Prediction of zanamivir efficiency over the possible 2009 Influenza A (H1N1) mutants by multiple molecular dynamics simulations and free energy calculations

Journal of Molecular Modeling

Volumn 17, Issue 10, 2011, Pages 2465-2473

  Pan, Dabo ^a   Sun, Huijun ^b   Bai, Chongliang ^a   Shen, Yulin ^c   Jin, Nengzhi ^c   Liu, Huanxiang ^a,b   Yao, Xiaojun ^b  

^a LANZHOU UNIVERSITY   (China)

^b LANZHOU UNIVERSITY   (China)

^c Gansu Computing Center   (China)

Author keywords

2009 H1N1 Influenza A virus; Drug resistance; Molecular dynamics simulation; Molecular mechanics generalized Born surface area (MM GBSA); Zanamivir

Indexed keywords

ZANAMIVIR;

2009 H1N1 INFLUENZA; ANTIVIRAL RESISTANCE; ARTICLE; DRUG EFFICACY; ENERGY; HYDROGEN BOND; MOLECULAR DYNAMICS; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; VIRUS MUTANT;

ANTIVIRAL AGENTS; DRUG RESISTANCE, VIRAL; HUMANS; HYDROGEN BONDING; INFLUENZA A VIRUS, H1N1 SUBTYPE; MOLECULAR DYNAMICS SIMULATION; MUTATION; NEURAMINIDASE; PROTEIN BINDING; PROTEIN STABILITY; ZANAMIVIR;

INFLUENZA A VIRUS;

EID: 80255127591     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-010-0929-8     Document Type: Article

References (40)

1. RJ Garten CT Davis CA Russell, et al. 2009 Antigenic and genetic characteristics of swine-origin 2009 A (H1N1) influenza viruses circulating in humans Science 325 197 201 10.1126/science.1176225 1:CAS:528: DC%2BD1MXos1Srt7w%3D
2. CDC (2010) Antiviral Drugs and H1N1 Flu (Swine Flu). http://www.cdc.gov/ h1n1flu/antiviral.htm. Accessed 10 July 2010)
3. Y Abed B Nehmé M Baz G Boivin 2008 Activity of the neuraminidase inhibitor A-315675 against oseltamivir-resistant influenza neuraminidases of N1 and N2 subtypes Antivir Res 77 163 166 10.1016/j.antiviral.2007.08.008 1:CAS:528:DC%2BD1cXotlOktA%3D%3D
4. PJ Collins LF Haire YP Lin J Liu RJ Russell PA Walker JJ Skehel SR Martin AJ Hay SJ Gamblin 2008 Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants Nature 453 1258 1261 10.1038/nature06956 1:CAS:528:DC%2BD1cXnslGks7k%3D (Pubitemid 351913590)
5. G Boivin N Goyette 2002 Susceptibility of recent Canadian influenza A and B virus isolates to different neuraminidase inhibitors Antivir Res 54 143 147 10.1016/S0166-3542(01)00219-4 1:CAS:528:DC%2BD38XjtVShsb0%3D (Pubitemid 34327680)
6. T Zürcher PJ Yates J Daly A Sahasrabudhe M Walters L Dash M Tisdale JL McKimm-Breschkin 2006 Mutations conferring zanamivir resistance in human influenza virus N2 neuraminidases compromise virus fitness and are not stably maintained in vitro J Antimicrob Chemoth 58 723 732 10.1093/jac/dkl321 (Pubitemid 44390944)
7. VP Mishin FG Hayden LV Gubareva 2005 Susceptibilities of antiviral-resistant influenza viruses to novel neuraminidase inhibitors Antimicrob Agents Chemoth 49 4515 4520 10.1128/AAC.49.11.4515-4520.2005 1:CAS:528:DC%2BD2MXht1Siu7%2FI (Pubitemid 41552580)
8. CF Arias M Escalera-Zamudio L Soto-Del Río Mde AG Cobián-Güemes P Isa S López 2009 Molecular Anatomy of 2009 Influenza Virus A (H1N1) Arch Med Res 40 643 654 10.1016/j.arcmed.2009.10.007 1:CAS:528:DC%2BC3cXjs1amu7w%3D
9. LV Gubareva RG Webster FG Hayden 2002 Detection of influenza virus resistance to neuraminidase inhibitors by an enzyme inhibition assay Antivir Res 53 47 61 10.1016/S0166-3542(01)00192-9 1:CAS:528:DC%2BD3MXnvFCrt7k%3D (Pubitemid 33001554)
10. http://www.cdc.gov/mmwr/preview/mmwrhtml/mm5832a3.htm (accessed August 9, 2010)
11. ZW Cao LY Han CJ Zheng ZL Ji X Chen HH Lin YZ Chen 2005 Computer prediction of drug resistance mutations in proteins Drug Discov Today 10 521 529 10.1016/S1359-6446(05)03377-5 1:CAS:528:DC%2BD2MXivV2hs7c%3D
12. R Chachra RC Rizzo 2008 Origins of resistance conferred by the R292K neuraminidase mutation via molecular dynamics and free energy calculations J Chem Theor Comput 4 1526 1540 10.1021/ct800068v 1:CAS:528:DC%2BD1cXps1ygsLo%3D
13. T Hou WA McLaughlin W Wang 2008 Evaluating the potency of HIV-1 protease drugs to combat resistance Proteins 71 1163 1174 10.1002/prot.21808 1:CAS:528:DC%2BD1cXlt1Wlurs%3D (Pubitemid 351564043)
14. J Zhang T Hou W Wang JS Liu 2010 Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance Proc Natl Acad Sci USA 107 1321 1326 10.1073/pnas.0907304107 1:CAS:528: DC%2BC3cXhslOktbk%3D
15. J Srinivasan TE Cheatham P Cieplak PA Kollman DA Case 1998 Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices J Am Chem Soc 120 9401 9409 10.1021/ja981844+ 1:CAS:528:DyaK1cXlsVyqtLo%3D (Pubitemid 28452628)
16. PA Kollman I Massova C Reyes B Kuhn S Huo L Chong M Lee T Lee Y Duan W Wang O Donini P Cieplak J Srinivasan DA Case TE Cheatham 2000 Calculating structures and free energies of complex molecules: combining molecular Molecular mechanics and continuum models Acc Chem Res 33 889 897 10.1021/ar000033j 1:CAS:528:DC%2BD3cXmvFGiu7g%3D (Pubitemid 32056774)
17. V Tsui DA Case 2000 Theory and applications of the generalized born solvation model in macromolecular simulations Biopolymers 56 275 291 10.1002/1097-0282(2000)56:4<275::AID-BIP10024>3.0.CO;2-E 1:CAS:528:DC%2BD38XkvFGmtQ%3D%3D (Pubitemid 34105875)
18. A Onufriev D Bashford DA Case 2000 Modification of the generalized Born model suitable for macromolecules J Phys Chem B 104 3712 3720 10.1021/jp994072s 1:CAS:528:DC%2BD3cXhvVGit70%3D
19. M Feig CL Brooks 2002 Evaluating CASP4 predictions with physical energy functions Proteins 49 232 245 10.1002/prot.10217 1:CAS:528:DC%2BD38XnsFeksb0%3D
20. C Gourmala Y Luo F Barbault Y Zhang S Ghalem F Maurel B Fan 2007 Elucidation of the LewisX-LewisX carbohydrate interaction with molecular dynamics simulations: A glycosynapse model J Mol Struct THEOCHEM 821 22 29 10.1016/j.theochem.2007.06.027 1:CAS:528:DC%2BD2sXhtFSrtbjM
21. m J Med Chem 50 2240 2244 10.1021/jm060542c 1:CAS:528:DC%2BD2sXjvFChtrk%3D (Pubitemid 46683076)
22. H Liu X Yao C Wang J Han 2010 In silico identification of the potential drug resistance sites over 2009 Influenza A (H1N1) virus neuraminidase Mol Pharmaceutics 7 894 904 10.1021/mp100041b 1:CAS:528:DC%2BC3cXls1Shu7o%3D
23. T Rungrotmongkol M Malaisree N Nunthaboot P Sompornpisut S Hannongbua 2010 Molecular prediction of oseltamivir efficiency against probable influenza A (H1N1-2009) mutants: molecular modeling approach Amino Acids 39 393 398 10.1007/s00726-009-0452-3 1:CAS:528:DC%2BC3cXotVaisLw%3D
24. DeLano WL (2002) The PyMOL Molecular Graphics System DeLano Scientific, Palo Alto, CA, USA. http://www.pymol.org
25. Q Li J Qi W Zhang CJ Vavricka Y Shi J Wei E Feng J Shen J Chen D Liu J He J Yan H Liu H Jiang M Teng X Li GF Gao 2010 The 2009 pandemic H1N1 neuraminidase N1 lacks the 150-cavity in its active site Nat Struct Mol Biol 17 1266 1268 10.1038/nsmb.1909 1:CAS:528:DC%2BC3cXhtFOht7fI
26. DA Case TE Cheatham T Darden H Gohlke R Luo KM Merz A Onufriev C Simmerling B Wang RJ Woods 2005 The Amber biomolecular simulation programs J Comput Chem 26 1668 1688 10.1002/jcc.20290 1:CAS:528:DC%2BD2MXht1SlsbbM (Pubitemid 43076180)
27. Y Duan C Wu S Chowdhury MC Lee G Xiong W Zhang R Yang P Cieplak R Luo T Lee J Caldwell J Wang PA Kollman 2003 A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations J Comput Chem 24 1999 2012 10.1002/jcc.10349 1:CAS:528: DC%2BD3sXovVygsbc%3D
28. MC Lee Y Duan 2004 Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model Proteins: Struct Funct Bioinform 55 620 634 10.1002/prot.10470 1:CAS:528:DC%2BD2cXjvFemtL8%3D (Pubitemid 38620087)
29. JM Wang RM Wolf JW Caldwell PA Kollman DA Case 2004 Development and testing of a general amber force field J Comput Chem 25 1157 1174 10.1002/jcc.20035 1:CAS:528:DC%2BD2cXksFakurc%3D
30. WL Jorgensen J Chandrasekhar JD Madura RW Impey ML Klein 1983 Comparison of simple potential functions for simulating liquid water J Chem Phys 79 926 935 10.1063/1.445869 1:CAS:528:DyaL3sXksF2htL4%3D
31. HJC Berendsen JPM Postma WF van Gunsteren A DiNola JR Haak 1984 Molecular dynamics with coupling to an external bath J Chem Phys 81 3684 3690 10.1063/1.448118 1:CAS:528:DyaL2cXmtlGksbY%3D
32. U Essmann L Perera ML Berkowitz TA Darden 1995 Smooth particle mesh Ewald method J Chem Phys 103 8577 9593 10.1063/1.470117 1:CAS:528:DyaK2MXptlehtrw%3D
33. JP Ryckaert G Ciccotti HJC Berendsen 1977 Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J Comput Phys 23 327 341 10.1016/0021-9991(77)90098-5 1:CAS:528:DyaE2sXktVGhsL4%3D
34. D Sitkoff KA Sharp B Honig 1994 Accurate calculation of hydration free energies using macroscopic solvent models J Phys Chem 98 1978 1988 10.1021/j100058a043 1:CAS:528:DyaK2cXhsVGrsrs%3D
35. DA Case 1994 Normal mode analysis of protein dynamics Curr Opin Struct Biol 4 285 290 10.1016/S0959-440X(94)90321-2 1:CAS:528:DyaK2cXltVehsbY%3D (Pubitemid 24116915)
36. JN Varghese PW Smith SL Sollis 1998 Drug design against a shifting target: a structural basis for resistance to inhibitors in a variant of influenza virus neuraminidase Structure 6 735 746 10.1016/S0969-2126(98)00075-6 1:CAS:528:DyaK1cXkvV2juro%3D (Pubitemid 28301207)
37. BJ Smith JL McKimm-Breshkin M McDonald 2002 Structural studies of the resistance of influenza virus neuramindase to inhibitors J Med Chem 45 2207 2212 10.1021/jm010528u 1:CAS:528:DC%2BD38XjtF2hu7g%3D (Pubitemid 34525800)
38. J McKimm-Breschkin A Sahasrabudhe T Blick 2001 Mechanisms of resistance of influenza virus to neuraminidase inhibitors Int Congress Series 1219 855 861 10.1016/S0531-5131(01)00364-8 1:CAS:528:DC%2BD38XkslahtL0%3D
39. CA Chang W Chen MK Gilson 2007 Ligand configurational entropy and protein binding Proc Natl Acad Sci USA 104 1534 1539 10.1073/pnas.0610494104 1:CAS:528:DC%2BD2sXhslars7o%3D (Pubitemid 46214625)
40. H Gohlke G Klebe 2002 Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors Angew Chem Int Edn 41 2644 2676 10.1002/1521-3773(20020802)41:15<2644::AID- ANIE2644>3.0.CO;2-O 1:CAS:528:DC%2BD38Xmt1entbw%3D