Binding pattern of the long acting neuraminidase inhibitor laninamivir towards influenza A subtypes H5N1 and pandemic H1N1

Journal of Molecular Graphics and Modelling

Volumn 38, Issue , 2012, Pages 148-154

  Meeprasert, Arthitaya ^a   Khuntawee, Wasinee ^a   Kamlungsua, Kittiwat ^a   Nunthaboot, Nadtanet ^b   Rungrotmongkol, Thanyada ^a   Hannongbua, Supot ^a  

^a CHULALONGKORN UNIVERSITY   (Thailand)

^b MAHASARAKHAM UNIVERSITY   (Thailand)

Author keywords

H5N1; Laninamivir; Molecular dynamics simulation; Neuraminidase; Pandemic H1N1

Indexed keywords

H5N1; LANINAMIVIR; MOLECULAR DYNAMICS SIMULATIONS; NEURAMINIDASE; PANDEMIC H1N1;

HYDROGEN BONDS; MOLECULAR DYNAMICS; VIRUSES;

DRUG INTERACTIONS;

LANINAMIVIR; OSELTAMIVIR; PERAMIVIR; SODIUM CHLORIDE; ZANAMIVIR;

ARTICLE; DRUG STRUCTURE; HYDROGEN BOND; IC 50; INFLUENZA VIRUS A H1N1; INFLUENZA VIRUS A H5N1; MOLECULAR DYNAMICS; MUTATION; NONHUMAN; PRIORITY JOURNAL; SIMULATION; VIRUS STRAIN; WILD TYPE;

ANTIVIRAL AGENTS; CATALYTIC DOMAIN; ENZYME INHIBITORS; HUMANS; HYDROGEN BONDING; INFLUENZA A VIRUS, H1N1 SUBTYPE; INFLUENZA A VIRUS, H5N1 SUBTYPE; MOLECULAR DOCKING SIMULATION; MUTATION; NEURAMINIDASE; OSELTAMIVIR; PROTEIN BINDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; STATIC ELECTRICITY; VIRAL PROTEINS; ZANAMIVIR;

CERCOPITHECINE HERPESVIRUS 1; ORTHOMYXOVIRIDAE;

EID: 84867418403     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2012.06.007     Document Type: Article

References (45)

1. P.J. Collins, L.F. Haire, Y.P. Lin, J. Liu, R.J. Russell, P.A. Walker, J.J. Skehel, S.R. Martin, A.J. Hay, and S.J. Gamblin Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants Nature 453 2008 1258 1261
2. G. Neumann, T. Noda, and Y. Kawaoka Emergence and pandemic potential of swine-origin H1N1 influenza virus Nature 459 2009 931 939
3. M. Yamashita, T. Tomozawa, M. Kakuta, A. Tokumitsu, H. Nasu, and S. Kubo CS-8958, a prodrug of the new neuraminidase inhibitor R-125489, shows long-acting anti-influenza virus activity Antimicrobial Agents and Chemotherapy 53 2009 186 192
4. S. Kubo, T. Tomozawa, M. Kakuta, A. Tokumitsu, and M. Yamashita Laninamivir prodrug CS-8958, a long-acting neuraminidase inhibitor, shows superior anti-influenza virus activity after a single administration Antimicrobial Agents and Chemotherapy 54 2010 1256 1264
5. N. Sugaya, and Y. Ohashi Long-acting neuraminidase inhibitor laninamivir octanoate (CS-8958) versus oseltamivir as treatment for children with influenza virus infection Antimicrobial Agents and Chemotherapy 54 2010 2575 2582
6. C.J. Vavricka, Q. Li, Y. Wu, J. Qi, M. Wang, Y. Liu, F. Gao, J. Liu, E. Feng, J. He, J. Wang, H. Liu, H. Jiang, and G.F. Gao Structural and functional analysis of laninamivir and its octanoate prodrug reveals group specific mechanisms for influenza NA inhibition PLoS Pathogens 7 2011 e1002249
7. T. Rungrotmongkol, P. Yotmanee, N. Nunthaboot, and S. Hannongbua Computational studies of influenza A virus at three important targets: hemagglutinin, neuraminidase and M2 protein Current Pharmaceutical Design 17 2011 1720 1739
8. D. Birnkrant, and E. Cox The emergency use authorization of peramivir for treatment of 2009 H1N1 influenza New England Journal of Medicine 361 2009 2204 2207
9. T. Honda, T. Masuda, S. Yoshida, M. Arai, S. Kaneko, and M. Yamashita Synthesis and anti-influenza virus activity of 7-O-alkylated derivatives related to zanamivir Bioorganic and Medicinal Chemistry Letters 12 2002 1925 1928
10. K. Koyama, M. Takahashi, M. Oitate, N. Nakai, H. Takakusa, S.-i. Miura, and O. Okazaki CS-8958, a prodrug of the novel neuraminidase inhibitor R-125489, demonstrates a favorable long-retention profile in the mouse respiratory tract Antimicrobial Agents and Chemotherapy 53 2009 4845 4851
11. Y. Makoto R-118958, a unique anti-influenza agent showing high efficacy for both prophylaxis and treatment after a single administration: from the in vitro stage to phase I study International Congress Series 1263 2004 38 42
12. H.T. Nguyen, T.G. Sheu, V.P. Mishin, A.I. Klimov, and L.V. Gubareva Assessment of pandemic and seasonal influenza A (H1N1) virus susceptibility to neuraminidase inhibitors in three enzyme activity inhibition assays Antimicrobial Agents and Chemotherapy 54 2010 3671 3677
13. M. Yamashita Laninamivir its prodrug CS-8958: long-acting neuraminidase inhibitors for the treatment of influenza Antiviral Chemistry and Chemotherapy 21 2010 71 84
14. B.K. Mai, and M.S. Li Neuraminidase inhibitor R-125489 - a promising drug for treating influenza virus: steered molecular dynamics approach Biochemical and Biophysical Research Communications 410 2011 688 691
15. R.J. Russell, L.F. Haire, D.J. Stevens, P.J. Collins, Y.P. Lin, G.M. Blackburn, A.J. Hay, S.J. Gamblin, and J.J. Skehel The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design Nature 443 2006 45 49
16. D.A. Case, T.A. Darden, T.E.I. Cheatham, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, W. Crowley, R.C. Walker, W. Zhang, K.M. Merz, B. Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossváry, K.F. Wong, F. Paesani, J. Vanicek, X. Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, D.H. Mathews, M.G. Seein, C. Sagui, V. Babin, and P.A. Kollman AMBER 10 2008
17. Q. Li, J. Qi, W. Zhang, C.J. 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, and G.F. Gao The 2009 pandemic H1N1 neuraminidase N1 lacks the 150-cavity in its active site Nature Structural & Molecular Biology 17 2010 1266 1268
18. W. Jorgensen, J. Chandrasekhar, J. Madura, R. Impey, and M. Klein Comparison of simple potential functions for simulating liquid water Journal of Chemical Physics 79 1983 926 935
19. T. Udommaneethanakit, T. Rungrotmongkol, U. Bren, V. Frecer, and M. Stanislav Dynamic behavior of avian influenza A virus neuraminidase subtype H5N1 in complex with oseltamivir, zanamivir, peramivir, and their phosphonate analogues Journal of Chemical Information and Modeling 49 2009 2323 2332
20. U. Arsawang, O. Saengsawang, T. Rungrotmongkol, P. Sornmee, K. Wittayanarakul, T. Remsungnen, and S. Hannongbua How do carbon nanotubes serve as carriers for gemcitabine transport in a drug delivery system? Journal of Molecular Graphics and Modelling 29 2011 591 596
21. W. Khuntawee, T. Rungrotmongkol, and S. Hannongbua Molecular dynamic behavior and binding affinity of flavonoid analogues to the cyclin dependent kinase 6/cyclin D complex Journal of Chemical Information and Modeling 52 2012 76 83
22. P. Sornmee, T. Rungrotmongkol, O. Saengsawang, U. Arsawang, T. Remsungnen, and S. Hannongbua Understanding the molecular properties of doxorubicin filling inside and wrapping outside single-walled carbon nanotubes Journal of Computational and Theoretical Nanoscience 8 2011 1385 1391
23. M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, J.A. Montgomery Jr., T. Vreven, K.N. Kudin, J.C. Burant, J.M. Millam, S.S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G.A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J.E. Knox, H.P. Hratchian, J.B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, P.Y. Ayala, K. Morokuma, G.A. Voth, P. Salvador, J.J. Dannenberg, V.G. Zakrzewski, S. Dapprich, A.D. Daniels, M.C. Strain, O. Farkas, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J.V. Ortiz, Q. Cui, A.G. Baboul, S. Clifford, J. Cioslowski, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, C. Gonzalez, and J.A. Pople Gaussian 03, Revision C.02 2004 Gaussian, Inc. Wallingford, CT
24. J. Wang, R.M. Wolf, J.W. Caldwell, P.A. Kollman, and D.A. Case Development and testing of a general amber force field Journal of Computational Chemistry 25 2004 1157 1174
25. J.P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes Journal of Computational Physics 23 1977 327 341
26. D.M. York, T.A. Darden, and L.G. Pedersen The effect of long-range electrostatic interactions in simulations of macromolecular crystals: a comparison of the Ewald and truncated list methods Journal of Chemical Physics 99 1993 8345 8348
27. B.K. Mai, M.H. Viet, and M.S. Li Top leads for swine influenza A/H1N1 virus revealed by steered molecular dynamics approach Journal of Chemical Information and Modeling 50 2010 2236 2247
28. M. Malaisree, T. Rungrotmongkol, P. Decha, P. Intharathep, O. Aruksakunwong, and S. Hannongbua Understanding of known drug-target interactions in the catalytic pocket of neuraminidase subtype N1 Proteins: Structure, Function, and Bioinformatics 71 2008 1908 1918
29. D. Pan, H. Sun, C. Bai, Y. Shen, N. Jin, H. Liu, and X. Yao 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 17 2011 2465 2473
30. T. Rungrotmongkol, P. Intharathep, M. Malaisree, N. Nunthaboot, N. Kaiyawet, P. Sompornpisut, S. Payungporn, Y. Poovorawan, and S. Hannongbua Susceptibility of antiviral drugs against 2009 influenza A (H1N1) virus Biochemical and Biophysical Research Communications 385 3 2009 390 394
31. L. Le, E. Lee, K. Schulten, and T.N. Truong Molecular modeling of swine influenza A/H1N1 Spanish H1N1, and avian H5N1 flu N1 neuraminidases bound to Tamiflu and Relenza PLoS Currents 1 2009 RRN1015
32. P. Bonnet, and R.A. Bryce Molecular dynamics and free energy analysis of neuraminidase-ligand interactions Protein Science 13 2004 946 957
33. D.-Q. Wei, Q.-S. Du, H. Sun, and K.-C. Chou Insights from modeling the 3D structure of H5N1 influenza virus neuraminidase and its binding interactions with ligands Biochemical and Biophysical Research Communications 344 3 2006 1048 1055
34. M. Malaisree, T. Rungrotmongkol, N. Nunthaboot, O. Aruksakunwong, P. Intharathep, P. Decha, P. Sompornpisut, and S. Hannongbua Source of oseltamivir resistance in avian influenza H5N1 virus with the H274Y mutation Amino Acids 37 2009 725 732
35. L. Le, E.H. Lee, D.J. Hardy, T.N. Truong, and K. Schulten Molecular dynamics simulations suggest that electrostatic funnel directs binding of Tamiflu to influenza N1 neuraminidases PLoS Computational Biology 6 2010 e1000939
36. A.J. Oakley, S. Barrett, T.S. Peat, J. Newman, V.A. Streltsov, L. Waddington, T. Saito, M. Tashiro, and J.L. McKimm-Breschkin Structural and functional basis of resistance to neuraminidase inhibitors of influenza B viruses Journal of Medicinal Chemistry 53 2010 6421 6431
37. J.N. Varghese, P.W. Smith, S.L. Sollis, T.J. Blick, A. Sahasrabudhe, J.L. McKimm-Breschkin, and P.M. Colman Drug design against a shifting target: a structural basis for resistance to inhibitors in a variant of influenza virus neuraminidase Structure (London, England: 1993) 6 1998 735 746
38. T. Rungrotmongkol, M. Malaisree, N. Nunthaboot, P. Sompornpisut, and S. Hannongbua Molecular prediction of oseltamivir efficiency against probable influenza A (H1N1-2009) mutants: molecular modeling approach Amino Acids 39 2010 393 398
39. T. Rungrotmongkol, V. Frecer, W. De-Eknamkul, S. Hannongbua, and S. Miertus Design of oseltamivir analogs inhibiting neuraminidase of avian influenza virus H5N1 Antiviral Research 82 2009 51 58
40. J.J. Shie, J.M. Fang, S.Y. Wang, K.C. Tsai, Y.S. Cheng, A.S. Yang, S.C. Hsiao, C.Y. Su, and C.H. Wong Synthesis of Tamiflu and its phosphonate congeners possessing potent anti-influenza activity Journal of the American Chemical Society 129 2007 11892 11893
41. T. Rungrotmongkol, T. Udommaneethanakit, V. Frecer, and S. Miertus Combinatorial design of avian influenza neuraminidase inhibitors containing pyrrolidine core with a reduced susceptibility to viral drug resistance Combinatorial Chemistry & High Throughput Screening 13 2010 268 277
42. H. Gohlke, C. Kiel, and D.A. Case Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes Journal of Molecular Biology 330 2003 891 913
43. T. Rungrotmongkol, N. Nunthaboot, M. Malaisree, N. Kaiyawet, P. Yotmanee, A. Meeprasert, and S. Hannongbua Molecular insight into the specific binding of ADP-ribose to the nsP3 macro domains of chikungunya and Venezuelan equine encephalitis viruses: molecular dynamics simulations and free energy calculations Journal of Molecular Graphics and Modelling 29 2010 347 353
44. V. Zoete, M. Meuwly, and M. Karplus Study of the insulin dimerization: binding free energy calculations and per-residue free energy decomposition Proteins: Structure, Function, and Bioinformatics 61 2005 79 93
45. H. Liu, X. Yao, C. Wang, and J. Han In silico identification of the potential drug resistance sites over 2009 influenza A (H1N1) virus neuraminidase Molecular Pharmacology 7 2010 894 904