Student Projects for UMass Chemistry 423 Spring 2011: Difference between revisions
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New page: '''This sandbox is in use for UMass Chemistry 423. Others please do not edit this page. Thanks!''' ''' Spring 2011 Chem423 Team Projects: Understanding Drug Mechanisms''' == Project Inst... |
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''' | <StructureSection load='1wat' size='400' side='right' scene='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4' caption=''> | ||
Instructions and signup page (1-6 below) were posted in Sandbox423 for all students to edit. Students created projects (7-8 below, and additional links in section 3) on separate sandbox pages. | |||
''' Spring 2011 Chem423 Team Projects: Understanding Drug Mechanisms''' | ''' Spring 2011 Chem423 Team Projects: Understanding Drug Mechanisms''' | ||
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{{Clear}} | {{Clear}} | ||
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Monday 4/25/11 | Monday 4/25/11 | ||
Nick DeGraan-Weber, Jackie Dorhout, Rachael Jayne, Mike Reardon - flu neuraminidase in complex with tamiflu | Nick DeGraan-Weber, Jackie Dorhout, Rachael Jayne, Mike Reardon - [[#Flu Neuraminidase|flu neuraminidase in complex with tamiflu]] | ||
John Hickey, Josh Drolet, Josephine Harrington, Andrea Simoni - influenza M2 proton channel | John Hickey, Josh Drolet, Josephine Harrington, Andrea Simoni - [[#Influenza M2 Proton Channel|influenza M2 proton channel]] | ||
[[UMass Chem 423 Student Projects 2011-1]]: | |||
Wednesday 4/27/11 | Wednesday 4/27/11 | ||
Brittany Forkus, Katie Geldart, Elizabeth Schutsky, Breanna Zerfas - | Brittany Forkus, Katie Geldart, Elizabeth Schutsky, Breanna Zerfas - Beta Adrenergic GPCR | ||
Lucia Tringali, Shaina Boyle, Jaclyn Somadelis , Dany Mbakop -- HIV Protease | Lucia Tringali, Shaina Boyle, Jaclyn Somadelis , Dany Mbakop -- HIV Protease | ||
Andy Kim, Zach Brentzel, Tyler Vlass, Zach Hitzig -- Acetylcholinesterase | Andy Kim, Zach Brentzel, Tyler Vlass, Zach Hitzig -- Acetylcholinesterase | ||
Friday 4/29/11 | Friday 4/29/11 | ||
Varun Chalupadi, Anthony Laviola, Tiffany Brucker, Alan Stebbins - | Varun Chalupadi, Anthony Laviola, Tiffany Brucker, Alan Stebbins - Cyclooxygenase | ||
[[UMass Chem 423 Student Projects 2011-2]]: | |||
Inna Brockman, Robert Nathan, Sarena Horava, Nick Cadirov - p38 kinase | Inna Brockman, Robert Nathan, Sarena Horava, Nick Cadirov - p38 kinase | ||
David Peltier, Donald Einck, Ethan Leighton, Chris Coakley - Rituximab Fab | David Peltier, Donald Einck, Ethan Leighton, Chris Coakley - Rituximab Fab | ||
Monday 5/2/11 | Monday 5/2/11 | ||
Max Moulton, Sally Stras, Jordan Schleeweis, Anh Huynh -- HIV reverse transcription | Max Moulton, Sally Stras, Jordan Schleeweis, Anh Huynh -- HIV reverse transcription | ||
Chris Brueckner, Daniel Roy, John Clarkson, Justin Srodulski -- Ketamine in binding complex with NMDA receptor | Chris Brueckner, Daniel Roy, John Clarkson, Justin Srodulski -- Ketamine in binding complex with NMDA receptor | ||
Lyes Khendek, Paul Breslin, William Rowley, Joe Perito, Ashley Rivera - G-Quadruplex | Lyes Khendek, Paul Breslin, William Rowley, Joe Perito, Ashley Rivera - G-Quadruplex | ||
==Students looking for group members== | ==Students looking for group members== | ||
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It is also useful to click the "selection halos:" box under the picture. That shows you what you have in your selection. | It is also useful to click the "selection halos:" box under the picture. That shows you what you have in your selection. | ||
=='''Flu Neuraminidase'''== | |||
[[Image:neuraminidase-and-tamiflu.jpg|left|300px]]<br /> | |||
{{clear}} | |||
===Introduction=== | |||
Neuraminidase protein is one of two glycoproteins that coats the envelope of the influenza virus. Neuraminidase's particular function is the removal of sialic acid from the host cell, allowing the replicated influenza viruses to escape the host cell and spread to other cells. | |||
Tamiflu, a drug designed to combat influenza, binds to and inhibits the function of neuraminidase, disabling its function and consequently disallowing the influenza virus to spread between cells. | |||
Influenza is a disease caused by the various species and genera of the influenza RNA virus. The disease, commonly referred to as "the Flu," is highly contagious and travels around the world in seasonal epidemics. It is responsible for the deaths of between 250,000 and 500,000 people each year, and these numbers can sometimes reach the millions in particularly pandemic years. The virus is particularly lethal to people with weakened immune systems, since the virus can enable the spread of dangerous secondary infections such as pneumonias within the host. | |||
The typical symptoms of the Flu include chills, fever, a sore throat, muscle pains, severe headache, coughing, and weakness or fatigue, as well as general discomfort. | |||
===Overall Structure=== | |||
Influenza (flu) Neuraminidase is a homotetramer, with four identical subunits. Each subunit consists mostly of antiparallel beta sheets and three alpha helices, with a beta-propeller folding pattern (<scene name='Sandbox45/Secondary_structure/2'>Secondary Structure</scene>). | |||
As shown, the alpha helices lie toward the center of the protein. | |||
The <scene name='Sandbox45/Active_site/1'>Active Site</scene> is a pocket on the surface of the protein, lined with highly conserved residues. Shown <scene name='Sandbox45/Tamiflu_bound/1'>here</scene> is the ligand Oseltamivir (Tamiflu) bound to one of the four subunits. When Tamiflu is bound, it tightly blocks the virus release sites on nonresistant strains of flu neuraminidase because it binds with the hydrophilic residues exposed on the surface. | |||
Different conformations account for drug resistance of flu neuraminidase. 2hu4 is the “closed” conformation of the wild type 3hu0. For example, a mutation at the site H274Y, <scene name='Sandbox45/Mutation_at_his274/1'>shown here</scene> on the closed-form wild type, causes a change in the usual binding site for Tamiflu, possibly affecting resistance. | |||
Research on the structures of the different mutants of flu Neuraminidase suggests that the slight change in the binding site affects the drug resistance of the molecule. In a specific case presented by Wang , et al., the H5N1 mutant being observed has a hydrophobic Tyr347 compared to the hydrophilic Asn347 of the wild type and closed form. Since Tamiflu binds to hydrophilic regions of the pore, this change has the potential to greatly affect the binding affinity, hence the mutant’s resistance to oseltamivir. | |||
===Drug Binding Site=== | |||
Flu neuraminidase is a homotetramer, and each of the four protein chains has a catalytic site. The catalytic sites are shown <scene name='Sandbox45/2hu4_tetramer_tamiflu/1'>here</scene> with Tamiflu shown in purple. | |||
Tamiflu was designed specifically to fit to the binding site of neuraminidase by induced fit. The binding site contains a loop of residues 147-152. When it binds at the active site, Tamiflu pulls a loop made of Asp151 and Glu119 <scene name='Sandbox45/2hu4_activesite_loop/2'>residues</scene> closer to the inhibitor, thereby enclosing the Tamiflu inhibitor. | |||
There are five specific residues that are in contact with the Tamiflu substrate - Arg292, Glu276, Arg152, Arg371, and Arg118. They are <scene name='Sandbox45/2hu4_active_site/1'>shown here</scene> in the active site. | |||
Tamiflu does not work on all types of the flu virus, and some are becoming immune to it. However, it was recently discovered that one of the subunits has a larger surface-accessible cavity in the substrate binding region. The larger end of this cavity is not in contact with Tamiflu when the substrate is bound. This presents an opportunity to design another drug with greater specificity to this pocket. | |||
===Additional Features=== | |||
Neuraminidase breaks the <scene name='Sandbox45/Sialic_acid_and_neuraminidase/1'>sialic acid</scene> groups from glycoproteins. <scene name='Sandbox45/Sialic_acid_and_hemagglutinin/1'>Hemagglutinin</scene> from on the virus attaches to the sialic acid groups. The virus is from the cell and is released when neuraminidase breaks the sialic acid groups. This will allow flu replication to happen and a neuraminidase inhibitor, such as Tamiflu, is required to stop neuraminidase. The interaction of Tamiflu with N1 neuraminidase is shown with this <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/Morph_2hty_to_2hu4/8'>morph</scene> (1). Tamiflu in this model is bound when it is visible and the loop in moved in towards the drug through induced fit. | |||
When neuraminidase breaks the sialic acid groups, the virus (virion) is released. This will allow replication of the virus. The inhibitor prevents the breaking of the sialic acid groups, so no virion is released and replicated. | |||
===Credits=== | |||
Introduction - Mike Reardon | |||
Overall Structure - Rachael Jayne | |||
Drug Binding Site - Jackie Dorhout | |||
Additional Features - Nick DeGraan-Weber | |||
===References=== | |||
(1) Martz, E.; Hodis, E.; Canner, D.; Samish, I.; Prilusky, J.; Goodsell, D. S.; Strong, M. Avian Influenza Neuraminidase, Tamiflu and Relenza. http://www.proteopedia.org/wiki/index.php/Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza 2011. | |||
(2) Influenza (Seasonal). World Health Organization. http://www.who.int/mediacentre/factsheets/fs211/en/ 2011 | |||
(3) "Influenza: Viral Infections: Merck Manual Home Edition". http://www.merck.com/mmhe/sec17/ch198/ch198d.html 2011 | |||
(2) OCA 7nn9 - Native Influenza Virus Neuraminidase Subtype N9. http://www.proteopedia.org/wiki/index.php/7nn9 2011. | |||
(3) OCA 2hu4 - N1 Neuraminidase in Complex with Oseltamivir 2. http://www.proteopedia.org/wiki/index.php/2hu4 2011. | |||
(4) Goodsell, David. Molecule of the Month: Influenza Neuraminidase- RCSB PDB. http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb113_1.html 2009. | |||
(5) Russell, R.J.; Haire, L.F.; Stevens, D.J.; Collins, P.J.; Lin, Y.P.; Blackburn, G.M.; Hay, A.J.; Gamblin, S.J.; Skehel, J.J. N1 neuraminidase in complex with oseltamivir 2. http://www.rcsb.org/pdb/explore.do?structureId=2hu4. | |||
(6) Garcia-Sosa, Alfonso; Sild, Sulev; Maran, Uko. Design of Multi-Binding-Site Inhibitors, Ligand Efficiency, and Consensus Screening of Avian Influenza H5N1 Wild-Type Neuraminidase and of the Oseltamivir-Resistant H274Y Variant. Journal of Chemical Information and Modeling. http://pubs.acs.org/doi/full/10.1021/ci800242z. 2009. | |||
(7) Wang, Shu-Qing; Dub, Qi-Shi; Huang, Ri-Bo; Zhang, Da-Wei; Chou, Kuo-Chen. Insights from investigating the interaction of oseltamivir (Tamiflu) with neuraminidase of the 2009 H1N1 swine flu virus. http://www.scirp.org/kcchou/papers/BBRC_2009_H1N1_Tamiflu.pdf. 2009. | |||
(8) Neuraminidase Inhibitors. http://www.fluwiki.info/pmwiki.php?n=Consequences.NeuraminidaseInhibitors. 2009. | |||
(9) Investor Update. http://www.roche.com/investors/ir_update/inv-update-2009-09-13.htm. 2009. | |||
=='''Influenza M2 Proton Channel'''== | |||
===Introduction=== | |||
Influenza A, better known as the flu, an infection of the nose, throat, and lungs caused by the influenza virus. Basic symptoms include aches, chills, fever, loss of energy and dizziness, but complications can include pneumonia, encephalitis, bronchitis, and death—about 36,000 people every year die of complications from the flu (CDC). | |||
The <scene name='Student_Projects_for_UMass_Chemistry_423_Spring_2011/Cv/1'>M2 protein is a proton-selective ion channel protein </scene> that plays an important role in the life cycle of the influenza A virus. The channel itself is a homotetramer with four identical M2 units, where each M2 protein is a helix stabilized by two disulfide bonds. At a low pH, the channel allows hydrogen ions to enter the viral particle form the endosome, effectively lowering the pH on the interior of the virus. This in turn causes the dissociation of the viral matrix protein M1 from the ribonucleoprotein, a critical step in “uncoating” the virus to introduce its contents to the cytoplasm of the host cell (Stouffer). The M2 protein itself consists of three major protein domains: a stretch of 24 amino acids on the N-terminal end that are exposed to the external environment, 22 (largely hydrophobic) amino acids in the transmembrane region, and 52 amino acids on the C-terminal end which are exposed to the inside of the viral particle (Schnell). | |||
The function of the M2 channel can be inhibited by the antiviral drug Amantadine, an inhibition that effectively blocks the virus from taking over the host cell. Amantadine inhibits the replication of influenza A viruses by interfering with the uncoating of the virus within the cell. Amantadine is an M2 inhibitor that blocks the ion channel formed by the M2 protein that spans the viral membrane. By blocking this channel, Amantadine effectively prevents the acidification and subsequent release of viral elements into the host cell. Unfortunately, the M2 gene is susceptible to mutations. When one of five (of the 22) amino acids in the transmembrane region is suitably substituted, Amantadine no longer binds in such a way that would block the motion of the protons into the virus. As of 2009, the CDC noted that a full 100% of Influenza A viruses of types H3N2 and 2009 pandemic flu samples cultured in the United States showed a resistance to Amantadine (CDC). | |||
===Overall Structure=== | |||
The M2 proton channel , made up of 97 residues, is a homotetramer transmembrane protein made up of 4 helices. The amino terminus of the protein is exposed to the outside environment, while the carboxy terminus is exposed to the internal environment. At pH 7.5, <scene name='Sandbox_111/Residue_18-23/1'>residues 18-23</scene> form the N-terminus. <scene name='Sandbox_111/Residue_25-46/1'>Residues 25-46</scene> create a transmembrane helix which forms a channel. Furthermore, residues 47-50 create a ‘short flexible loop,’ and residues 51-59 form a C-terminal amphipathic helix (Schnell). | |||
The loop created by residues 47-50 at the C-terminus connects the amphipathic helices to the transmembrane domain. The amphipathic helices lie perpendicular to the transmembrane helices. These amphipathic helices form a base that is resistant to changes in pH and therefore acts to stabilize the protein. It should be noted that the transmembrane helices are left handed while the amphipathic helices forming the base are right handed. These amphipathic helicves are also arranged head to tail (Schnell). | |||
The pore created by the four tansmembrane helices is constricted at the N-terminus by the methyl groups on Val 27. On the other end of the pore, interactions between Trp41 also create a blockage. The four helices are packed so tightly that van der Waals forces are created between the indole rings of Trp41. This forms a gate. Together, the interactions between Trp41 and Val27 block the passage of water through the pore. Furthermore, hydrogen bonds between Asp44 and Trp41 stabilize the gate. When the pH is lowered, the imidazole rings of His37 are protonated and the helices undergo electrostatic repulsion. This in turn breaks the Asp44 and Trp41 interactions and the gate will open. As previously mentioned, the base created by the amphipathic helices prevents the protein from dissociating. However, cysteins at the N-terminus create disulphide bonds that also act to prevent dissociation (Schnell). | |||
===Drug Binding Site=== | |||
Amantadine binds with high affinity to a site in the M2 protein spanning five residues: Leu 26, Val 27, Ala 30, Ser 31, and Gly 34 (Cady). This high affinity is seen at pH’s closer to neutral. In lower pH’s the protein is only somewhat bound to amantadine. Therefore, when determining the mechanism by which amantadine blocks the channel experiments must be conducted at neutral pH. <scene name='Sandbox_111/Binding/10'>Binding of amantadine</scene> to the M2 protein is illustrated for viewing of the bonds. | |||
When amantadine isn't present, the <scene name='Sandbox_111/No_amantadine/3'>pore</scene> created in the M2 complex is open, allowing viral particles to pass through. In the presence of amantadine, this pore is <scene name='Sandbox_111/Amantadine_present/1'>occluded</scene>, which prevents entry of the viral particles. | |||
===Additional Features=== | |||
<scene name='Sandbox_111/His37/1'>His37</scene> – His37 has been found to exhibit significant proton selectivity. This suggests that His37 is involved in the opening of the conductive channel. The channel is non-conductive when His37 is not protonated, and conductive when it is in the protonated state (Pielak/Chou). | |||
<scene name='Sandbox_111/Trp41_ring/1'>Trp41</scene> – Replacing Trp41 with a substitute amino acid results in increased channel current in in both directions. As such, the Trp 41 site is important to directional selectivity, in that it regulates the direction of the proton channel flow. This is accomplished in part because it forms a ring that prevents water from entering the channel and reaching the His37, and thus deprotonating if the pH is high, from the C-terminus(Pielak/Chou). | |||
In addition, the proton transport channel is used to equalize the pH in the channel with that of the cytoplasm in the host cell. This prevents rearrangement of the haemmagglutanin during its transport to the host cell. (Schnell) | |||
===References=== | |||
Cady, S.D., Schmidt-Rohr, K., Wang, J., Soto, C., DeGrado, W.F., Hong, M. "Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers," (2010) ''Nature'' '''463''': 689-692. | |||
Stouffer AL, Acharya R, Salom D, Levine AS, Di Costanzo L, Soto CS, Tereshko V, Nanda V, Stayrook S, DeGrado WF (2008). "Structural basis for the function and inhibition of an influenza virus proton channel". Nature 451 (7178): 596-9 | |||
Schnell JR, Chou JJ (2008). "Structure and mechanism of the M2 proton channel of influenza A virus". Nature 451 (7178): 591–5. | |||
Pielak RM, Schnell JR, Chou JJ: Mechanism of drug inhibition and drug resistance of influenza A M2 channel. Proc Natl Acad Sci, 106(18):7379-84 (2009). | |||
"CDC Recommends against the Use of Amantadine and Rimantadine for the Treatment or Prophylaxis of Influenza in the United States during the 2005–06 Influenza Season". CDC Health Alert. Centers for Disease Control and Prevention | |||
Hay AJ, Wolstenholme AJ, Skehel JJ, Smith MH. The molecular basis of the specific anti-influenza action of amantadine. EMBO J 1985; 4: 3021-4. | |||
Stephenson I, Nicholson KG. Influenza: vaccination and treatment. Eur Respir J 2001; 17: 1282-93. | |||
Pielak RM, Chou JJ. "Infuenza M2 proton channels". BBAMEM-80262; No. of pages: 8; 4C: 2, 3, 5, 6. | |||
===Credits=== | |||
Introduction -- Josephine Harrington | |||
Overall structure -- Andrea Simoni | |||
Drug binding site -- Joshua Drolet | |||
Additional features -- John Hickey | |||
