CELLMED (셀메드)

Cellmed Orthocellular Medicine and Pharmaceutical Association (셀메드 세포교정의약학회)
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Molecular dynamics simulations approaches for discovering anti-influenza drug

  • Cho, Sungjoon (Department of Biological Science, Hoseo University) ;
  • Choi, Youngjin (Department of Food Science and Technology & Research Institute for Basic Science, Hoseo University)
  • Received : 2016.09.30
  • Accepted : 2016.11.18
  • Published : 2016.11.30
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Abstract

The emergence of influenza virus and antigenic drift are potential cause of world-wide pandemic. There are some commercially available drugs in the market to treat influenza. During past decade, however, critical resistances have been raised for biological targets. Because of structural complexity and flexibility of target proteins, applying a computational modeling tool is very beneficial for developing alternative anti-influenza drugs. In this review, we introduced molecular dynamics (MD) simulations approach to reflect full conformational flexibility of proteins during molecular modeling works. Case studies of MD works were summarized for the drug discovery and drug resistance mechanism of anti-influenza pharmaceuticals.

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References

  1. Amaro RE, Minh DD, Cheng LS, Lindstrom WM Jr, Olson AJ, Lin JH, Li WW, McCammon JA. Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design. J Am Chem Soc. 2007;129:7764-7765. https://doi.org/10.1021/ja0723535
  2. Astrahan P, Kass I, Cooper MA, Arkin IT. A novel method of resistance for influenza against a channel-blocking antiviral drug. Proteins. 2004;55:251-257. https://doi.org/10.1002/prot.20018
  3. Bright RA, Shay DK, Shu B, Cox NJ, Klimov AI. Adamantane resistance among influenza A viruses isolated early during the 2005-2006 influenza season in the United States. JAMA. 2006;295:891-894. https://doi.org/10.1001/jama.295.8.joc60020
  4. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Martin Karplus. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem. 1983;4:187-217. https://doi.org/10.1002/jcc.540040211
  5. Case DA, Cheatham TE III, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, Woods RJ. The Amber biomolecular simulation programs. J Comput Chem. 2005;26:1668-1688. https://doi.org/10.1002/jcc.20290
  6. Cheng LS, Amaro RE, Xu D, Li WW, Arzberger PW, McCammon JA. Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem. 2008;51:3878-3894. https://doi.org/10.1021/jm8001197
  7. Collins PJ, Haire LF, Lin YP, Liu J, Russell RJ, Walker PA, Skehel JJ, Martin SR, Hay AJ, Gamblin SJ. Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants. Nature. 2008;453:1258-1261. https://doi.org/10.1038/nature06956
  8. Cox NJ, Subbarao K. Global epidemiology of influenza: past and present. Annu Rev Med. 2000;51:407-421. https://doi.org/10.1146/annurev.med.51.1.407
  9. de Jong MD, Hien TT, Farrar J. Oseltamivir resistance in influenza A (H5N1) infection, N Engl J Med. 2006;354:1423-1424. https://doi.org/10.1056/NEJMc060077
  10. Duggal A, Pinto R, Rubenfeld G, Fowler RA, Global variability in reported mortality for critical illness during the 2009-10 influenza A (H1N1) pandemic: A systematic review and meta-regression to guide reporting of outcomes during disease outbreaks. PLoS One. 2016;11:e0155044. https://doi.org/10.1371/journal.pone.0155044
  11. Du J, Cross TA, Zhou HX. Recent progress in structure-based anti-influenza drug design. Drug Discov Today. 2012;17:1111-1120. https://doi.org/10.1016/j.drudis.2012.06.002
  12. Hay AJ, Wolstenholme AJ, Skehel JJ, Smith MH. The molecular basis of the specific anti-influenza action of amantadine. EMBO J. 1985;4:3021-3024.
  13. Jackson RJ, Cooper KL, Tappenden P, Rees A, Simpson EL, Read RC, Nicholson KG. Oseltamivir, zanamivir and amantadine in the prevention of influenza: A systematic review. J Infection. 2011;62:14-25. https://doi.org/10.1016/j.jinf.2010.10.003
  14. Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules, Nat Struct Biol. 2002;9:646-652. https://doi.org/10.1038/nsb0902-646
  15. Katsuno K, Burrows J, Duncan K, van Huijsduijnen RH, Kaneko T, Kita K, Mowbray C, Schmatz D, Warner P, Slingby BT. Hit and lead criteria in drug discovery for infectious diseases of the developing world. Nat Rev Drug Discov. 2015;14:751-758. https://doi.org/10.1038/nrd4683
  16. Kirkwood JG. Statistical mechanics of fluid mixtures. J Chem Phys. 1935;3:300-313. https://doi.org/10.1063/1.1749657
  17. Kiso M, Mitamura K, Sakai-Tagawa Y, Shiraishi K, Kawakami C, Kimura K, Hayden FG, Sugaya N, Kawaoka Y. Resistant influenza A viruses in children treated with oseltamivir: descriptive study. Lancet. 2004;364:759-765. https://doi.org/10.1016/S0140-6736(04)16934-1
  18. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE 3rd. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res. 2000;33:889-897. https://doi.org/10.1021/ar000033j
  19. Lei H, Duan Y. Improved sampling methods for molecular simulation. Curr Opin Struct Biol. 2007;17:187-191. https://doi.org/10.1016/j.sbi.2007.03.003
  20. Leonov H, Astrahan P, Krugliak M, Arkin IT. How do aminoadamantanes block the influenza M2 channel, and how does resistance develop? J Am Chem Soc. 2011;133:9903-9911. https://doi.org/10.1021/ja202288m
  21. Li L, Li Y, Zhang L, Hou T. Theoretical studies on the susceptibility of oseltamivir against variants of 2009 A/H1N1 influenza neuraminidase. J Chem Inf Model. 2012;52:2715-2729. https://doi.org/10.1021/ci300375k
  22. Li Q, Zhou L, Zhou M, Chen Z, Li F, Wu H, Xiang N, Chen E, Tang F, Wang D, Meng L, Hong Z, Tu W, Cao Y, Li L, Ding F, Liu B, Wang M, Xie R, Gao R, Li X, Bai T, Zou S, He J, Hu J, Xu Y, Chai C, Wang S, Gao Y, Jin L, Zhang Y, Luo H, Yu H, He J, Li Q, Wang X, Gao L, Pang X, Liu G, Yan Y, Yuan H, Shu Y, Yang W, Wang Y, Wu F, Uyeki TM, Feng Z. Epidemiology of human infections with avian influenza A (H7N9) virus in China. N Engl J Med. 2014;370:520-532. https://doi.org/10.1056/NEJMoa1304617
  23. Lu SJ, Chong FC. Combining molecular docking and molecular dynamics to predict the binding modes of flavonoid derivatives with the neuraminidase of the 2009 H1N1 influenza A virus. Int J Mol Sci. 2012;13:4496-4507. https://doi.org/10.3390/ijms13044496
  24. McCammon JA, Gelin BR, Karplus M. Dynamics of folded proteins. Nature. 1977;267:585-590. https://doi.org/10.1038/267585a0
  25. McNicholl IR, McNicholl JJ. Neuraminidase inhibitors: zanamivir and oseltamivir. Ann Pharmacother. 2001;35:57-70. https://doi.org/10.1345/aph.10118
  26. Mortier J, Rakers C, Bermudez M, Murgueitio MS, Riniker S, Wolber G. The impact of molecular dynamics on drug design: applications for the characterization of ligand-macromolecule complexes. Drug Discov Today. 2015;20:686-702. https://doi.org/10.1016/j.drudis.2015.01.003
  27. Oster L, Tapani S, Xue Y, Kack H. Successful generation of structural information for fragment-based drug discovery. Drug Discov Today. 2015;20:1104-1111. https://doi.org/10.1016/j.drudis.2015.04.005
  28. Yamaya M, Nadine L, Kubo H, Saito K, Saito R, Nishimura H. The effects of neuraminidase inhibitors on the release of oseltamivir-sensitive and oseltamivir-resistant influenza viruses from primary cultures of human tracheal epithelium. J Med Virol. 2015;87:25-34. https://doi.org/10.1002/jmv.23974
  29. Pinto LH, Holsinger LJ, Lamb RA. Influenza virus M2 protein has ion channel activity. Cell. 1992;69:517-528. https://doi.org/10.1016/0092-8674(92)90452-I
  30. Radkiewicz JL, Brooks CL. Protein dynamics in enzymatic catalysis: exploration of dihydrofolate reductase. J Am Chem Soc. 2000;122:225-231. https://doi.org/10.1021/ja9913838
  31. Russell RJ, Haire LF, Stevens DJ, Collins PJ, Lin YP, Blackburn GM, Hay AJ, Gamblin SJ, Skehel JJ. The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design. Nature. 2006;443:45-49. https://doi.org/10.1038/nature05114
  32. Sadasivam K, Kolandaivel P. Computational studies of pandemic 1918 and 2009 H1N1 hemagglutinins bound to avian and human receptor analogs. J Biomol Struct Dynamics. 2015;34:272-289.
  33. Salsbury FR Jr. Molecular dynamics simulations of protein dynamics and their relevance to drug discovery. Curr Opin Pharmacol. 2010;10:738-744. https://doi.org/10.1016/j.coph.2010.09.016
  34. van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. GROMACS: Fast, flexible, and free. J Comput Chem. 2005;26:1701-1718. https://doi.org/10.1002/jcc.20291
  35. van Kerkhove MD, Vandemaele KA, Shinde V, Jaramillo-Gutierrez G, Koukounari A, Donnelly CA, Carlino LO, Owen R, Paterson B, Pelletier L, Vachon J, Gonzalez C, Hongjie Y, Zijian F, Chuang SK, Au A, Buda S, Krause G, Haas W, Bonmarin I, Taniguichi K, Nakajima K, Shobayashi T, Takayama Y, Sunagawa T, Heraud JM, Orelle A, Palacios E, van der Sande MA, Wielders CC, Hunt D, Cutter J, Lee VJ, Thomas J, Santa-Olalla P, Sierra-Moros MJ, Hanshaoworakul W, Ungchusak K, Pebody R, Jain S, Mounts AW; WHO Working Group for Risk Factors for Severe H1N1pdm Infection. Risk factors for severe outcomes following 2009 influenza A (H1N1) infection: a global pooled analysis. PLoS Med. 2011;8:e1001053. https://doi.org/10.1371/journal.pmed.1001053
  36. von Itzstein M. The war against influenza: discovery and development of sialidase inhibitors. Nat Rev Drug Discov. 2007;6:967-974. https://doi.org/10.1038/nrd2400
  37. Wang C, Lamb RA, Pinto LH. Activation of the M2 ion channel of influenza virus: a role for the transmembrane domain histidine residue. Biophys J. 1995;69:1363-1371. https://doi.org/10.1016/S0006-3495(95)80003-2
  38. Wang J, Hou T, Xu X. Recent advances in free energy calculations with a combination of molecular mechanics and continuum models. Curr Comput Aid Drug Design. 2006;2:287-306. https://doi.org/10.2174/157340906778226454
  39. Wang T, Wu MB, Zhang RH, Chen ZJ, Hua C, Lin JP, Yang LR. Advances in computational structure-based drug design and application in drug discovery. Curr Topics Med Chem. 2016;16:901-916.
  40. Woods CJ, Malaisree M, Long B, McIntosh-Smith S, Mulholland AJ. Analysis and assay of oseltamivir-resistant mutants of influenza neuraminidase via direct observation of drug unbinding and rebinding in simulation. Biochemistry. 2013;52:8150-8164. https://doi.org/10.1021/bi400754t
  41. Woods CJ, Malaisree M, Pattarapongdilok N, Sompornpisut P, Hannongbua S, Mulholland AJ. Long time scale GPU dynamics reveal the mechanism of drug resistance of the dual mutant I223R/H275Y neuraminidase from H1N1-2009 influenza virus. Biochemistry. 2012;51:4364-4375. https://doi.org/10.1021/bi300561n
  42. Zwanzig RW, Kirkwood JG, Oppenheim I, Alder BJ. Statistical mechanical theory of transport processes. VII. The coefficient of thermal conductivity of monatomic liquids. J Chem Phys. 1954;22:783-790. https://doi.org/10.1063/1.1740193