In depth analysis on the binding sites of adamantane derivatives in HCV (hepatitis C virus) p7 channel based on the NMR structure

PLoS ONE

Volumn 9, Issue 4, 2014, Pages

  Du, Qi Shi ^a,d   Wang, Shu Qing ^b   Chen, Dong ^a,c   Meng, Jian Zong ^c   Huang, Ri Bo ^a,c  

^a NATIONAL ENGINEERING RESEARCH CENTER FOR NON FOOD BIOREFINERY   (China)

^b TIANJIN MEDICAL UNIVERSITY   (China)

^c GUANGXI UNIVERSITY   (China)

^d GORDON LIFE SCIENCE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMANTADINE; AROMATIC AMINO ACID; HISTIDINE; ION CHANNEL; P7 CHANNEL; PHENYLALANINE; RIMANTADINE; TRYPTOPHAN; UNCLASSIFIED DRUG; ADAMANTANE; ANTIVIRUS AGENT; VIRUS PROTEIN;

AMINO ACID COMPOSITION; ANTIVIRAL ACTIVITY; ARTICLE; DISSOCIATION CONSTANT; DRUG BINDING SITE; DRUG DESIGN; DRUG POTENCY; DRUG PROTEIN BINDING; DRUG STRUCTURE; HEPATITIS C VIRUS; HYDROPHOBICITY; LIGAND BINDING; MATHEMATICAL MODEL; MOLECULAR INTERACTION; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE; PROTEIN STRUCTURE; PROTON TRANSPORT; ANALOGS AND DERIVATIVES; BINDING SITE; CHEMISTRY; DRUG DEVELOPMENT; DRUG EFFECTS; HEPACIVIRUS; HEPATITIS C; HUMAN; METABOLISM; MOLECULAR DOCKING; PROTEIN CONFORMATION; THERMODYNAMICS; VIROLOGY;

ADAMANTANE; ANTIVIRAL AGENTS; BINDING SITES; DRUG DISCOVERY; HEPACIVIRUS; HEPATITIS C; HUMANS; ION CHANNELS; MOLECULAR DOCKING SIMULATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; THERMODYNAMICS; VIRAL PROTEINS;

EID: 84899511220     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0093613     Document Type: Article

References (46)

1. Choo QL, Kuo G, Weiner AJ, Overby LR, Bradley DW, et al. (1989) Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science 244: 359-562.
2. Fusco DN, Chung RT (2012) Novel Therapies for Hepatitis C: Insights from the Structure of the Virus. Annu Rev Med 63: 373-387.
3. Wasley A, Alter MJ (2000) Epidemiology of hepatitis C: geographic differences and temporal trends. Semin Liver Dis 20: 1-16. (Pubitemid 30421405)
4. Zoulim F, Chevallier M, Maynard M, Trepo C (2003) Clinical consequences of hepatitis C virus infection. Rev Med Virol 13: 57-68. (Pubitemid 36125505)
5. Dubuisson J, Helle F, Cocquerel L (2008) Early steps of the hepatitis C virus life cycle. Cell Microbiol 10: 821-827. (Pubitemid 351386938)
6. Ghany MG, Strader DB, Thomas DL, Seeff LB (2009) Diagnosis, management, and treatment of hepatitis C: an update. Hepatology 49: 1335-1374.
7. Schoggins JW, Wilson SJ, Panis M, Murphy MY, Jones CT, et al. (2011) A diverse range of gene products are effectors of the type I interferon antiviral response. Nature 472: 481-485.
8. Griffin S, StGelais C, Owsianka AM, Patel AH, Rowlands D, et al. (2008) Genotype-dependent sensitivity of hepatitis C virus to inhibitors of the p7 ion channel. Hepatology 48: 1779-1790.
9. Steinmann E, Whitfield T, Kallis S, Dwek RA, Zitzmann N, et al. (2007) Antiviral effects of amantadine and iminosugar derivatives against hepatitis C virus. Hepatology 46: 330-338. (Pubitemid 47344767)
10. Griffin SD, Beales LP, Clarke DS, Worsfold O, Evans SD, et al. (2003) The p7 protein of hepatitis C virus forms an ion channel that is blocked by the antiviral drug, amantadine. FEBS Lett 535: 34-38. (Pubitemid 36126351)
11. Pavlović D, Neville DCA, Argaud O, Blumberg B, Dwek RA, et al. (2003) The hepatitis C virus p7 protein forms an ion channel that is inhibited by long-alkylchain iminosugar derivatives. Proc Natl Acad Sci USA 100: 6104-6108. (Pubitemid 36576938)
12. Montserret R, Saint N, Vanbelle C, Salvay AG, Simorre JP, et al. (2010) NMR structure and ion channel activity of the p7 protein from hepatitis C virus. J Biol Chem 285: 31446-31461.
13. Premkumar A, Wilson L, Ewart GD, Gage PW (2004) Cation-selective ion channels formed by p7 of hepatitis C virus are blocked by hexamethylene amiloride. FEBS Lett 557: 99-103. (Pubitemid 38115876)
14. Wozniak AL, Griffin S, Rowlands D, Harris M, Yi M, et al. (2010) Intracellular proton conductance of the hepatitis C virus p7 protein and its contribution to infectious virus production. PLoS Pathog 6: e1001087.
15. Mihm U, Grigorian N, Welsch C, Herrmann E, Kronenberger B, et al. (2006) Amino acid variations in hepatitis C virus p7 and sensitivity to antiviral combination therapy with amantadine in chronic hepatitis C. Antivir Ther 11: 507-519. (Pubitemid 44024859)
16. Yang BO, Xie SQ, Berardi MJ, Zhao XH, Dev J, et al. (2013) Unusual architecture of the p7 channel from hepatitis C virus. Nature 498: 521-5.
17. Schnell JR, Chou JJ (2008) Structure and mechanism of the M2 proton channel of influenza A virus. Nature 451: 591-595. (Pubitemid 351186272)
18. Stouffer AL, Acharya R, Salom D, Levine AS, Di Costanzo L, et al. (2008) Structural basis for the function and inhibition of an influenza virus proton channel. Nature 451: 596-599. (Pubitemid 351186271)
19. Huang RB, Du QS, Wang CH, Chou KC (2008) An in-depth analysis of the biological functional studies based on the NMR M2 channel structure of influenza A virus. Biochemical and Biophysical Research Communications 377: 1243-1247.
20. Gu RX, Liu LA, Wei DQ, Du JG, Liu L, et al. (2011) Free energy calculations on the two drug binding sites in the M2 proton channel. J Am Chem Soc 133: 10817-10825.
21. Li H, Robertson AD, Jensen JH (2005) Very fast Empirical prediction and rationalization of protein pKa values. PROTEINS: Structure, Function, and Bioinformatics 61: 704-721. (Pubitemid 41753142)
22. Bas DC, Rogers DM, Jensen JH (2008) Very fast prediction and rationalization of pKa values for protein-ligand complexes. PROTEINS: Structure, Function, and Bioinformatics 73: 765-783. (Pubitemid 352788657)
23. Olsson MHM, Sondergard CR, Rostkowski M, Jensen JH (2011) PROPKA3: Consistent treatment of internal and surface residues in empirical pKa predictions. J Chem Theory Comput 7: 525-537.
24. Sondergaard CR, Olsson MHM, Rostkowski M, Jensen JH (2011) Improved treatment of ligands and coupling effects in empirical calculation and rationalization of pKa values. J Chem Theory and Computation 7: 2284-2295.
25. Morris GM, Huey R, Olson AJ (2008) Using AutoDock for ligand-receptor docking. Curr. Protoc. Bioinformatics, Chapter 8, Unit 8 14.
26. Fuhrmann J, Rurainski A, Lenhof HP, Neumann DA (2010) New Lamarckian genetic algorithm for flexible ligand-receptor docking. J Comput Chem 31: 1911-1918.
27. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, et al. (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19: 1639-1662. (Pubitemid 128590223)
28. Liao SM, Du QS, Meng JZ, Pang ZW, Huang RB (2013) The multiple roles of histidine in protein interactions. Chemistry central Journal 7: 44.
29. Du QS, Wang QY, Du LQ, Chen D, Huang RB (2013) Theoretical study on the polar hydrogen-π (Hp-π) interactions between protein side chains. Chemistry Central Journal 7: 92.
30. Du QS, Long SY, Meng JZ, Huang RB (2012) Empirical formulation and parameterization of cation-p interactions for protein modeling. J Comput Chem 33: 153-162.
31. Du QS, Liao SM, Meng JZ, Huang RB (2012) Energies and physicochemical properties of cation-π interactions in biological structures. J Molecular Graphics and Modeling 34: 38-45.
32. Wang QY, Lu J, Liao SM, Du QS, Huang RB (2013) Unconventional interaction forces in protein structures and in ligand-host complex structures. Current Topics in Medicinal Chemistry 13: 1141-1151.
33. Purvis GD, Bartlett RJ (1982) A full coupled-cluster singles and doubles model: The inclusion of disconnected triples. J Chem Phys 76: 1910-1919.
34. Lee TJ, Rice JE (1988) An efficient closed-shell singles and doubles coupled-cluster method. Chem Phys Lett 23: 406-415.
35. Scuseria GE, Schaefer HF III (1989) Is coupled cluster singles and doubles (CCSD) more computationally intensive than quadratic configuration interaction (QCISD)? J Chem Phys 90: 3700-3703.
36. Scuseria GE, Janssen CL, Schaefer HF III (1988) An efficient reformulation of the closed-shell coupled cluster single and double excitation (CCSD) equations. J Chem Phys 89: 7382-7388.
37. Spector R (1988) Transport of amantadine and rimantadine through the blood-brain barrier. J Pharmacol Exp Ther 244: 516-519.
38. StGelais C, Foster TL, Verow M, Atkins E, Fishwick CWG, et al. (2009) Determinants of hepatitis C virus p7 ion channel function and drug sensitivity identified in vitro. J Virol 83: 7970-7981.
39. Wermuth CG, Ganellin CR, Lindberg P, Mitscher LA (1998) Glossary of terms used in medicinal chemistry (IUPAC Recommendations 1998). Pure and Applied Chemistry 70: 1129-1143.
40. Ponder JW, Case DA (2003) Force fields for protein simulations. Adv Prot Chem 66: 27-85. (Pubitemid 37392314)
41. Warshel A, Sharma PK, Kato M, Parson WW (2006) Modeling Electrostatic Effects in Proteins. Biochim Biophys Acta 1764: 1647-1676. (Pubitemid 46070172)
42. Leckband D, Israelachvili J (2001) Intermolecular forces in biology. Quart Rev Biophys 34: 105-267. (Pubitemid 33139917)
43. Krieger E, Joo K, Lee J, Raman S, et al. (2009) Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins 77 (Suppl 9): 114-122.
44. Rosenberg MR, Casarott MG (2010) Coexistence of two adamantane binding sites in the influenza A M2 ion channel. Proc Natl Acad Sci USA 107: 13866-13871.
45. Pielak RM, Chou JJ (2010) Flu channel drug resistance: a tale of two sites. Protein & Cell 1: 246-258.
46. Foster TL, Verow M, Wozniak AL, Bentham MJ, et al. (2011) Resistance mutations define specific antiviral effects for inhibitors of the hepatitis C virus p7 ion channel. Hepatology 54: 79-90.