MbtI structure has a mobile element (residues 268-293 and 324-336) that can adopt a <scene name='69/694235/Irp9_closed_state/2'>closed</scene> or <scene name='69/694235/2g5f_with_open_loop/1'>open conformation</scene> depending on whether or not ligands are bound to the active site(Harrison 2006). The closed conformation partially obstructs the active site. <ref name= "5a"/>.
MbtI structure has a mobile element (residues 268-293 and 324-336) that can adopt a <scene name='69/694235/Irp9_closed_state/2'>closed</scene> or <scene name='69/694235/2g5f_with_open_loop/1'>open conformation</scene> depending on whether or not ligands are bound to the active site(Harrison 2006). The closed conformation partially obstructs the active site. <ref name= "5a"/>.
Inhibition studies have also shown a switch in binding mode at the MbtI active site for inhibitors carrying a substituted enolpyruvyl group compared to the chorismate substrate(Chi 2006, Turvey 2012, Turvey 2010). Crystal structures and fluorescent-based thermal shift assays show that substituents larger than a methyl group are accommodated in the active site of MbtI through localized flexibility in the peptide backbone(Chi 2006). Positioning of the <scene name='69/694235/3st6_structure_bindingpocket/3'>active site residues</scene> of MbtI in [[3ST6]] with the inhibitor AMT bound is highly similar to the positioning of the <scene name='69/694235/3log_bindingpocket/2'>active site residues</scene> in closed form of MbtI [[3log]] with succinic acid bound <ref name= "5a"/>. The AMT inhibitor contains an unmodified enolpyruvyl side chain and resembles the structure of the natural substrate, chorismate. [[3log]] and [[3ST6]] are shown to share a similar binding mode, termed binding mode 1. Isochorismate inhibitors with modified enolpyruvl side chains ([[3VEH]], [[3RV9]], [[3RV8]], [[3RV7]], [[3RV6]]) utilize a novel binding mode, termed mode 2, which involves the <scene name='69/694235/3veh_structure_bindingpocket2/2'>reorientation of the isochorismate analogue within the active site</scene>. Movement of the peptide backbone away from the closed form of MbtI is required to accommodate the enolpyruyl modified inhibitors.
Inhibition studies have also shown a switch in binding mode at the MbtI active site for inhibitors carrying a substituted enolpyruvyl group compared to the chorismate substrate(Chi 2006, Turvey 2012, Turvey 2010). Crystal structures and fluorescent-based thermal shift assays show that substituents larger than a methyl group are accommodated in the active site of MbtI through localized flexibility in the peptide backbone(Chi 2006). Positioning of the <scene name='69/694235/3st6_structure_bindingpocket/3'>active site residues</scene> of MbtI in [[3ST6]] with the inhibitor AMT bound is highly similar to the positioning of the <scene name='69/694235/3log_bindingpocket/3'>active site residues</scene> in closed form of MbtI [[3log]] with succinic acid bound <ref name= "5a"/>. The AMT inhibitor contains an unmodified enolpyruvyl side chain and resembles the structure of the natural substrate, chorismate. [[3log]] and [[3ST6]] are shown to share a similar binding mode, termed binding mode 1. Isochorismate inhibitors with modified enolpyruvl side chains ([[3VEH]], [[3RV9]], [[3RV8]], [[3RV7]], [[3RV6]]) utilize a novel binding mode, termed mode 2, which involves the <scene name='69/694235/3veh_structure_bindingpocket2/2'>reorientation of the isochorismate analogue within the active site</scene>. Movement of the peptide backbone away from the closed form of MbtI is required to accommodate the enolpyruyl modified inhibitors.
==Molecular Mechanism==
==Molecular Mechanism==
'''Magnesium cation effect'''
'''Magnesium cation effect'''
[[Image:Screen Shot 2015-04-25 at 11.08.58 PM.png |300 px|left|thumb|'''Table 1:''' pKa values of active site residues of MbtI with and without Magnesium. Ferrer 2-11.]] The presence of the [http://en.wikipedia.org/wiki/Magnesium_in_biology magnesium ion] induces <scene name='69/694235/Mg_coordination/1'>changes in the structure</scene> of the active site and in the substrate, as well as causes significant pKa shifts in some of the key residues involved in the catalytic activity(Table 1) . The <scene name='69/694235/3rv6_mg_shell/3'>coordination shell</scene> of the magnesium cation in the active site of MbtI is composed of two water molecules, Glu434, Glu294, and the two oxygen atoms of the C1 carboxylate group of chorismate <ref name= "8a">PMID:22307014</ref>. In the presence of the magnesium ion, the positively charged Lys295 is displaced from the active site and the negatively charged Glu297 is faced toward the active site. Magnesium cation also orients the C1 carboxylate group coplanar to the ring of chorismate, reducing the electron density on the C2 center and favoring nucleophilic attack.
[[Image:Screen Shot 2015-04-25 at 11.08.58 PM.png |300 px|left|thumb|'''Table 1:''' pKa values of active site residues of MbtI with and without Magnesium. Ferrer 2-11.]] The presence of the [http://en.wikipedia.org/wiki/Magnesium_in_biology magnesium ion] induces changes in the structure of the active site and in the substrate, as well as causes significant pKa shifts in some of the key residues involved in the catalytic activity (Table 1).The <scene name='69/694235/3rv6_mg_shell/4'>coordination shell</scene>of the magnesium cation in the active site of MbtI in [[3rv6]] with phenyl-AMT inhibitor bound is composed of two water molecules, Glu434, Glu294, and the two oxygen atoms of the C1 carboxylate group of chorismate. In the presence of the magnesium ion, the positively charged Lys295 is displaced from the active site and the negatively charged Glu297 is faced toward the active site. Magnesium cation also orients the C1 carboxylate group coplanar to the ring of chorismate, reducing the electron density on the C2 center and favoring nucleophilic attack<ref name= "8a">PMID:22307014</ref>.
Salicylate synthase from Mycobacterium_tuberculosis (MtbI) is a highly promiscuous enzyme that has four distinct activities in vivo: isochorismate synthase (IS), isochorismate pyruvate lyase (IPL), salicylate synthase (SS) and chorismate mutate (CM)(Ferrer 2012). MtbI belongs to the chorismate-utilizing enzyme family, which consists of structural homologues (Ipr9, MenF, EntC, and MbtI) that isomerize chromate to isochorismate and share a fold of two α/β subdomains, each comprising of a antiparallel β-sheet with helices packed against it(Ferrer 2012, Lamb 2011). These enzymes are present in bacteria, fungi, plants and apicomplexan parasites and catalyze the initial reactions of menaquinone, siderophore, and tryptophan biosynthesis(ferrer 2012, Lamb 2011, Voss 1999). The IS, IPL, and SS activity of MbtI require the presence of a magnesium ion within the active site, while CM activity is only observed in absence of the magnesium cation(ferrer 2012). IS, IPL, and SS activity are also modulated by the pH of the medium(ferrer 2012). Isochorismate is the primary product at pH values below 7.5 and salicylate is the primary product formed at pH 8(ferrer 2012, Zwahlen 2006).
The salicylate synthase activity of MbtI catalyzes the first committed step in the synthesis of the iron chelating siderophore, mycobactin T, in Mycobacterium tuberculosis (Figure 1)[1]. Mycobactin T is synthesized by the proteins encoded by the mbt and mbt2 gene clusters [1]. The gene Rv2386c is essential for the in vitro growth of "M. tuberculosis" and codes the enzyme MbtI (turvey, 2010). This complex secondary metabolite is essential for both virulence and survival of M. tuberculosis(ferrer 2012, Voss 1999, Harrison 2006). Therefore, inhibitors of salicylate synthase may serve as potential TB therapies with a novel mode of action [2][3][4][1][5][6]
Figure 1: Pathways catalyzed by wild-type MbtI[7].
Structure
File:Active site cleft.pngFigure 2: This shows a single sub unit of MbtI, with the active site cleft located at the lower left hand side of the image.
The crystal asymmetric unit was found to contain four MbtI molecules, however crystal packing and size exclusion chromatography data suggest a monomeric enzyme [8]. There are no significant structural changes between the four monomers excepts from the localized differences in the active site [8]. The overall molecular structure consist of a polypeptide of 450 residues that forms one large single domain with a similar fold to other chromate-utilizing enzymes [8]. The core of the protein is formed by 21 Beta sheets folded into a twisted beta-sandwich. The protein's core is then surrounded by 10 alpha helices[8]. The active site was identified by comparison to the product bound forms of Irp9 and TrpE and is situated in a cleft that is about 12Å in length, 10Å deep, and 7Å wide. One side of the groove is formed by β21, C-terminal helix, and α11. The other side of the groove is formed by β16-17 loop, helix α7, and β15-α6 loop. The β19-20 and β12-13 loops make up the bottom of the active side cleft (Harrison 2006)
MbtI structure has a mobile element (residues 268-293 and 324-336) that can adopt a closed or open conformation depending on whether or not ligands are bound to the active site(Harrison 2006). The closed conformation partially obstructs the active site. [1].
Inhibition studies have also shown a switch in binding mode at the MbtI active site for inhibitors carrying a substituted enolpyruvyl group compared to the chorismate substrate(Chi 2006, Turvey 2012, Turvey 2010). Crystal structures and fluorescent-based thermal shift assays show that substituents larger than a methyl group are accommodated in the active site of MbtI through localized flexibility in the peptide backbone(Chi 2006). Positioning of the active site residues of MbtI in 3ST6 with the inhibitor AMT bound is highly similar to the positioning of the active site residues in closed form of MbtI 3log with succinic acid bound [1]. The AMT inhibitor contains an unmodified enolpyruvyl side chain and resembles the structure of the natural substrate, chorismate. 3log and 3ST6 are shown to share a similar binding mode, termed binding mode 1. Isochorismate inhibitors with modified enolpyruvl side chains (3VEH, 3RV9, 3RV8, 3RV7, 3RV6) utilize a novel binding mode, termed mode 2, which involves the reorientation of the isochorismate analogue within the active site. Movement of the peptide backbone away from the closed form of MbtI is required to accommodate the enolpyruyl modified inhibitors.
Molecular Mechanism
Magnesium cation effect
Table 1: pKa values of active site residues of MbtI with and without Magnesium. Ferrer 2-11.
The presence of the magnesium ion induces changes in the structure of the active site and in the substrate, as well as causes significant pKa shifts in some of the key residues involved in the catalytic activity (Table 1).The coordination shellof the magnesium cation in the active site of MbtI in 3rv6 with phenyl-AMT inhibitor bound is composed of two water molecules, Glu434, Glu294, and the two oxygen atoms of the C1 carboxylate group of chorismate. In the presence of the magnesium ion, the positively charged Lys295 is displaced from the active site and the negatively charged Glu297 is faced toward the active site. Magnesium cation also orients the C1 carboxylate group coplanar to the ring of chorismate, reducing the electron density on the C2 center and favoring nucleophilic attack[9].
Isochorismate pyruvate lyase (IPL)
Isochorismate is converted to salicylate and pyruvate through abstraction of the C2 hydrogen followed by protonation of C9 atom and the breakage of the C3-O7 bond. Histidine residue (His334) was proposed to act as a base, abstracting the C2 proton of isochorismate through a second order elimination mechanism. However, recent studies have shown that this residue lies more than 13 A away from C2 atom and no other water molecules appear close enough to the C2 atom to act as a base. IPL reaction has been proposed to proceed through an intramolecular pericyclic mechanisms, involving a concerted hydrogen transfer from C2 to C9 and breakage of the C3-O7 bond.
Currently, isochorismate is believed to be formed from chorismate through a proposed Sn2 mechanism involving nucleophilic attack of an activated water molecule to the C2 center followed by either a concerted or stepwise elimination of the C4 hydroxyl group [11]. Lys205 has been proposed to act as the catalytic base, activating a water molecule in the active site by abstracting one of its protons. However, mutational analysis of Lys205 suggested that the lysine reside is not the sole determinant in the activation of a water molecule for nucleophilic attack of the C2 center. Studies have shown that Lys205 is protonated at neutral pH and therefore can't act as a base to activate the water molecule, agreeing with the mutational analysis data. Instead of Lys205, Glu297 residue has been proposed to act as a base in the activation of the water molecule. The magnesium ion forces the negatively charged Glu297 residue to face toward the active site and the pKa of Glu297 (3.9) suggest an unprotonated state. Furthermore, Glu297 forms a hydrogen bond with a water molecule within the active site as well as with Lys205, which is in turn hydrogen bonded to C1 carboxylate group of chorismate and the oxygen of the nucleophilic water molecule. The glutamic residue (Gly252) could protonate the C4 leaving hydroxyl group. The pKa of Gly252 (7.7) suggest that is it is the only protonated glutamate residue in the active site at pH 7 and thus able to protonate the C4 leaving group. The pKa of Gly252 also accounts for the accumulation of isochorismate at pH values below 7.5.
A magnesium ion in the active site orients the C1 carboxyl group of chorismate. A lysine residue then serves as a general base for the activation of a water molecule to attack at C2. The catalytic mechanism for conversion of isochorismate to salicylate by MbtI is a sigmatropic, pericyclic mechanism that is pH-dependent. Chromate mutase activity is only observed in the absence of magnesium ion in the active site while salicylate synthase activity is depended on magnesium ion. The active site of MbtI is altered by the removal of the magnesium cofactor causing chromate mutase activity. MbtI has differing binding modes for chromate that leads to different substrate conformations/transition states and resulting in different products.
Mycobacterium tuberculosis is the causative agent of Tuberculosis (TB), an infectious disease that affects one-third of the worlds population. Two TB-related conditions exist: latent TB infection and active TB disease. Currently, there are four regimens that are approved for the treatment of latent TB infection through the use of the antibiotics isoniazid, rifampin, and rifapentine.TB disease can also be treated through various antibiotic regimens. There are 10 drugs currently approved by the FDA for treating TB disease. The first-line anti-TB agents are the antibiotics isoniazid, rifampin, ethambutol, and pyrazinamide [14]. Although various treatments for TB infection and TB disease exist, the emergence of multi-drug and extensively-drug resistant strains of M. tuberculosis has increased the need for anti-tubercular agents with novel modes of action.
Iron is essential for mycobacterial growth and pathogenesis, therefore the pathways for iron acquisition are potential targets for antibacterial therapies.M. tuberculosis obtains iron through two different pathways: chelating iron from the host through the siderophore mycobactin and the degradation of heme released from damaged red blood cells.
Mycobactin is a siderophore synthesized by the proteins encoded by the mbt and mbt2 gene clusters [1]. The gene Rv2386c is essential for the in vitro growth of "M. tuberculosis" and codes the enzyme MbtI. (turvey, 2010)
MbtI catalyses the first committed step in the biosynthesis of the siderophore mycobactin and is a potential target for inhibition. The salicylate synthase activity of MbtI produces salicylate and pyruvate from chorismate through an isochorismate intermediate. Inhibition of MbtI activity would decrease the production of salicylate and therefore the synthesis of mycobactin; leading to a decrease in iron acquisition and pathogenesis of M. tuberculosis[15] .
Figure 3: Reaction catalyzed by MbtI in the mycobactin biosynthesis pathway[3].
Inhibition Studies
MbtI Inhibition studies aid in the future design of anti-tubercular agents and broad-spectrum antibiotics with a novel mode of action. Mimics of the enzyme-bound intermediate of MbtI, isochorismate, prove to be significantly more potent inhibitors than mimics of the substrate, chorismate [2]. The isochorismate mimic based on a 2,3-dihydroxybenzoate scaffold showed low-micromolar inhibition constants against MbtI that were an order of magnitude more potents than the natural substrates. The most potent inhibitors contained hydrophobic enol ether side chains at C3 instead of the enol-pyruvyl side chains seen in chorismate and isochorismate (Turvey 2010). Increased potency of inhibitors with a substituted enolpyruvyl group has been attributed to a change in the binding mode through localized flexibility of the peptide backbone.
Two binding mode at the MbtI active site have been observed based on the structure of the inhibitor.
IsochorismateSpecifically, 2-hydroxybenzoate-based inhibitors that contain extended hydrophobic enol ether side chains at C3 in place of the enol-pyruvate side chain found in chorismate and isochorismate.
↑ 1.01.11.21.31.41.5Chi G, Manos-Turvey A, O'Connor PD, Johnston JM, Evans GL, Baker EN, Payne RJ, Lott JS, Bulloch EM. Implications of Binding Mode and Active Site Flexibility for Inhibitor Potency against the Salicylate Synthase from Mycobacterium tuberculosis. Biochemistry. 2012 Jun 7. PMID:22607697 doi:10.1021/bi3002067
↑ 3.03.1Manos-Turvey A, Cergol KM, Salam NK, Bulloch EM, Chi G, Pang A, Britton WJ, West NP, Baker EN, Lott JS, Payne RJ. Synthesis and evaluation of M. tuberculosis salicylate synthase (MbtI) inhibitors designed to probe plasticity in the active site. Org Biomol Chem. 2012 Dec 14;10(46):9223-36. doi: 10.1039/c2ob26736e. Epub 2012, Oct 29. PMID:23108268 doi:https://dx.doi.org/10.1039/c2ob26736e
↑Voss, James J., Kerry Rutter, Benjamin G. Schroedor, Hua Su, and YaQi Zhu. "The salicylate-derived mycobactin siderophores of Mycobacterium tuberculosis are essential for growth in macrophages." Proceedings of the National Academy of Sciences 97.3 (2000): 1252-57. Web. 14 Mar. 2015.
↑He Z, Stigers Lavoie KD, Bartlett PA, Toney MD. Conservation of mechanism in three chorismate-utilizing enzymes. J Am Chem Soc. 2004 Mar 3;126(8):2378-85. PMID:14982443 doi:https://dx.doi.org/10.1021/ja0389927
↑Ferrer S, Marti S, Moliner V, Tunon I, Bertran J. Understanding the different activities of highly promiscuous MbtI by computational methods. Phys Chem Chem Phys. 2012 Mar 14;14(10):3482-9. doi: 10.1039/c2cp23149b. Epub, 2012 Feb 3. PMID:22307014 doi:https://dx.doi.org/10.1039/c2cp23149b
↑Ferrer S, Marti S, Moliner V, Tunon I, Bertran J. Understanding the different activities of highly promiscuous MbtI by computational methods. Phys Chem Chem Phys. 2012 Mar 14;14(10):3482-9. doi: 10.1039/c2cp23149b. Epub, 2012 Feb 3. PMID:22307014 doi:https://dx.doi.org/10.1039/c2cp23149b
↑Ferrer S, Marti S, Moliner V, Tunon I, Bertran J. Understanding the different activities of highly promiscuous MbtI by computational methods. Phys Chem Chem Phys. 2012 Mar 14;14(10):3482-9. doi: 10.1039/c2cp23149b. Epub, 2012 Feb 3. PMID:22307014 doi:https://dx.doi.org/10.1039/c2cp23149b
↑He Z, Stigers Lavoie KD, Bartlett PA, Toney MD. Conservation of mechanism in three chorismate-utilizing enzymes. J Am Chem Soc. 2004 Mar 3;126(8):2378-85. PMID:14982443 doi:https://dx.doi.org/10.1021/ja0389927
↑Ferrer S, Marti S, Moliner V, Tunon I, Bertran J. Understanding the different activities of highly promiscuous MbtI by computational methods. Phys Chem Chem Phys. 2012 Mar 14;14(10):3482-9. doi: 10.1039/c2cp23149b. Epub, 2012 Feb 3. PMID:22307014 doi:https://dx.doi.org/10.1039/c2cp23149b
↑Ferrer S, Marti S, Moliner V, Tunon I, Bertran J. Understanding the different activities of highly promiscuous MbtI by computational methods. Phys Chem Chem Phys. 2012 Mar 14;14(10):3482-9. doi: 10.1039/c2cp23149b. Epub, 2012 Feb 3. PMID:22307014 doi:https://dx.doi.org/10.1039/c2cp23149b
↑Tuberculosis (TB). Ed. Sam Posner. Centers for Disease Control and Prevention, n.d. Web. 9 Apr. 2015.
↑De Voss, James J., Kerry Rutter, Benjamin G. Schroeder, Hua Su, and YaQi Zhu. The salicylate-derived mycobacterium siderophore of Mycobacterium tuberculosis are essential for growth in macrophages. "Proceedings of the National Science Academy" 97.3 (2000): 1252-57. Web. 5 Apr. 2015.
