Molecular modeling of swine influenza A/H1N1, Spanish H1N1, and avian H5N1 flu N1 neuraminidases bound to Tamiflu and Relenza

PLoS Currents

Volumn , Issue AUG, 2009, Pages 1-10

  Le, Ly ^a   Lee, Eric ^b   Schulten, Klaus ^b   Truong, Thanh N ^c  

^a INSTITUTE FOR COMPUTATIONAL SCIENCE AND TECHNOLOGY   (Viet Nam)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^c UNIVERSITY OF UTAH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84873439661     PISSN: None     EISSN: 21573999     Source Type: Journal    
DOI: 10.1371/currents.RRN1015     Document Type: Article

References (21)

1. Ohuchi M, Asaoka N, Sakai T, Ohuchi R. Roles of neuraminidase in the initial stage of influenza virus infection. Microbes Infect. 2006 Apr;8(5):1287-93. Epub 2006 Feb 8. PubMed PMID: 16682242.
2. Laver G (2006) Antiviral drugs for influenza: Tamiflu past, present and future. Future Virology 1: 577-586
3. von Itzstein M, Wu WY, Kok GB, Pegg MS, Dyason JC, Jin B, Phan Tho V, Smythe ML, White HF, Oliver SW, Colman PM, Varghese JN, Ryan DM, Woods JM, Bethell RC, Hotham VJ, Cameron JM, Penn CR (1993) Rational design of potent sialidase-based inhibitors of influenza virus replication. Nature (London) 363: 418-423
4. de Jong JC, Heinen PP, Loeffen WLA, van Nieuwstadt AP, Claas ECJ, Bestebroer TM, Bijlsma K, Verweij C, Osterhaus ADME, Rimmelzwaan GF, Fouchier RAM, Kimman TG (2001) Antigenic and molecular heterogeneity in recent swine influenza A(H1N1) virus isolates with possible implications for vaccination policy. Vaccine 19: 4452-4464
5. Anonymous (2009) Update: drug susceptibility of swine-origin influenza A (H1N1) viruses, April 2009. MMWR Morbidity and mortality weekly report 58: 433-435
6. Humphrey W, Dalke A, Schulten K (1996) VDM: visual molecular dynamics. Journal of Molecular Graphics 14: 33-38, plates, 27-28
7. Xu X, Zhu, X., Dwek, R.A., Stevens, J., Wilson, I.A. (2008) Structural characterization of the 1918 influenza virus H1N1 neuraminidase Journal of Virology 82: 10493-10501
8. Russell RJ, Haire LF, Stevens DJ, Collins PJ, Lin YP, Blackburn GM, Hay AJ, Gamblin SJ, Skehel JJ (2006) The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design. Nature (London, United Kingdom) 443: 45-49
9. Collins PJ, Haire LF, Lin YP, Liu J, Russell RJ, Walker PA, Skehel JJ, Martin SR, Hay AJ, Gamblin SJ (2008) Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants. Nature (London, United Kingdom) 453: 1258-1261
10. MacKerell AD, Jr., Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, III, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M (1998) All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins. Journal of Physical Chemistry B 102: 3586-3616
11. MacKerell AD, Jr,. Feig, M., Brooks, C.L., III, (2004) Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations,. Journal of Computational Chemistry 25: 1400-1415
12. Saam J, Ivanov I, Walther M, Holzhütter H, and Kuhn H. (2007) Molecular dioxygen enters the active site of 12/15-lipoxygenase via dynamic oxygen access channels. Proc. Natl. Acad. Sci., 104(33), 13319-13324
13. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics 79: 926-935
14. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K (2005) Scalable molecular dynamics with NAMD. Journal of Computational Chemistry 26: 1781-1802
15. 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 Jun 27;129(25):7764-5. Epub 2007 Jun 1. PubMed PMID: 17539643.
16. Aruksakunwong O, Malaisree M, Decha P, Sompornpisut P, Parasuk V, Pianwanit S, Hannongbua S. On the lower susceptibility of oseltamivir to influenza neuraminidase subtype N1 than those in N2 and N9. Biophys J. 2007 Feb 1;92(3):798-807. Epub 2006 Nov 3. PubMed PMID: 17085491; PubMed Central PMCID: PMC1779986.
17. Malaisree M, Rungrotmongkol T, Decha P, Intharathep P, Aruksakunwong O, Hannongbua S. Understanding of known drug-target interactions in the catalytic pocket of neuraminidase subtype N1. Proteins. 2008 Jun;71(4):1908-18. PubMed PMID: 18175324.
18. Chachra R, Rizzo RC (2008) Origins of Resistance Conferred by the R292K Neuraminidase Mutation via Molecular Dynamics and Free Energy Calculations. Journal of Chemical Theory and Computation 4: 1526-1540
19. von Itzstein M, Dyason JC, Oliver SW, White HF, Wu WY, Kok GB, Pegg MS. A study of the active site of influenza virus sialidase: an approach to the rational design of novel anti-influenza drugs. J Med Chem. 1996 Jan 19;39(2):388-91. PubMed PMID: 8558506.
20. Taylor NR, von Itzstein M. Molecular modeling studies on ligand binding to sialidase from influenza virus and the mechanism of catalysis. J Med Chem. 1994 Mar 4;37(5):616-24. PubMed PMID: 8126701.
21. Wang NX, Zheng JJ. Computational studies of H5N1 influenza virus resistance to oseltamivir. Protein Sci. 2009 Apr;18(4):707-15. PubMed PMID: 19309695.