Molecular docking investigation for Indonesian H274Y mutant neuraminidase type 1 with neuraminidase inhibitors

Abstract

The aim of this study is to get insight the interaction between Indonesian H274Y mutant neuraminidase with four inhibitors. Not only to seek preferable inhibitor to be used, but also to investigate the interaction occurred, especially hydrogen bonds formed. Hydrogen bonds analysis and its interaction energies calculation showed that zanamivir is the most preferable inhibitor with 13 hydrogen bonds formed and –439.96 kcal/mol. Laninamivir would be an alternative inhibitor since it has 10 hydrogen bonds and –307.19 kcal/mol. The investigation of ΔSAS showed almost all active site residues buried when interacted with inhibitors. Only a few residues have an increases ΔSAS. Lipinski rule analysis showed that zanamivir and laninamivir would be best taken by injection or inhalation.

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Herlambang, S. and Saleh, R. (2012) Molecular docking investigation for Indonesian H274Y mutant neuraminidase type 1 with neuraminidase inhibitors. American Journal of Molecular Biology, 2, 49-59. doi: 10.4236/ajmb.2012.21006.

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1] Sedyaningsih, E.R., Isfandari, S., Soendoro, S. and Supari, S.F. (2008) Towards mutual trust, transparency and equity in virus sharing mechanism: The avian influenza case of Indonesia. Annals Academy of Medicine Singapore, 37, 482-488.
[2] http://www.who.int/csr/disease/avian_influenza/avianinfluenza_factsheetJan2006/en/index.html
[3] Cheung, C.L., Rayner, J.M., Smith, G.J.D., Wang, P., Naipospos, T.S.P., Zhang, J., Yuen, K.Y., Webster, R.G., Peiris, J.S.M. and Chen, H. (2006) Distribution of amantadine-resistant H5N1 avian influenza variants in Asia. The Journal of Infectious Diseases, 193, 1626-1629. doi:10.1086/504723
[4] Tu, Q., Pinto, L.H., Luo, G., Shaughnessy, M.A., Mullaney, D., Kurtz, S., Krystal, M. and Lamb, R.A. (1996) Characterization of M2 ion channel activity by BL-1743, an inhibitor of influenza A virus. Journal of Virology, 70, 4246-4252.
[5] Li, K.S., Guan, Y., Wang, J., Smith, G.J., Xu, K.M., Duan, L., et al. (2004) Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia. Nature, 430, 209-213. doi:10.1038/nature02746
[6] Puthavathana, P., Auewarakul, P., Charoenying, P.C., Sangsiriwut, K., Pooruk, P., Boonnak, K., et al. (2005) Molecular characterization of the complete genome of human influenza H5N1 virus isolates from Thailand. Journal of General Virology, 86, 423-433. doi:10.1099/vir.0.80368-0
[7] Hay, A.J., et al. (1993) Options for the control of influenza virus II. Excerpta Medica, Amsterdam, 281-288.
[8] Hay, A.J., Wolstenholme, A.J., Skehel, J.J. and Smith, M.H. (1985) The molecular basis of the specific anti-influenza action of amantadine. The EMBO Journal, 4, 3021-3024.
[9] Hayden, F.G., Sperber, S.J., Belshe, R.B., Clover, R.D., Hay, A.J. and Pyke, S. (1991) Recovery of drug resistant influenza A virus during therapeutic use of rimantadine. Antimicrob Agents Chemother, 35, 1741-1747.
[10] Peiris, J.S., Yu, W.C., Leung, C.W., et al. (2004) Re-emergence of fatal human influenza A subtype H5N1 disease. Lancet, 363, 617-619. doi:10.1016/S0140-6736(04)15595-5
[11] Le, Q.M., Kiso, M., Someya, K., et al. (2005) Avian flu: Isolation of drug-resistant H5N1 virus. Nature, 437, 1108. doi:10.1038/4371108a
[12] Jefferson, T., Demicheli, V., Rivetti, D., Jones, M., Di Pietrantonj, C., Rivetti, A. (2006) Antivirals for influenza in healthy adults: Systematic review. Lancet, 367, 303- 313. doi:10.1016/S0140-6736(06)67970-1
[13] Bright, R.A., Shay, D.K., Shu, B., et al. (2006) Adamantane resistance among influenza A viruses isolated early during the 2005-2006 influenza season in the United States. Journal of the American Medical Association (JAMA), 295, 891-894. doi:10.1001/jama.295.8.joc60020
[14] Hayden, F.G., Belshe, R.B., Clover, R.D., Hay, A.J., Oakes, M.G. and Soo, W. (1989) Emergence and apparent transmission of rimantadine-resistant influenza A virus in families. New England Journal of Medicine, 321, 1696-1702. doi:10.1056/NEJM198912213212502
[15] Hall, C.B., Dolin, R., Gala, C.L., et al. (1987) Children with influenza A infection: Treatment with rimantadine. Pediatrics, 80, 275-282.
[16] Shiraishi, K., Mitamura, K., Sakai-Tagawa, Y., Goto, H., Sugaya, N. and Kawaoka, Y. (2003) High frequency of resistant viruses harboring different mutations in amantadine-treated children with influenza. Journal of Infectious Diseases, 188, 57-61. doi:10.1086/375799
[17] Englund, J.A., Champlin, R.E., Wyde, P.R., et al. (1998) Common emergence of amantadine- and rimantadine-resistant influenza A viruses in symptomatic immunocompromised adults. Clinical Infectious Diseases, 26, 1418-1424. doi:10.1086/516358
[18] Hayden, F.G. (2001) Perpectives on antiviral use during pandemic influenza. Philosophical Transactions of the Royal Society B: Biological Sciences, 356, 1877-1884.
[19] Russell, R.J., Haire, L.F., Stevens, D.J., Collins, P.J., Lin, Y.P., Blackburn, G.M., Hay, A.J., Gamblin, S.J. and Skehel, J.J. (2006) The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design. Nature London, United Kingdom, 443, 45-49. doi:10.1038/nature05114
[20] Chachra, R. and Rizzo, R.C. (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. doi:10.1021/ct800068v
[21] McKimm-Breschkin, J.L., Sahasrabudhe, A., Blick, T.J., McDonald, M., Colman, P.M., Hart, G.J., Bethell, R.C. and Varghese, J.N. (1998) Mutations in a conserved residue in the influenza virus neuraminidase active site decreases sensitivity to Neu5Ac2en derivatives. Journal of Virology, 72, 2456-2462.
[22] Mishin, V.P., Hayden, F.G. and Gubareva, L.V. (2005) Susceptibilities of antiviral-resistant influenza viruses to novel neuraminidase inhibitors. Antimicrobial Agents and Chemotherapy, 49, 4515-4520. doi:10.1128/AAC.49.11.4515-4520.2005
[23] Sheu, T.G., Deyde, V.M., Okomo-Adhiambo, M., Garten, R.J., Xu, X., Bright, R.A., Butler, E.N., Wallis, T.R., Klimov, A.I. and Gubareva, L.V. (2008) Surveillance for neuraminidase inhibitor resistance among human influenza A and B viruses circulating worldwide from 2004 to 2008. Antimicrobial Agents and Chemotherapy, 52, 3284-3292.
[24] Wetherall, N.T., Trivedi, T., Zeller, J., Hodges-Savola, C., McKimm-Breschkin, J.L., Zambon, M. and Hayden, F.G. (2003) Evaluation of neuraminidase enzyme assays using different substrates to measure susceptibility of influenza clinical isolates to neuraminidase inhibitors: Report of the neuraminidase inhibitor susceptibility network. Journal of Clinical Microbiology, 41, 742-750. doi:10.1128/JCM.41.2.742-750.2003
[25] McKimm-Breschkin, J.L., Trivedi, T., Hampson, A., Hay, A., Klimov, A., Tashiro, M., Hayden, F.G. and Zambon, M. (2003) Neuraminidase sequence analysis and susceptibilities of influenza virus clinical isolates to zanamivir and oseltamivir. Antimicrobial Agents and Chemotherapy, 47, 2264-2272. doi:10.1128/AAC.47.7.2264-2272.2003
[26] Yen, H., Ilyushina, N.A., Salomon, R., Hoffmann, E., Webster, R.G. and Govorkova, E.A. (2007) Neuraminidase inhibitor-resistant recombinant A/Vietnam/1203/04 (H5N1) influenza viruses retain their replication efficiency and pathogenicity in vitro and in vivo. Journal of Virology, 81, 12418-12426. doi:10.1128/JVI.01067-07
[27] Meijer, A., Lackenby, A., Hungnes, O., Lina, B., van der Werf, S., Schweiger, B., Opp, M., Paget, J., van de Kassteele, J., Hay, J. and Zambon, M. (2009) Oseltamivir-resistant influenza virus A (H1N1), Europe, 2007-08 season. Emerging Infectious Diseases, 15, 552- 560. doi:10.3201/eid1504.081280
[28] Monto, A.S., McKimm-Breschkin, J.L., Macken, C., Hampson, A.W., Hay, A., Klimov, A., Tashiro, M., Webster, R.G., Aymard, M., Hayden, F.G. and Zambon, M. (2006) Detection of influenza viruses resistant to neuraminidase inhibitors in global surveillance during the first 3 years of their use. Antimicrobial Agents and Chemotherapy, 50, 2395-2402. doi:10.1128/AAC.01339-05
[29] Tamura, D., Mitamura, K., Yamazaki, M., Fujino, M., Nirasawa, M., Kimura, K., Kiso, M., Shimizu, H., Kawakami, C., Hiroi, S., Takahashi, S., Hata, M., Minagawa, H., Kimura, Y., Kaneda, S., Sugita, S., Horimoto, T., Sugaya, N. and Kawaoka, Y. (2009) Oseltamivir-resistant influenza A viruses circulating in Japan. Journal of Clinical Microbiology, 47, 1424-1427. doi:10.1128/JCM.02396-08
[30] McNicholl, I.R. and McNicholl, J.J. (2001) Neuraminidase inhibitors: Zanamivir and oseltamivir. Annals of Pharmacotherapy, 35, 57-70. doi:10.1345/aph.10118
[31] Russell, R.J., Haire, L.F., Stevens, D.J., Collins, P.J., Lin, Y.P., Blackburn, G.M., Hay, A.J., Gamblin, S.J. and Skehel, J.J. (2006) The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design, Nature, 443, 45-49. doi:10.1038/nature05114
[32] Collins, P.J., Haire, L.F., Lin, Y.P., Liu, J., Russell, R.J., Walker, P.A., Skehel, J.J., Martin, S.R., Hay, A.J. and Gamblin, S.J. (2008) Crystal structures of oseltamivir- resistant influenza virus neuraminidase mutants, Nature, 453, 1258-1261. doi:10.1038/nature06956
[33] http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/nph-select.cgi?go=database
[34] Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J.H., Zhang, Z., Miller, W. and Lipman D.J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25, 3389-3402. doi:10.1093/nar/25.17.3389
[35] Zdobnov, E.M. and Apweiler, R. (2001) InterProScan—An integration platform for the signature-recognition methods in InterPro. Bioinformatics, 17, 847-848.
[36] Arnold, K., Bordoli, L., Kopp, J. and Schwede, T. (2006). The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling. Bioinformatics, 22, 195-201. doi:10.1093/bioinformatics/bti770
[37] Kiefer, F., Arnold, K., Künzli, M., Bordoli, L. and Schwede, T. (2009). The SWISS-MODEL repository and associated resources. Nucleic Acids Research, 37, D387-D392. doi:10.1093/nar/gkn750
[38] Schwede, T., Kopp, J., Guex, N. and Peitsch, M.C. (2003) SWISS-MODEL: An automated protein homology-mo- deling server. Nucleic Acids Research, 31, 3381-3385. doi:10.1093/nar/gkg520
[39] Guex, N. and Peitsch, M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modelling. Electrophoresis, 18, 2714-2723. doi:10.1002/elps.1150181505
[40] Peitsch, M.C. (1995) Protein modeling by E-mail. Bio/ Technology, 13, 658-660.
[41] http://www.pdb.org/pdb/home/home.do
[42] Sali, A., Pottertone, L., Yuan, F., van Vlijmen, H. and Karplus, M. (1995) Evaluation of comparative protein modeling by MODELLER. Proteins, 23, 318-326. doi:10.1002/prot.340230306
[43] Fiser, R.K. and Sali, A. (2000) Modeling of loops in protein structures. Protein Science, 9, 1753-1773. doi:10.1110/ps.9.9.1753
[44] Laskowski, R.A., MacArthur, M.W., Moss, D.S. and Thornton, J.M. (1993) PROCHECK—A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26, 283-291. doi:10.1107/S0021889892009944
[45] Morris, A.L., MacArthur, M.W., Hutchinson, E.G. and Thornton, J.M. (1992) Stereochemical quality of protein structure coordinates. Proteins: Structure, Function, and Bioinformatics, 12, 345-364. doi:10.1002/prot.340120407
[46] Shen, M.-Y. and Sali, A. (2006) Statistical potential for assessment and prediction of protein structures. Protein Science, 15, 2507-2524. doi:10.1110/ps.062416606
[47] Lüthy, R., Bowie, J.U. and Eisenberg, D. (1992) Assessment of protein models with three-dimensional profiles. Nature, 356, 83-85. doi:10.1038/356083a0
[48] Ramachandran, G.N., Ramakrishnan, C. and Sasisekharan, V. (1963) Stereochemistry of polypeptide chain configurations. Journal of Molecular Biology, 7, 95-99. doi:10.1016/S0022-2836(63)80023-6
[49] Kabsch, W. and Sander, C. (1983) Biopolymers dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637. doi:10.1002/bip.360221211
[50] http://pubchem.ncbi.nlm.nih.gov/
[51] Wu, G., Robertson, D.H., Brooks, C.L.III and Vieth, M. (2003) Detailed analysis of grid-based molecular docking: A case study of CDOCKER—A CHARMm-based MD docking algorithm. Journal of Computational Chemistry, 24, 1549. doi:10.1002/jcc.10306
[52] Stoll, V., Stewart, K.D., Maring, C.J., Muchmore, S., Giranda, V., Gu, Y.Y., Wang, G., Chen, Y., Sun, M., Zhao, C., Kennedy, A.L., Madigan, D.L., Xu, Y., Saldivar, A., Kati, W., Laver, G., Sowin, T., Sham, H.L., Greer, J. and Kempf, D. (2003) Influenza neuraminidase inhibitors: Structure-based design of a novel inhibitor series. Biochemistry, 42, 718-727. doi:10.1021/bi0205449
[53] Lipinski, C.A., Lombardo, F., Dominy, B.W. and Feeney, P.J. (1997) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 23, 3-25. doi:10.1016/S0169-409X(96)00423-1
[54] Hatakeyama, S., Sugaya, N., Ito, M., Yamazaki, M., Ichikawa, M., Kimura, K., Kiso, M., Shimizu, H., Kawakami, C., Koike, K., Mitamura, K. and Kawaoka, Y. (2007) Emergence of influenza B viruses with reduced sensitivity to neuraminidase inhibitors. Journal of the American Medical Association (JAMA), 297, 1435-1442. doi:10.1001/jama.297.13.1435
[55] Hayden, F.G. (2006) Antiviral resistance in influenza viruses—Implications for management and pandemic response. New England Journal of Medicine, 354, 785-788. doi:10.1056/NEJMp068030
[56] Kiso, M., Mitamura, K., Sakai-Tagawa, Y., Shiraishi, K., Kawakami, C., Kimura, K., Hayden, F. G., Sugaya, N. and Kawaoka, Y. (2004) Resistant influenza A viruses in children treated with oseltamivir: Descriptive study. Lancet, 364, 759-765. doi:10.1016/S0140-6736(04)16934-1
[57] Lackenby, A., Hungnes, O., Dudman, S.G., Meijer, A., Paget, W.J., Hay, A.J. and Zambon, M.C. (2008) Emergence of resistance to oseltamivir among influenza A (H1N1) viruses in Europe. Eurosurveillance, 13, 1-2.
[58] Le, Q.M., Kiso, M., Someya, K., Sakai, Y.T., Nguyen, T.H., Nguyen, K.H.L., Pham, N.D., Ngyen, H.H., Yamada, S., Muramoto, Y., Horimoto, T., Takada, A., Goto, H., Suzuki, T., Suzuki, Y. and Kawaoka, Y. (2005) Avian flu: Isolation of drug-resistant H5N1 virus. Nature (London), 437, 1108. doi:10.1038/4371108a
[59] Yamashita, M., Tomozawa, T., Kakuta, M., Tokumitsu, A., Nasu, H. and Kubo, S. (2009) CS-8958, a Prodrug of the new neuraminidase inhibitor R-125489, shows long-acting anti-influenza virus activity. Antimicrobial Agents and Chemotherapy, 53, 186-192. doi:10.1128/AAC.00333-08
[60] Kiso, M., Kubo, S., Ozawa, M., Le, Q.M., Nidom, C.A., et al. (2001) Efficacy of the new neuraminidase inhibitor CS-8958 against H5N1 influenza viruses. PLoS Pathogens, 6, 1-10.

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