Computational study on new natural polycyclic compounds of H1N1 influenza virus neuraminidase

Journal of Molecular Modeling

Volumn 18, Issue 8, 2012, Pages 3445-3453

  Wang, Ye ^a   Wu, Di ^a   Yu, Dahai ^a   Wang, Zhiyong ^a   Tian, Li ^a   Wang, Yanyan ^a   Han, Weiwei ^a   Fang, Xuexun ^a  

^a JILIN UNIVERSITY   (China)

Author keywords

A H1N1 influenza virus; Homology modeling; Molecular docking; Neuraminidase; Virtual screening

Indexed keywords

OSELTAMIVIR; POLYCYCLIC AROMATIC COMPOUND; VIRUS SIALIDASE; ZANAMIVIR;

ARTICLE; AVIAN INFLUENZA VIRUS; CHEMICAL INTERACTION; CHEMICAL STRUCTURE; CONJUGATION; ENERGY; HYDROPHOBICITY; INFLUENZA VIRUS A H1N1; INFLUENZA VIRUS A H5N1; MOLECULAR DOCKING; NONHUMAN; PRIORITY JOURNAL; VIRUS EXAMINATION;

ANTIVIRAL AGENTS; CATALYTIC DOMAIN; COMPUTER SIMULATION; HYDROGEN BONDING; INFLUENZA A VIRUS, H1N1 SUBTYPE; MODELS, MOLECULAR; MOLECULAR STRUCTURE; NEURAMINIDASE; OSELTAMIVIR; POLYCYCLIC COMPOUNDS; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; STRUCTURAL HOMOLOGY, PROTEIN; THERMODYNAMICS; ZANAMIVIR;

AVIAN INFLUENZA VIRUS; INFLUENZA A VIRUS; ORTHOMYXOVIRIDAE;

EID: 84864677874     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-011-1349-0     Document Type: Article

References (42)

1. Wang YT, Chan CH, Su ZY, Chen CL (2010) Homology modeling, docking, and molecular dynamics reveal HR1039 as a potent inhibitor of 2009 A (H1N1) influenza neuraminidase. Biophys Chem 147:74-80
2. Mercader AG, Pomilio AB (2010) QSAR study of flavonoids and flavonoids as influenza H1N1 virus neuraminidase inhibitors. Eur J Med Chem 45:1724-1730
3. Wiley DC, Skehel JJ (1987) The structure and function of the hemagglutinin membrane glycoprotein of influenza virus. Annu Rev Biochem 56:365-394
4. Murti KG, Webster RG (1986) Distribution of hemagglutinin and neuraminidase on influenza virions as revealed by immunoelectron microscopy. Virology 149:36-43 (Pubitemid 16174976)
5. Liu AL, Wang HD, Lee SM, Wang YT, Du GH (2008) Structure-activity relationship of flavonoids as influenza virus neuraminidase inhibitors and their in vitro anti-viral activities. Bioorg Med Chem 16:7141-7147
6. McKimm-Breschkin JL (2000) Resistance of influenza viruses to neuraminidase inhibitors-a review. Antiviral Res 47:1-17 (Pubitemid 30621392)
7. Du QS, Wang SQ, Chou KC (2007) Study of drug resistance of chicken influenza A virus (H5N1) from homology-modeled 3D structures of neuraminidases. Biochem Biophys Res Commun 354:634-640
8. Khan AU, Shakil S, Lal SK (2009) Efficacy of neuraminidase (NA) inhibitors against H1N1 strains of different geographical regions: an in silico approach. Indian J Microbiol 49:370-376
9. Yen HL, Ilyushina NA, Salomon R, Hoffmann E, Webster RG, Govorkova EA (2007) Neuraminidase inhibitor-resistant recombinant A/Vietnam/1203/04 (H5N1) influenza viruses retain their replication efficiency and pathogenicity in vitro and in vivo. J Virol 81:12418-12426 (Pubitemid 350085855)
10. Kiso M, Mitamura K, Sakai-Tagawa Y, Shiraishi K, Kawakami C, Kimura K, Hayden FG, Sugaya N, Kawaoka Y (2004) Resistant influenza A viruses in children treated with oseltamivir: descriptive study. Lancet 364:759-765 (Pubitemid 39165094)
11. Ison MG, Gubareva LV, Atmar RL, Treanor J, Hayden FG (2006) Recovery of drug-resistant influenza virus from immunocompromised patients: a case series. J Infect Dis 193:760-764
12. Li Y, Leung KT, Yao F, Ooi LS, Ooi VE (2006) Antiviral flavans from the leaves of pithecellobium clypearia. J Nat Prod 69:833-835 (Pubitemid 44021417)
13. Miki K, Nagai T, Suzuki K, Tsujimura R, Koyama K, Kinoshita K, Furuhata K, Yamada H, Takahashi K (2007) Anti-influenza virus activity of biflavonoids. Bioorg Med Chem Lett 17:772-775 (Pubitemid 46108558)
14. Ginsburg H, Deharo E (2011) A call for using natural compounds in the development of new antimalarial treatments - an introduction. Malar J 10:S1
15. BioEdit (2011) BioEdit version 5.0.6, Caredata.com, Inc
16. 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 453:1258-1261 (Pubitemid 351913590)
17. Saisubramanian N, Edwinoliver NG, Nandakumar N, Kamini NR, Puvanakrishnan R (2006) Efficacy of lipase from Aspergillus niger as an additive in detergent formulations: a statistical approach. J Ind Microbiol Biotechnol 33:669-676 (Pubitemid 44065571)
18. Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL Workspace: Aweb-based environment for protein structure homology modeling. Bioinformatics 22:195-201 (Pubitemid 43205406)
19. Schwede T, Kopp J, Guex N, Peitsch MC (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res 31:3381-3385 (Pubitemid 37442164)
20. Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18:2714-2723 (Pubitemid 28059943)
21. Nayeem A, Sitkoff D, Krystek S Jr (2006) A comparative study of available software for high-accuracy homology modeling: from sequence alignments to structural models. Protein Sci 15:808-824
22. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283-291
23. Trott O, Olson A (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31:455-461
24. Huey R, Morris GM, Olson AJ, Goodsell DS (2007) A semiempirical free energy force field with charge-based desolvation. J Comput Chem 28:1145-1152 (Pubitemid 46506716)
25. Natural Products Databse (NPD) (2011) http://wiki.compbio.ucsf. edu/wiki/index.php/Natural-products-database
26. Irwin JJ (2008) Using ZINC to acquire a virtual screening library. Curr Protoc Bioinf 22:14.6.1-14.6.23
27. Irwin JJ, Shoichet BK (2005) ZINC-a free database of commercially available compounds for virtual screening. J Chem Inf Model 45:177-182 (Pubitemid 40736970)
28. Open Babel toolbox (2011) http://openbabel.sourceforge.net/
29. Raccoon (2011) http://autodock.scripps.edu/resources/raccoon/
30. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE (1999) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19:1639-1662
31. Affinity User Guide (1999) Accelrys Inc, San Diego
32. Insight II (2000) version 2000, Accelrys Inc, San Diego
33. Yu K, Luo C, Qin G, Xu Z, Li N, Liu H, Shen X, Ma J, Wang Q, Yang C, Zhu W, Jiang H (2009) Why are oseltamivir and zanamivir effective against the newly emerged influenza A virus (A/H1N1) ? Cell Res 19:1221-1224
34. Kitchen D, Decornez H, Furr J, Bajorath J (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov 3(11):935-949 (Pubitemid 39529931)
35. Huanxiang L, Xiaojun Y, Chengqi W, Jian H (H1N1) In silico identification of the potential drug resistance sites over 2009 influenza A virus neuraminidase. Mol Pharm 7:894-904
36. 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 443:45-49 (Pubitemid 44344043)
37. Govorkova EA, Leneva IA, Goloubeva OG, Bush K, Webster RG (2001) Comparison of efficacies of RWJ-270201, zanamivir, and oseltamivir against H5N1, H9N2, and other avian influenza viruses. Antimicrob Agents Chemother 45:2723-2732 (Pubitemid 32906663)
38. Bantia S, Parker CD, Ananth SL, Horn LL, Andries K, Chand P, Kotian PL, Dehghani A, El-Kattan Y, Lin T, Hutchison TL, Montgomery JA, Kellog DL, Babu YS (2001) Comparison of the anti-influenza virus activity of RWJ-270201 with those of oseltamivir and zanamivir. Antimicrob Agents Chemother 45:1162-1167 (Pubitemid 32230997)
39. Boivin G, Goyette N (2002) Susceptibility of recent Canadian influenza A and B virus isolates to different neuraminidase inhibitors. AntiViral Res 54:143-147 (Pubitemid 34327680)
40. Steiner T, Koellner G (2001) Hydrogen bonds with π-acceptors in proteins: frequencies and role in stabilizing local 3D structures. J Mol Biol 305:535-557 (Pubitemid 33032860)
41. Weiss MS, Brandl M, Sühnel J, Pal D, Hilgenfeld R (2001) More hydrogen bonds for the (structural) biologist. Trends Biochem Sci 26:521-523 (Pubitemid 32823428)
42. Hunter CA, Singh J, Thornton JM (1991) Pi-pi interactions: the geometry and energetic of phenylalanine-phenylalanine interactions in proteins. J Mol Biol 218:837-846 (Pubitemid 121003380)