Skip to main content
SpringerLink
Log in

Prediction of selective inhibition of neuraminidase from various influenza virus strains by potential inhibitors

  • Published:
Biochemistry (Moscow), Supplement Series B: Biomedical Chemistry Aims and scope Submit manuscript

Abstract

A universal model of inhibition of neuraminidases from various influenza virus strains by a particular inhibitor has been developed. It is based on known 3D structures for neuraminidases from three influenza virus strains (A/Tokyo/3/67, A/tern/Australia/G70C/75, B/Lee/40) and modeling of the 3D structure of neuraminidases from other strains (A/PR/8/34 and A/Aichi/2/68). Using docking and molecular dynamics, we have modeled 235 enzyme-ligand complexes for 185 compounds with known IC50 values. Selection of final variants among three intermediate results obtained for each enzyme-ligand pair and calculation of independent variables for generation of linear regression equations were performed using MM-PBSA/MM-GBSA. This resulted in the set of equations for individual strains and the equations pooling all the data. Thus using this approach it is possible to predict inhibition for neuraminidase from each the considered strains by a particular inhibitor and to predict the range of its action on neuraminidases from various influenza virus strains.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Breslav, N.V., Shevchenko, E.S., Abramov, D.D., Prolipov, A.G., Zhuravleva, M.M., Oskerko, T.A., Kolobukhina, L.V., Merkulova, L.N., Shchelkanov, M.Yu., Burtseva, E.I., and L’vov, D.K., Vopr. Virusol., 2013, vol. 58, no.1, pp. 28–32.

    Google Scholar 

  2. Air, G.M. and Laver, W.G., Proteins: Structure, Function, and Bioinformatics, 1989, vol. 6, no. 4, pp. 341–356.

    Article  CAS  Google Scholar 

  3. Mishin, V.P., Hayden, F.G., and Gubareva, L.V., Antimicrob. Agents Chemother., 2005, vol. 11, pp. 4515–4520.

    Article  Google Scholar 

  4. Moscona, A., N. Engl. J. Med., 2005, vol. 353, pp. 1363–1373.

    Article  CAS  Google Scholar 

  5. McKimm-Breschkin, J., Trivedi, T., Hampson, A., et al., Antimicrob. Agents Chemother., 2003, vol. 47, pp. 2264–2272.

    Article  CAS  Google Scholar 

  6. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E., Nucl. Acids Res., 2000, vol. 28, pp. 235–242.

    Article  CAS  Google Scholar 

  7. Babu, Y.S., Chand, P., Bantia, S., Kotian, P., Dehghani, A., El-Kattan, Y., Lin, T.H., Hutchison, T.L., Elliott, A.J., Parker, C.D., Ananth, S.L., Horn, L.L., Laver, G.W., and Montgomery, J.A., J. Med. Chem., 2000, vol. 43, no. 19, pp. 3482–3486.

    Article  CAS  Google Scholar 

  8. Whittington, A. and Bethell, R., Expert Opin. Ther. Patents, 1995, vol. 5, no. 8, pp. 793–803.

    Article  CAS  Google Scholar 

  9. Sebaug, J.L., Pharmaceutical Statistics, 2011, vol. 10, no. 2, pp. 128–134.

    Article  Google Scholar 

  10. SYBYL-X, Tripos, St. Louis, MO, USA.

  11. Kuntz, I.D., Blaney, J.M., Oatley, S.J., Langridge, R., and Ferrin, T.E., J. Mol. Biol., 1982, vol. 161, pp. 269–288.

    Article  CAS  Google Scholar 

  12. Case, D.A., Darden, T., Cheatham, T.E., III, Simmerling, C., Wang, J., Duke, R.E., Luo, R., Merz, K.M., Pearlman, D.A., and Crowley, M., AMBER 9, San Francisco: University of California, 2006.

    Google Scholar 

  13. Shcherbakov, A.M., Levina, I.S., Kulikova, L.E., Fedyushkina, I.V., Skvortsov, V.S., Veselovsky, A.V., Kuznetsov, Yu.V., and Zavarzin, I.V., Biomed. Khim., 2016, vol. 62, no. 3, pp. 290–294. doi 10.18097/PBMC20166203290

    Article  Google Scholar 

  14. Kollman, P.A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., Donini, O., Cieplak, P., Srinivasan, J., Case, D.A., and Cheatham, T.E., III, Acc. Chem. Res., 2000, vol. 33, pp. 889–897.

    Article  CAS  Google Scholar 

  15. Nguyen, T.T., Viet, M.H., and Li, M.S., The Scientific World Journal, 2014, Article ID 536084, 14 pages. doi 10.1155/2014/536084

    Google Scholar 

  16. Chand, P., Babu, Y.S., and Bantia, S.J., J. Med. Chem., 1997, vol. 40, pp. 4030–4052.

    Article  CAS  Google Scholar 

  17. Atigadda, V.R., Brouillette, W.J., Duarte, F., Ali, S.M., Babu, Y.S., Bantia, S., Chand, P., Chu, N., Montgomery, J.A., Walsh, D.A., Sudbeck, E.A., Finley, J., Luo, M., Air, G.M., and Laver, G.M., J. Med. Chem., 1999, vol. 42, pp. 2332–2343.

    Article  CAS  Google Scholar 

  18. Williams, M.A., Lew, W., Mendel, D.B., Tai, C.Y., Escarpe, P.A., Laver, W.G., Stevens, R.C., and Kim, C.U., Bioorg. Med. Chem. Lett., 1997, vol. 7, pp. 1837–1842.

    Article  CAS  Google Scholar 

  19. Kim, C.U., Lew, W., Williams, M.S., Wu, H., Zhang, L., Chen, X., Escarpe, P.A., Mendel, D.B., Laver, W.G., and Stevens, R.C., J. Med. Chem., 1998, vol. 41, pp. 2451–2460.

    Article  CAS  Google Scholar 

  20. Lew, W., Wu, H., Mendel, D.B., Escarpe, P.A., Chen, X., Laver, G., Graves, B.J., and Kim, C.U., Bioorg. Med. Chem. Lett., 1998, vol. 8, pp. 3321–3324.

    Article  CAS  Google Scholar 

  21. Kim, C.U., Lew, W., Williams, M.A., Liu, H.T., Zhang, L.J., Swaminathan, S., Bischofberger, N., Chen, M.S., Mendel, D.B., Tai, C.Y., Laver, W.G., and Steven, R.C., J. Am. Chem. Soc., 1997, vol. 119, pp. 681–690.

    Article  CAS  Google Scholar 

  22. Bantia, S., Parker, C.D., Ananth, S.L., Horn, L.L., Andries, K., Chand, P., Kotian, P.L., Dehghani, A., El-Kattan, Y., Lin, T., and Hutchison, T.L., Antimicrob. Agents Chemother., 2001, vol. 45, no. 4, pp. 1162–1167.

    Article  CAS  Google Scholar 

  23. Wang, G.T., Chen, Y., Wang, S., Gentles, R., Sowin, T., Kati, W., Muchmore, S., Giranda, V., Stewart, K., Sham, H., Kempf, D., and Laver, W.G., J. Med. Chem., 2001, vol. 44, pp. 1192–1201.

    Article  CAS  Google Scholar 

  24. Gao, L., Zu, M., Wu, S., Liu, A.L., and Du, G.H., Bioorgan. Med. Chem. Letts., 2011, vol. 21, no. 19, pp. 5964–5970.

    Article  CAS  Google Scholar 

  25. Smith, P.W., Sollis, S.L., and Howes, P.D., J. Med. Chem., 1998, vol. 41, pp. 787–797.

    Article  CAS  Google Scholar 

  26. Wyatt, P.G., Coomber, B.A., Evans, D.N., Jack, T.I., Fulton, H.E., Wonacott, A.J., Colman, P., and Varghese, J., Bioorgan. Med. Chem. Letts., 2001, vol. 11, no. 5, pp. 669–673.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute of Biomedical Chemistry, ul. Pogodinskaya 10, Moscow, 119121, Russia

    A. V. Mikurova, A. V. Rybina & V. S. Skvortsov

Authors
  1. A. V. Mikurova
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. V. Rybina
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. V. S. Skvortsov
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to A. V. Mikurova.

Additional information

Original Russian Text © A.V. Mikurova, A.V. Rybina, V.S. Skvortsov, 2017, published in Biomeditsinskaya Khimiya.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Mikurova, A.V., Rybina, A.V. & Skvortsov, V.S. Prediction of selective inhibition of neuraminidase from various influenza virus strains by potential inhibitors. Biochem. Moscow Suppl. Ser. B 11, 166–185 (2017). https://doi.org/10.1134/S1990750817020044

Download citation

  • Received:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S1990750817020044

Keywords

Search

Navigation