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Molecular dynamics simulations approaches for discovering anti-influenza drug

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초록

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.

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.

참고문헌 (42)

  1. Amaro RE, "Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design", J Am Chem Soc, 129, pp.7764~7765 (2007)
  2. Astrahan P, "A novel method of resistance for influenza against a channel-blocking antiviral drug", Proteins, 55, pp.251~257 (2004)
  3. Bright RA, "Adamantane resistance among influenza A viruses isolated early during the 2005-2006 influenza season in the United States", JAMA, 295, pp.891~894 (2006)
  4. Brooks BR, "CHARMM : A program for macromolecular energy, minimization, and dynamics calculations", J Comput Chem, 4, pp.187~217 (1983)
  5. Case DA, "The Amber biomolecular simulation programs", J Comput Chem, 26, pp.1668~1688 (2005)
  6. Cheng LS, "Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase", J Med Chem, 51, pp.3878~3894 (2008)
  7. Collins PJ, "Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants", Nature, 453, pp.1258~1261 (2008)
  8. Cox NJ, "Global epidemiology of influenza : past and present", Annu Rev Med, 51, pp.407~421 (2000)
  9. de Jong MD, "Oseltamivir resistance in influenza A (H5N1) infection", N Engl J Med, 354, pp.1423~1424 (2006)
  10. Duggal A, "Global variability in reported mortality for critical illness during the 2009-10 influenza A (H1N1) pandemic: A systematic review and metaregression to guide reporting of outcomes during disease outbreaks", PLoS One, 11, pp.e0155044~ (2016)
  11. Du J, "Recent progress in structure-based anti-influenza drug design", Drug Discov Today, 17, pp.1111~1120 (2012)
  12. Hay AJ, "The molecular basis of the specific anti-influenza action of amantadine", EMBO J, 4, pp.3021~3024 (1985)
  13. Jackson RJ, "Oseltamivir, zanamivir and amantadine in the prevention of influenza : A systematic review", J Infection, 62, pp.14~25 (2011)
  14. Karplus M, "Molecular dynamics simulations of biomolecules", Nat Struct Biol, 9, pp.646~652 (2002)
  15. Katsuno K, "Hit and lead criteria in drug discovery for infectious diseases of the developing world", Nat Rev Drug Discov, 14, pp.751~758 (2015)
  16. Kirkwood JG, "Statistical mechanics of fluid mixtures", J Chem Phys, 3, pp.300~313 (1935)
  17. Kiso M, "Resistant influenza A viruses in children treated with oseltamivir : descriptive study", Lancet, 364, pp.759~765 (2004)
  18. Kollman PA, "Calculating structures and free energies of complex molecules : combining molecular mechanics and continuum models", Acc Chem Res, 33, pp.889~897 (2000)
  19. Lei H, "Improved sampling methods for molecular simulation", Curr Opin Struct Biol, 17, pp.187~191 (2007)
  20. Leonov H, "How do aminoadamantanes block the influenza M2 channel, and how does resistance develop?", J Am Chem Soc, 133, pp.9903~9911 (2011)
  21. Li L, "Theoretical studies on the susceptibility of oseltamivir against variants of 2009 A", H1N1influenza neuraminidase, 2012, pp.52, 2715~2729
  22. Li Q, "Epidemiology of human infections with avian influenza A(H7N9)virus in China", N Engl J Med, 370, pp.520~532 (2014)
  23. Lu SJ, "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, 13, pp.4496~4507 (2012)
  24. McCammon JA, "Dynamics of folded proteins", Nature, 267, pp.585~590 (1977)
  25. McNicholl IR, "Neuraminidase inhibitors : zanamivir and oseltamivir", Ann Pharmacother, 35, pp.57~70 (2001)
  26. Mortier J, "The impact of molecular dynamics on drug design : applications for the characterization of ligand-macromolecule complexes", Drug Discov Today, 20, pp.686~702 (2015)
  27. Ö ster L, "Successful generation of structural information for fragment-based drug discovery", Drug Discov Today, 20, pp.1104~1111 (2015)
  28. Yamaya M, "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, 87, pp.25~34 (2015)
  29. Pinto LH, "Influenza virus M2 protein has ion channel activity", Cell, 69, pp.517~528 (1992)
  30. Radkiewicz JL, "Protein dynamics in enzymatic catalysis : exploration of dihydrofolate reductase", J Am Chem Soc, 122, pp.225~231 (2000)
  31. Russell RJ, "The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design", Nature, 443, pp.45~49 (2006)
  32. Sadasivam K, "Computational studies of pandemic 1918 and 2009 H1N1 hemagglutinins bound to avian and human receptor analogs", J Biomol Struct Dynamics, 34, pp.272~289 (2015)
  33. Salsbury FR Jr, "Molecular dynamics simulations of protein dynamics and their relevance to drug discovery", Curr Opin Pharmacol, 10, pp.738~744 (2010)
  34. van der Spoel D, "GROMACS : Fast, flexible, and free", J Comput Chem, 26, pp.1701~1718 (2005)
  35. van Kerkhove MD, Vandemaele KA, Shinde V, JaramilloGutierrez G, Koukounari A, Donnelly CA, Carlino LO, Owen R, Paterson B, Pelletier L, "Risk factors for severe outcomes following 2009influenza A (H1N1) infection: a global pooled analysis", PLoS Med, 8, pp.e1001053~ (2011)
  36. von Itzstein M, "The war against influenza : discovery and development of sialidase inhibitors", Nat Rev Drug Discov, 6, pp.967~974 (2007)
  37. Wang C, "Activation of the M2 ion channel of influenza virus : a role for the transmembrane domain histidine residue", Biophys J, 69, pp.1363~1371 (1995)
  38. Wang J, "Recent advances in free energy calculations with a combination of molecular mechanics and continuum models", Curr Comput Aid Drug Design, 2, pp.287~306 (2006)
  39. Wang T, "Advances in computational structure-based drug design and application in drug discovery", Curr Topics Med Chem, 16, pp.901~916 (2016)
  40. Woods CJ, "Analysis and assay of oseltamivir-resistant mutants of influenza neuraminidase via direct observation of drug unbinding and rebinding in simulation", Biochemistry, 52, pp.8150~8164 (2013)
  41. Woods CJ, "Long time scale GPU dynamics reveal the mechanism of drug resistance of the dual mutant I223R", H275Y neuraminidase from H1N1-2009 influenza virus, 2012, pp.51, 4364~4375
  42. Zwanzig RW, "Statistical mechanical theory of transport processes. VII. The coefficient of thermal conductivity of monatomic liquids", J Chem Phys, 22, pp.783~790 (1954)

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