quinolone" is a result of the heterocyclic (due to the presence of an inner-ring Nitrogen), bicyclic core-containing structure of Ciprofloxacin, which structure is characteristic of all quinolones<ref>Siegmund, K., et al. (2005). Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids [Research], 33(15)'', 4838-4848.</ref>. Ciprofloxacin is further characterized as a "fluoroquinolone" since it contains a fluorine atom at the R6 position of its bicyclic core<ref>Peterson, L. (2001). Quinolone-Molecular Structure-Activity Relationships: What We Have Learned About Improving Antimicrobial Activity. ''Clinical Infectious Diseases, 33(3)'', S180-S186.</ref>. Indeed, all fluoroquinolones contain this R6 fluorine moiety. A general molecular structure for all fluoroquinolones is shown. The R6 fluorine occurs on the left ring of the bicyclic core.<br />
<br />
[[Image:Flg.jpg]]<ref>Image from: http://cid.oxfordjournals.org/content/33/Supplement_3/S180.full.</ref><br />
<br />
<br />
=== Administration ===<br />
Ciprofloxacin is usually administered either as CIPRO® Oral Suspension (Ciprofloxacin) or as CIPRO® Tablets (Ciprofloxacin hydrochloride)<ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. Both administration types are oral. <br />
<br />
CIPRO® Oral Suspension (Ciprofloxacin) is a 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula: C₁₇H₁₈FN₃O₃. Ciprofloxacin has a molecular weight of 331.35 g/mol and occurs as a yellowish, crystalline substance<ref>Molecular weight from Chemexper.com.</ref><ref>CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin is shown (base empirical formula).<br />
<br />
[[Image:cipro.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://textbookofbacteriology.net/themicrobialworld/cipro.gif&imgrefurl=http://textbookofbacteriology.net/themicrobialworld/control.html&usg=__wtzKLHB3NssfnODEB224br5-Bcw=&h=200&w=250&sz=2&hl=en&start=0&zoom=1&tbnid=o7VT7s6FFIUrWM:&tbnh=160&tbnw=199&ei=Hk10TaypBcL58AbyvIjKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=527&vpy=300&dur=1709&hovh=160&hovw=200&tx=155&ty=82&oei=EU10TcvOCMbdtge5msiLDw&page=1&ndsp=16&ved=1t:429,r:7,s:0.</ref><br />
<br />
CIPRO® Tablet[s] (Ciprofloxacin hydrochloride) is the monohydrochloride monohydrate salt of 1-cyclopropyl-6-floro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid with empirical formula C₁₇H₁₈FN₃O₃•HCl•H₂O. Ciprofloxacin hydrochloride has a molecular weight of 385.5 g/mol and also occurs as a yellowish, crystalline substance<ref>Molecular weight from: CIPRO® (ciprofloxacin hydrochloride) TABLETS - CIPRO® (ciprofloxacin*) ORAL SUSPENSION - Drug Information Packet. Bayer HealthCare Pharmaceuticals. Schering Plough Corporation.</ref>. A simple molecular structure of Ciprofloxacin hydrochloride is shown.<br />
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[[Image:ciproHCl.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://images.rxlist.com/images/rxlist/ciloxan_s.gif&imgrefurl=http://www.rxlist.com/ciloxan_ophthalmic_ointment-drug.htm&usg=__UqTKseSe8hD85c5RLGIz2_dbAg0=&h=142&w=232&sz=2&hl=en&start=16&zoom=1&tbnid=70Q2WG5hppsQ5M:&tbnh=100&tbnw=164&ei=T010TenMFYH_8Aa6gvDKDw&prev=/images%3Fq%3Dciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:10%2C624&um=1&itbs=1&iact=hc&vpx=1064&vpy=399&dur=309&hovh=106&hovw=174&tx=98&ty=76&oei=EU10TcvOCMbdtge5msiLDw&page=2&ndsp=18&ved=1t:429,r:17,s:16&biw=1280&bih=647.</ref><br />
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Ciprofloxacin may also be administered intravenously and in the form of eye or ear drops<ref>Ciprofloxacin. (2010). Pcm.me. http://pcm.me/ciprofloxacin/.</ref>.<br />
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== Synthesis ==<br />
A six-step pathway for Ciprofloxacin synthesis is shown below. This particular pathway is characterized by the initiation of a cyclic chloro-fluoro precursor followed by closing of a nitrogen-containing ring and addition of piperazine ortho with respect to the R6 fluorine. It should be noted, however, that other systems for Ciprofloxacin synthesis have been postulated. <br />
[[Image:Cipro Synthesis.gif]]<ref>Image from: http://www.google.com/imgres?imgurl=http://www.chemdrug.com/databases/SYNTHESIS/SYN/09/09000601a.gif&imgrefurl=http://www.chemdrug.com/databases/8_0_dvpytumicutbciwa.html&usg=__TxiDuzCve6C_crxmcPYTpfW5d4s=&h=555&w=678&sz=6&hl=en&start=0&zoom=1&tbnid=xhquLksJBbMnjM:&tbnh=165&tbnw=201&ei=0Y93TdbGI-yI0QGspa25Bw&prev=/images%3Fq%3Dsynthesis%2Bof%2Bciprofloxacin%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26sa%3DN%26rls%3Dorg.mozilla:en-US:official%26biw%3D1280%26bih%3D647%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=346&vpy=105&dur=63&hovh=203&hovw=248&tx=170&ty=128&oei=0Y93TdbGI-yI0QGspa25Bw&page=1&ndsp=16&ved=1t:429,r:1,s:0</ref><br />
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== Characteristic Protein Targets and Interactions ==<br />
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Ciprofloxacin is known for its efficient ability to hinder bacterial DNA synthesis via inhibition of bacterial DNA Gyrase and DNA Topoisomerase IV. <ref>Ciprofloxacin Oral - Monograph - Ciprofloxacin Hydrochloride. 2009. Medscape.com. http://www.medscape.com/druginfo/monograph cid=med&drugid=7748&drugname=Ciprofloxacin+Oral&monotype=monograph&secid=8.</ref>. DNA Gyrase, a type II DNA topoisomerase, is a tetramer composed of 2 GyrA and 2 GyrB subunits. DNA Gyrase is responsible for introducing negative superhelical twists (gyrations, hence, "Gyrase") - as it removes positive superhelical twists - without which twists DNA replication would not occur. Topoisomerase IV, also a type II DNA topoisomerase, is composed of 2 ParC and 2 ParE subunits, and its overall structure is similar to that of DNA Gyrase. Specifically, ParC is homologous to GyrA, and ParE is homologous to GyrB. Topoisomerase IV is responsible for the separation of interlinked daughter chromosomes, which separation anticipates the segregation of daughter cells. The action of Ciprofloxacin on DNA Gyrase and on Topoisomerase IV is characterized by the stabilization of DNA in complex with either of these two proteins. This stabilization prevents normal motility (and, thus, progression) of the DNA replication fork, which prevention results in a full inhibition of DNA replication. This inhibition ultimately leads to cell death.<br />
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=== DNA Gyrase Target ===<br />
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<Structure load='2XCT' size='350' frame='true' align='right' caption='Twinned Structure of Staphylococcus aureus Gyrase Complex with Attached Ciprofloxacin and DNA' scene='Insert optional scene name here' /><br />
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A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from ''Staphylococcus aureus'' in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene>. The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>.<br />
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=== Topoisomerase IV Target ===<br />
<Structure load='3LTN' size='350' frame='true' align='right' caption='Example Inhibitor-Stabilized Topoisomerase IV-DNA Cleavage Complex from Streptococcus pneumoniae' scene='Insert optional scene name here' /><br />
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=== Efflux Pump Interaction ===<br />
Certain bacteria (''Escherichia coli'', for example) contain a proton motive-force dependent multidrug efflux pump, which, as the name suggests, grants the bacteria resistance to certain foreign substances <ref>Su, Chih-Chia, et al. (2006). Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway. ''Journal of Bacteriology, 188(20)'', 7290-7296. </ref>. In ''Escherichia coli'' the efflux system that confers particular drug resistance is a tripartite transmembrane resistance structure known as "AcrAB-TolC" <ref>Husain, F., Nikaido, H. (2010). Substrate path in the AcrB multidrug efflux pump of Escherichia coli. ''Molecular Microbiology, 78(2)'', 320-330. </ref>The drug molecule targeted for excretion is captured by the AcrB subunit (most likely from the periplasm or from the periplasm-intermembrane interface) and is then passed on to the TolC complex for final export. Of course, one could argue that the most important member of the AcrAB-TolC resistance complex is the member that is responsible for the initial attraction of the target compound, The AcrB subunit. Ciprofloxacin is one such drug that is captured by the AcrB subunit for exclusion from the bacterial cell. <br />
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<Structure load='1OYE' size='350' frame='true' align='right' caption='AcrB Multidrug Efflux Pump with Attached Ciprofloxacin' scene='Insert optional scene name here' /><br />
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== References ==<br />
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<references/></div>John Ripollone