메뉴 건너뛰기




Volumn 52, Issue 10, 2012, Pages 2715-2729

Theoretical studies on the susceptibility of oseltamivir against variants of 2009 A/H1N1 influenza neuraminidase

Author keywords

[No Author keywords available]

Indexed keywords

FREE ENERGY; HEALTH RISKS; MOLECULAR DYNAMICS; VIRUSES;

EID: 84867759741     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci300375k     Document Type: Article
Times cited : (64)

References (105)
  • 1
    • 84859520338 scopus 로고    scopus 로고
    • Two Years after Pandemic Influenza A/2009/H1N1: What Have We Learned?
    • Cheng, V. C. C.; To, K. K. W.; Tse, H.; Hung, I. F. N.; Yuen, K. Y. Two Years after Pandemic Influenza A/2009/H1N1: What Have We Learned? Clin. Microbiol. Rev. 2012, 25, 223-263
    • (2012) Clin. Microbiol. Rev. , vol.25 , pp. 223-263
    • Cheng, V.C.C.1    To, K.K.W.2    Tse, H.3    Hung, I.F.N.4    Yuen, K.Y.5
  • 3
    • 0019119577 scopus 로고
    • A revision of the system of nomenclature for influenza viruses: A WHO memorandum
    • Memorandums, M. L. A revision of the system of nomenclature for influenza viruses: a WHO memorandum Bull. W. H. O. 1980, 58, 585-591
    • (1980) Bull. W. H. O. , vol.58 , pp. 585-591
    • Memorandums, M.L.1
  • 4
    • 36749056771 scopus 로고    scopus 로고
    • The war against influenza: Discovery and development of sialidase inhibitors
    • Von Itzstein, M. The war against influenza: discovery and development of sialidase inhibitors Nat. Rev. Drug Discovery 2007, 6, 967-974
    • (2007) Nat. Rev. Drug Discovery , vol.6 , pp. 967-974
    • Von Itzstein, M.1
  • 5
    • 55249083577 scopus 로고    scopus 로고
    • Structural characterization of the 1918 influenza virus H1N1 neuraminidase
    • Xu, X.; Zhu, X.; Dwek, R. A.; Stevens, J.; Wilson, I. A. Structural characterization of the 1918 influenza virus H1N1 neuraminidase J. Virol. 2008, 82, 10493-10501
    • (2008) J. Virol. , vol.82 , pp. 10493-10501
    • Xu, X.1    Zhu, X.2    Dwek, R.A.3    Stevens, J.4    Wilson, I.A.5
  • 6
    • 0033897803 scopus 로고    scopus 로고
    • Resistance of influenza viruses to neuraminidase inhibitors-a review
    • McKimm-Breschkin, J. L. Resistance of influenza viruses to neuraminidase inhibitors-a review Antiviral Res. 2000, 47, 1-17
    • (2000) Antiviral Res. , vol.47 , pp. 1-17
    • McKimm-Breschkin, J.L.1
  • 8
    • 46849105028 scopus 로고    scopus 로고
    • Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase
    • Cheng, L. S.; Amaro, R. E.; Xu, D.; Li, W. W.; Arzberger, P. W.; McCammon, J. A. Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase J. Med. Chem. 2008, 51, 3878-3894
    • (2008) J. Med. Chem. , vol.51 , pp. 3878-3894
    • Cheng, L.S.1    Amaro, R.E.2    Xu, D.3    Li, W.W.4    Arzberger, P.W.5    McCammon, J.A.6
  • 9
  • 12
    • 0034084227 scopus 로고    scopus 로고
    • Discovery and Development of GS 4104 (oseltamivir) An Orally Active Influenza Neuraminidase Inhibitor
    • Lew, W.; Chen, X.; Kim, C. U. Discovery and Development of GS 4104 (oseltamivir) An Orally Active Influenza Neuraminidase Inhibitor Curr. Med. Chem. 2000, 7, 663-672
    • (2000) Curr. Med. Chem. , vol.7 , pp. 663-672
    • Lew, W.1    Chen, X.2    Kim, C.U.3
  • 13
    • 0032710055 scopus 로고    scopus 로고
    • Zanamivir: A review of its use in influenza
    • Dunn, C. J.; Goa, K. L. Zanamivir: a review of its use in influenza Drugs 1999, 58, 761-784
    • (1999) Drugs , vol.58 , pp. 761-784
    • Dunn, C.J.1    Goa, K.L.2
  • 14
    • 77953267929 scopus 로고    scopus 로고
    • In silico identification of the potential drug resistance sites over 2009 influenza A (H1N1) virus neuraminidase
    • Liu, H.; Yao, X.; Wang, C.; Han, J. In silico identification of the potential drug resistance sites over 2009 influenza A (H1N1) virus neuraminidase Mol. Pharmaceutics 2010, 7, 894-904
    • (2010) Mol. Pharmaceutics , vol.7 , pp. 894-904
    • Liu, H.1    Yao, X.2    Wang, C.3    Han, J.4
  • 15
    • 75549083531 scopus 로고    scopus 로고
    • Homology modeling, docking, and molecular dynamics reveal HR1039 as a potent inhibitor of 2009 A (H1N1) influenza neuraminidase
    • Wang, Y. T.; Chan, C.; Su, Z. Y.; Chen, C. L. Homology modeling, docking, and molecular dynamics reveal HR1039 as a potent inhibitor of 2009 A (H1N1) influenza neuraminidase Biophys. Chem. 2010, 147, 74-80
    • (2010) Biophys. Chem. , vol.147 , pp. 74-80
    • Wang, Y.T.1    Chan, C.2    Su, Z.Y.3    Chen, C.L.4
  • 16
    • 36048996081 scopus 로고    scopus 로고
    • Neuraminidase inhibitor-resistant recombinant A/Vietnam/1203/04 (H5N1) influenza viruses retain their replication efficiency and pathogenicity in vitro and in vivo
    • Yen, H. L.; Ilyushina, N. A.; Salomon, R.; Hoffmann, E.; Webster, R. G.; Govorkova, E. A. Neuraminidase inhibitor-resistant recombinant A/Vietnam/1203/04 (H5N1) influenza viruses retain their replication efficiency and pathogenicity in vitro and in vivo J. Virol. 2007, 81, 12418-12426
    • (2007) J. Virol. , vol.81 , pp. 12418-12426
    • Yen, H.L.1    Ilyushina, N.A.2    Salomon, R.3    Hoffmann, E.4    Webster, R.G.5    Govorkova, E.A.6
  • 19
    • 0035865919 scopus 로고    scopus 로고
    • Selection of influenza virus mutants in experimentally infected volunteers treated with oseltamivir
    • Gubareva, L. V.; Kaiser, L.; Matrosovich, M. N.; Soo-Hoo, Y.; Hayden, F. G. Selection of influenza virus mutants in experimentally infected volunteers treated with oseltamivir J. Infect. Dis. 2001, 183, 523-531
    • (2001) J. Infect. Dis. , vol.183 , pp. 523-531
    • Gubareva, L.V.1    Kaiser, L.2    Matrosovich, M.N.3    Soo-Hoo, Y.4    Hayden, F.G.5
  • 23
    • 80255127591 scopus 로고    scopus 로고
    • Prediction of zanamivir efficiency over the possible 2009 Influenza A (H1N1) mutants by multiple molecular dynamics simulations and free energy calculations
    • Pan, D.; Sun, H.; Bai, C.; Shen, Y.; Jin, N.; Liu, H.; Yao, X. Prediction of zanamivir efficiency over the possible 2009 Influenza A (H1N1) mutants by multiple molecular dynamics simulations and free energy calculations J. Mol. Model. 2011, 17, 2465-2473
    • (2011) J. Mol. Model. , vol.17 , pp. 2465-2473
    • Pan, D.1    Sun, H.2    Bai, C.3    Shen, Y.4    Jin, N.5    Liu, H.6    Yao, X.7
  • 24
  • 27
    • 0346996361 scopus 로고    scopus 로고
    • Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations
    • Masukawa, K. M.; Kollman, P. A.; Kuntz, I. D. Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations J. Med. Chem. 2003, 46, 5628-5637
    • (2003) J. Med. Chem. , vol.46 , pp. 5628-5637
    • Masukawa, K.M.1    Kollman, P.A.2    Kuntz, I.D.3
  • 28
    • 65249136476 scopus 로고    scopus 로고
    • Independent-trajectories thermodynamic-integration free-energy changes for biomolecular systems: Determinants of H5N1 avian influenza virus neuraminidase inhibition by peramivir
    • Lawrenz, M.; Baron, R.; McCammon, J. A. Independent-trajectories thermodynamic-integration free-energy changes for biomolecular systems: Determinants of H5N1 avian influenza virus neuraminidase inhibition by peramivir J. Chem. Theory Comput. 2009, 5, 1106-1116
    • (2009) J. Chem. Theory Comput. , vol.5 , pp. 1106-1116
    • Lawrenz, M.1    Baron, R.2    McCammon, J.A.3
  • 29
    • 79954432061 scopus 로고    scopus 로고
    • Molecular dynamics simulation of oseltamivir resistance in neuraminidase of avian influenza H5N1 virus
    • Shu, M.; Lin, Z.; Zhang, Y.; Wu, Y.; Mei, H.; Jiang, Y. Molecular dynamics simulation of oseltamivir resistance in neuraminidase of avian influenza H5N1 virus J. Mol. Model. 2011, 17, 587-592
    • (2011) J. Mol. Model. , vol.17 , pp. 587-592
    • Shu, M.1    Lin, Z.2    Zhang, Y.3    Wu, Y.4    Mei, H.5    Jiang, Y.6
  • 30
    • 38549150173 scopus 로고    scopus 로고
    • Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble
    • Landon, M. R.; Amaro, R. E.; Baron, R.; Ngan, C. H.; Ozonoff, D.; Andrew McCammon, J.; Vajda, S. Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble Chem. Biol. Drug Des. 2008, 71, 106-116
    • (2008) Chem. Biol. Drug Des. , vol.71 , pp. 106-116
    • Landon, M.R.1    Amaro, R.E.2    Baron, R.3    Ngan, C.H.4    Ozonoff, D.5    Andrew McCammon, J.6    Vajda, S.7
  • 31
    • 84861657255 scopus 로고    scopus 로고
    • Mutation-Induced Loop Opening and Energetics for Binding of Tamiflu to Influenza N8 Neuraminidase
    • Kar, P.; Knecht, V. Mutation-Induced Loop Opening and Energetics for Binding of Tamiflu to Influenza N8 Neuraminidase J. Phys. Chem. B. 2012, 116, 6137-6149
    • (2012) J. Phys. Chem. B. , vol.116 , pp. 6137-6149
    • Kar, P.1    Knecht, V.2
  • 32
    • 76549102880 scopus 로고    scopus 로고
    • Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance
    • Zhang, J.; Hou, T.; Wang, W.; Liu, J. S. Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 1321-1326
    • (2010) Proc. Natl. Acad. Sci. U. S. A. , vol.107 , pp. 1321-1326
    • Zhang, J.1    Hou, T.2    Wang, W.3    Liu, J.S.4
  • 33
    • 67949124553 scopus 로고    scopus 로고
    • Characterizing loop dynamics and ligand recognition in human-and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations
    • Amaro, R. E.; Cheng, X.; Ivanov, I.; Xu, D.; McCammon, J. A. Characterizing loop dynamics and ligand recognition in human-and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations J. Am. Chem. Soc. 2009, 131, 4702-4709
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 4702-4709
    • Amaro, R.E.1    Cheng, X.2    Ivanov, I.3    Xu, D.4    McCammon, J.A.5
  • 34
    • 34347230817 scopus 로고    scopus 로고
    • Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design
    • Amaro, R. E.; Minh, D. D. L.; Cheng, L. S.; Lindstrom, W. M., Jr; Olson, A. J.; Lin, J. H.; Li, W. W.; McCammon, J. A. Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design J. Am. Chem. Soc. 2007, 129, 7764-7765
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 7764-7765
    • Amaro, R.E.1    Minh, D.D.L.2    Cheng, L.S.3    Olson, A.J.4    Lin, J.H.5    Li, W.W.6    McCammon, J.A.7
  • 35
    • 19744364217 scopus 로고    scopus 로고
    • The molecular basis of resilience to the effect of the Lys103Asn mutation in non-nucleoside HIV-1 reverse transcriptase inhibitors studied by targeted molecular dynamics simulations
    • Rodríguez-Barrios, F.; Balzarini, J.; Gago, F. The molecular basis of resilience to the effect of the Lys103Asn mutation in non-nucleoside HIV-1 reverse transcriptase inhibitors studied by targeted molecular dynamics simulations J. Am. Chem. Soc. 2005, 127, 7570-7578
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 7570-7578
    • Rodríguez-Barrios, F.1    Balzarini, J.2    Gago, F.3
  • 36
    • 33947644064 scopus 로고    scopus 로고
    • Molecular dynamics and free energy studies on the wild-type and double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related inhibitors: Mechanism for binding and drug resistance
    • Hou, T.; Yu, R. Molecular dynamics and free energy studies on the wild-type and double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related inhibitors: mechanism for binding and drug resistance J. Med. Chem. 2007, 50, 1177-1188
    • (2007) J. Med. Chem. , vol.50 , pp. 1177-1188
    • Hou, T.1    Yu, R.2
  • 37
    • 42449147045 scopus 로고    scopus 로고
    • Evaluating the potency of HIV-1 protease drugs to combat resistance
    • Hou, T.; McLaughlin, W. A.; Wang, W. Evaluating the potency of HIV-1 protease drugs to combat resistance Proteins: Struct., Funct., Bioinf. 2008, 71, 1163-1174
    • (2008) Proteins: Struct., Funct., Bioinf. , vol.71 , pp. 1163-1174
    • Hou, T.1    McLaughlin, W.A.2    Wang, W.3
  • 38
    • 57749118013 scopus 로고    scopus 로고
    • Origins of resistance conferred by the R292K neuraminidase mutation via molecular dynamics and free energy calculations
    • Chachra, R.; Rizzo, R. C. Origins of resistance conferred by the R292K neuraminidase mutation via molecular dynamics and free energy calculations J. Chem. Theory Comput. 2008, 4, 1526-1540
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 1526-1540
    • Chachra, R.1    Rizzo, R.C.2
  • 39
    • 0037339235 scopus 로고    scopus 로고
    • Molecular dynamics studies of the wild-type and double mutant HIV-1 integrase complexed with the 5CITEP inhibitor: Mechanism for inhibition and drug resistance
    • Barreca, M. L.; Lee, K. W.; Chimirri, A.; Briggs, J. M. Molecular dynamics studies of the wild-type and double mutant HIV-1 integrase complexed with the 5CITEP inhibitor: mechanism for inhibition and drug resistance Biophys. J. 2003, 84, 1450-1463
    • (2003) Biophys. J. , vol.84 , pp. 1450-1463
    • Barreca, M.L.1    Lee, K.W.2    Chimirri, A.3    Briggs, J.M.4
  • 40
    • 61449101624 scopus 로고    scopus 로고
    • Predicting drug resistance of the HIV-1 protease using molecular interaction energy components
    • Hou, T.; Zhang, W.; Wang, J.; Wang, W. Predicting drug resistance of the HIV-1 protease using molecular interaction energy components Proteins: Struct., Funct., Bioinf. 2009, 74, 837-846
    • (2009) Proteins: Struct., Funct., Bioinf. , vol.74 , pp. 837-846
    • Hou, T.1    Zhang, W.2    Wang, J.3    Wang, W.4
  • 41
    • 84863653124 scopus 로고    scopus 로고
    • Understanding the effect of drug-resistant mutations of HIV-1 intasome on raltegravir action through molecular modeling study
    • Xue, W. W.; Qi, J.; Yang, Y.; Jin, X. J.; Liu, H. X.; Yao, X. J. Understanding the effect of drug-resistant mutations of HIV-1 intasome on raltegravir action through molecular modeling study Mol. Biosyst. 2012, 8, 2135-2144
    • (2012) Mol. Biosyst. , vol.8 , pp. 2135-2144
    • Xue, W.W.1    Qi, J.2    Yang, Y.3    Jin, X.J.4    Liu, H.X.5    Yao, X.J.6
  • 42
    • 84355166397 scopus 로고    scopus 로고
    • Molecular modeling study on the resistance mechanism of HCV NS3/4A serine protease mutants R155K, A156V and D168A to TMC435
    • Xue, W. W.; Pan, D. B.; Yang, Y.; Liu, H. X.; Yao, X. J. Molecular modeling study on the resistance mechanism of HCV NS3/4A serine protease mutants R155K, A156V and D168A to TMC435 Antiviral Res. 2012, 93, 126-137
    • (2012) Antiviral Res. , vol.93 , pp. 126-137
    • Xue, W.W.1    Pan, D.B.2    Yang, Y.3    Liu, H.X.4    Yao, X.J.5
  • 43
    • 84862832804 scopus 로고    scopus 로고
    • Exploring the molecular basis of dsRNA recognition by NS1 protein of influenza A virus using molecular dynamics simulation and free energy calculation
    • Pan, D. B.; Sun, H. J.; Shen, Y. L.; Liu, H. X.; Yao, X. J. Exploring the molecular basis of dsRNA recognition by NS1 protein of influenza A virus using molecular dynamics simulation and free energy calculation Antiviral Res. 2011, 92, 424-433
    • (2011) Antiviral Res. , vol.92 , pp. 424-433
    • Pan, D.B.1    Sun, H.J.2    Shen, Y.L.3    Liu, H.X.4    Yao, X.J.5
  • 44
    • 84861625628 scopus 로고    scopus 로고
    • Long Time Scale GPU Dynamics Reveal the Mechanism of Drug Resistance of the Dual Mutant I223R/H275Y Neuraminidase from H1N1-2009 Influenza Virus
    • Woods, C. J.; Malaisree, M.; Pattarapongdilok, N.; Sompornpisut, P.; Hannongbua, S.; Mulholland, A. J. Long Time Scale GPU Dynamics Reveal the Mechanism of Drug Resistance of the Dual Mutant I223R/H275Y Neuraminidase from H1N1-2009 Influenza Virus Biochemistry 2012, 51, 4364-4375
    • (2012) Biochemistry , vol.51 , pp. 4364-4375
    • Woods, C.J.1    Malaisree, M.2    Pattarapongdilok, N.3    Sompornpisut, P.4    Hannongbua, S.5    Mulholland, A.J.6
  • 45
    • 84867792168 scopus 로고    scopus 로고
    • Exploring the Cause of Oseltamivir Resistance Against Mutant H274Y Neuraminidase by Molecular Simulation Approach
    • Karthick, V.; Shanthi, V.; Rajasekaran, R.; Ramanathan, K. Exploring the Cause of Oseltamivir Resistance Against Mutant H274Y Neuraminidase by Molecular Simulation Approach J. Phys. Chem. B 2012, 1-13
    • (2012) J. Phys. Chem. B , pp. 1-13
    • Karthick, V.1    Shanthi, V.2    Rajasekaran, R.3    Ramanathan, K.4
  • 46
    • 70350510084 scopus 로고    scopus 로고
    • Dynamic behavior of avian influenza a virus neuraminidase subtype H5N1 in complex with oseltamivir, zanamivir, peramivir, and their phosphonate analogues
    • Udommaneethanakit, T.; Rungrotmongkol, T.; Bren, U.; Frecer, V.; Stanislav, M. Dynamic behavior of avian influenza a virus neuraminidase subtype H5N1 in complex with oseltamivir, zanamivir, peramivir, and their phosphonate analogues J. Chem. Inf. Model. 2009, 49, 2323-2332
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 2323-2332
    • Udommaneethanakit, T.1    Rungrotmongkol, T.2    Bren, U.3    Frecer, V.4    Stanislav, M.5
  • 47
    • 63449087331 scopus 로고    scopus 로고
    • Computational studies of H5N1 influenza virus resistance to oseltamivir
    • Wang, N. X.; Zheng, J. J. Computational studies of H5N1 influenza virus resistance to oseltamivir Protein Sci. 2009, 18, 707-715
    • (2009) Protein Sci. , vol.18 , pp. 707-715
    • Wang, N.X.1    Zheng, J.J.2
  • 48
    • 80053300058 scopus 로고    scopus 로고
    • Study of Tamiflu Sensitivity to Variants of A/H5N1 Virus Using Different Force Fields
    • Li, M. S.; Nguyen, T. T.; Mai, B. K. Study of Tamiflu Sensitivity to Variants of A/H5N1 Virus Using Different Force Fields J. Chem. Inf. Model. 2011, 51, 2266-2276
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 2266-2276
    • Li, M.S.1    Nguyen, T.T.2    Mai, B.K.3
  • 49
    • 77958551314 scopus 로고    scopus 로고
    • Correlation Analyses on Binding Affinity of Sialic Acid Analogues with Influenza Virus Neuraminidase-1 Using ab Initio MO Calculations on Their Complex Structures
    • Hitaoka, S.; Harada, M.; Yoshida, T.; Chuman, H. Correlation Analyses on Binding Affinity of Sialic Acid Analogues with Influenza Virus Neuraminidase-1 Using ab Initio MO Calculations on Their Complex Structures J. Chem. Inf. Model. 2010, 50, 1796-1805
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 1796-1805
    • Hitaoka, S.1    Harada, M.2    Yoshida, T.3    Chuman, H.4
  • 50
    • 73349096620 scopus 로고    scopus 로고
    • Infiltration of water molecules into the oseltamivir-binding site of H274Y neuraminidase mutant causes resistance to oseltamivir
    • Park, J. W.; Jo, W. H. Infiltration of water molecules into the oseltamivir-binding site of H274Y neuraminidase mutant causes resistance to oseltamivir J. Chem. Inf. Model. 2009, 49, 2735-2741
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 2735-2741
    • Park, J.W.1    Jo, W.H.2
  • 51
    • 79951524535 scopus 로고    scopus 로고
    • Molecular prediction of oseltamivir efficiency against probable influenza A (H1N1-2009) mutants: Molecular modeling approach
    • Rungrotmongkol, T.; Malaisree, M.; Nunthaboot, N.; Sompornpisut, P.; Hannongbua, S. Molecular prediction of oseltamivir efficiency against probable influenza A (H1N1-2009) mutants: molecular modeling approach Amino Acids 2010, 39, 393-398
    • (2010) Amino Acids , vol.39 , pp. 393-398
    • Rungrotmongkol, T.1    Malaisree, M.2    Nunthaboot, N.3    Sompornpisut, P.4    Hannongbua, S.5
  • 52
    • 0036224125 scopus 로고    scopus 로고
    • Susceptibility of recent Canadian influenza A and B virus isolates to different neuraminidase inhibitors
    • Boivin, G.; Goyette, N. Susceptibility of recent Canadian influenza A and B virus isolates to different neuraminidase inhibitors Antiviral Res. 2002, 54, 143-147
    • (2002) Antiviral Res. , vol.54 , pp. 143-147
    • Boivin, G.1    Goyette, N.2
  • 53
    • 33748702675 scopus 로고    scopus 로고
    • Mutations conferring zanamivir resistance in human influenza virus N2 neuraminidases compromise virus fitness and are not stably maintained in vitro
    • Zürcher, T.; Yates, P. J.; Daly, J.; Sahasrabudhe, A.; Walters, M.; Dash, L.; Tisdale, M.; McKimm-Breschkin, J. L. Mutations conferring zanamivir resistance in human influenza virus N2 neuraminidases compromise virus fitness and are not stably maintained in vitro J. Antimicrob. Chemother. 2006, 58, 723-732
    • (2006) J. Antimicrob. Chemother. , vol.58 , pp. 723-732
    • Zürcher, T.1    Yates, P.J.2    Daly, J.3    Sahasrabudhe, A.4    Walters, M.5    Dash, L.6    Tisdale, M.7    McKimm-Breschkin, J.L.8
  • 54
    • 27644439501 scopus 로고    scopus 로고
    • Susceptibilities of antiviral-resistant influenza viruses to novel neuraminidase inhibitors
    • Mishin, V. P.; Hayden, F. G.; Gubareva, L. V. Susceptibilities of antiviral-resistant influenza viruses to novel neuraminidase inhibitors Antimicrob. Agents Chemother. 2005, 49, 4515-4520
    • (2005) Antimicrob. Agents Chemother. , vol.49 , pp. 4515-4520
    • Mishin, V.P.1    Hayden, F.G.2    Gubareva, L.V.3
  • 57
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt, K. D.; Tatusova, T.; Maglott, D. R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins Nucleic Acids Res. 2007, 35, D61-D65
    • (2007) Nucleic Acids Res. , vol.35
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 58
    • 84860626102 scopus 로고    scopus 로고
    • Accelrys Inc. San Diego, CA, (accessed Sept. 2012).
    • Discovery Studio 2.5 Guide; Accelrys Inc.: San Diego, CA, 2009. http://www.accelrys.com (accessed Sept. 2012).
    • (2009) Discovery Studio 2.5 Guide
  • 60
  • 61
    • 28644432877 scopus 로고    scopus 로고
    • Very fast empirical prediction and rationalization of protein pKa values
    • Li, H.; Robertson, A. D.; Jensen, J. H. Very fast empirical prediction and rationalization of protein pKa values Proteins 2005, 61, 704-721
    • (2005) Proteins , vol.61 , pp. 704-721
    • Li, H.1    Robertson, A.D.2    Jensen, J.H.3
  • 62
    • 0242663237 scopus 로고    scopus 로고
    • A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    • Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations J. Comput. Chem. 2003, 24, 1999-2012
    • (2003) J. Comput. Chem. , vol.24 , pp. 1999-2012
    • Duan, Y.1    Wu, C.2    Chowdhury, S.3    Lee, M.C.4    Xiong, G.5    Zhang, W.6    Yang, R.7    Cieplak, P.8    Luo, R.9    Lee, T.10
  • 65
    • 3042524904 scopus 로고
    • A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model
    • Bayly, C. I.; Cieplak, P.; Cornell, W.; Kollman, P. A. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model J. Phys. Chem. 1993, 97, 10269-10280
    • (1993) J. Phys. Chem. , vol.97 , pp. 10269-10280
    • Bayly, C.I.1    Cieplak, P.2    Cornell, W.3    Kollman, P.A.4
  • 66
    • 0344796204 scopus 로고
    • Ion Water Interaction Potentials Derived from Free-Energy Perturbation Simulations
    • Åqvist, J. Ion Water Interaction Potentials Derived from Free-Energy Perturbation Simulations J. Phys. Chem. 1990, 94, 8021-8024
    • (1990) J. Phys. Chem. , vol.94 , pp. 8021-8024
    • Åqvist, J.1
  • 70
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 1977, 23, 327-341
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 71
    • 0027321958 scopus 로고
    • Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches
    • Miyamoto, S.; Kollman, P. A. Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches Proteins 1993, 16, 226-245
    • (1993) Proteins , vol.16 , pp. 226-245
    • Miyamoto, S.1    Kollman, P.A.2
  • 72
    • 33748495575 scopus 로고    scopus 로고
    • Computational study of the binding affinity and selectivity of the bacterial ammonium transporter AmtB
    • Luzhkov, V. B.; Almlöf, M.; Nervall, M.; Åqvist, J. Computational study of the binding affinity and selectivity of the bacterial ammonium transporter AmtB Biochemistry 2006, 45, 10807-10814
    • (2006) Biochemistry , vol.45 , pp. 10807-10814
    • Luzhkov, V.B.1    Almlöf, M.2    Nervall, M.3    Åqvist, J.4
  • 73
    • 36849122972 scopus 로고
    • High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases
    • Zwanzig, R. W. High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases J. Chem. Phys. 1954, 22, 1420-1426
    • (1954) J. Chem. Phys. , vol.22 , pp. 1420-1426
    • Zwanzig, R.W.1
  • 74
    • 47749107217 scopus 로고    scopus 로고
    • Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria
    • Jorgensen, W. L.; Thomas, L. L. Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria J. Chem. Theory Comput. 2008, 4, 869-876
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 869-876
    • Jorgensen, W.L.1    Thomas, L.L.2
  • 75
    • 0037008160 scopus 로고    scopus 로고
    • Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors
    • Gohlke, H.; Klebe, G. Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors Angew. Chem., Int. Ed. 2002, 41, 2644-2676
    • (2002) Angew. Chem., Int. Ed. , vol.41 , pp. 2644-2676
    • Gohlke, H.1    Klebe, G.2
  • 76
    • 33646471468 scopus 로고
    • Statistical mechanics of fluid mixtures
    • Kirkwood, J. G. Statistical mechanics of fluid mixtures J. Chem. Phys. 1935, 3, 300
    • (1935) J. Chem. Phys. , vol.3 , pp. 300
    • Kirkwood, J.G.1
  • 77
    • 0032560959 scopus 로고    scopus 로고
    • Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices
    • Srinivasan, J.; Cheatham, T. E., III; Cieplak, P.; Kollman, P. A.; David, A. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices J. Am. Chem. Soc. 1998, 120, 9401-9409
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 9401-9409
    • Srinivasan, J.1    Cieplak, P.2    Kollman, P.A.3    David, A.4
  • 78
    • 0034521981 scopus 로고    scopus 로고
    • Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
    • Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models Acc. Chem. Res. 2000, 33, 889-897
    • (2000) Acc. Chem. Res. , vol.33 , pp. 889-897
    • Kollman, P.A.1    Massova, I.2    Reyes, C.3    Kuhn, B.4    Huo, S.5    Chong, L.6    Lee, M.7    Lee, T.8    Duan, Y.9    Wang, W.10
  • 79
    • 33748637571 scopus 로고    scopus 로고
    • Recent advances in free energy calculations with a combination of molecular mechanics and continuum models
    • Wang, J. M.; Hou, T. J.; Xu, X. J. Recent advances in free energy calculations with a combination of molecular mechanics and continuum models Curr. Comput.-Aided Drug Des. 2006, 2, 287-306
    • (2006) Curr. Comput.-Aided Drug Des. , vol.2 , pp. 287-306
    • Wang, J.M.1    Hou, T.J.2    Xu, X.J.3
  • 80
    • 84857282935 scopus 로고    scopus 로고
    • Free Energy Calculations by the Molecular Mechanics Poisson-Boltzmann Surface Area Method
    • Homeyer, N.; Gohlke, H. Free Energy Calculations by the Molecular Mechanics Poisson-Boltzmann Surface Area Method Mol. Inf. 2012, 31, 114-122
    • (2012) Mol. Inf. , vol.31 , pp. 114-122
    • Homeyer, N.1    Gohlke, H.2
  • 81
    • 79951996670 scopus 로고    scopus 로고
    • Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. the accuracy of ranking poses generated from docking
    • Hou, T. J.; Wang, J.; Li, Y. Y.; Wang, W. Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking J. Comput. Chem. 2011, 32, 866-877
    • (2011) J. Comput. Chem. , vol.32 , pp. 866-877
    • Hou, T.J.1    Wang, J.2    Li, Y.Y.3    Wang, W.4
  • 82
    • 79952588669 scopus 로고    scopus 로고
    • Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. the accuracy of binding free energy calculations based on molecular dynamics simulations
    • Hou, T. J.; Wang, J. M.; Li, Y. Y.; Wang, W. Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations J. Chem. Inf. Model. 2011, 51, 69-82
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 69-82
    • Hou, T.J.1    Wang, J.M.2    Li, Y.Y.3    Wang, W.4
  • 83
    • 67649518877 scopus 로고    scopus 로고
    • Binding free energy calculations of N-sulphonyl-glutamic acid inhibitors of MurD ligase
    • Perdih, A.; Bren, U.; Solmajer, T. Binding free energy calculations of N-sulphonyl-glutamic acid inhibitors of MurD ligase J. Mol. Model. 2009, 15, 983-996
    • (2009) J. Mol. Model. , vol.15 , pp. 983-996
    • Perdih, A.1    Bren, U.2    Solmajer, T.3
  • 84
    • 0026596911 scopus 로고
    • Calculations of antibody-antigen interactions: Microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603
    • Lee, F. S.; Chu, Z. T.; Bolger, M. B.; Warshel, A. Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603 Protein Eng. 1992, 5, 215-228
    • (1992) Protein Eng. , vol.5 , pp. 215-228
    • Lee, F.S.1    Chu, Z.T.2    Bolger, M.B.3    Warshel, A.4
  • 85
    • 77749279875 scopus 로고    scopus 로고
    • DNA duplex stability: The role of preorganized electrostatics
    • Bren, U.; Lah, J.; Bren, M.; Martinek, V.; Florian, J. DNA duplex stability: the role of preorganized electrostatics J. Phys. Chem. B 2010, 114, 2876-2885
    • (2010) J. Phys. Chem. B , vol.114 , pp. 2876-2885
    • Bren, U.1    Lah, J.2    Bren, M.3    Martinek, V.4    Florian, J.5
  • 86
    • 0035822178 scopus 로고    scopus 로고
    • Binding affinities for a series of selective inhibitors of gelatinase-A using molecular dynamics with a linear interaction energy approach
    • Hou, T. J.; Zhang, W.; Xu, X. J. Binding affinities for a series of selective inhibitors of gelatinase-A using molecular dynamics with a linear interaction energy approach J. Phys. Chem. B 2001, 105, 5304-5315
    • (2001) J. Phys. Chem. B , vol.105 , pp. 5304-5315
    • Hou, T.J.1    Zhang, W.2    Xu, X.J.3
  • 87
    • 1842611470 scopus 로고    scopus 로고
    • Molecular dynamics and free energy analysis of neuraminidase-ligand interactions
    • Bonnet, P.; Bryce, R. A. Molecular dynamics and free energy analysis of neuraminidase-ligand interactions Protein Sci. 2004, 13, 946-957
    • (2004) Protein Sci. , vol.13 , pp. 946-957
    • Bonnet, P.1    Bryce, R.A.2
  • 88
    • 0036771626 scopus 로고    scopus 로고
    • Accelerated Poisson-Boltzmann calculations for static and dynamic systems
    • Luo, R.; David, L.; Gilson, M. K. Accelerated Poisson-Boltzmann calculations for static and dynamic systems J. Comput. Chem. 2002, 23, 1244-1253
    • (2002) J. Comput. Chem. , vol.23 , pp. 1244-1253
    • Luo, R.1    David, L.2    Gilson, M.K.3
  • 90
    • 0030044141 scopus 로고    scopus 로고
    • A study of the active site of influenza virus sialidase: An approach to the rational design of novel anti-influenza drugs
    • von Itzstein, M.; Dyason, J. C.; Oliver, S. W.; White, H. F.; Wu, W. Y.; Kok, G. B.; Pegg, M. S. A study of the active site of influenza virus sialidase: an approach to the rational design of novel anti-influenza drugs J. Med. Chem. 1996, 39, 388-391
    • (1996) J. Med. Chem. , vol.39 , pp. 388-391
    • Von Itzstein, M.1    Dyason, J.C.2    Oliver, S.W.3    White, H.F.4    Wu, W.Y.5    Kok, G.B.6    Pegg, M.S.7
  • 92
    • 33746508990 scopus 로고    scopus 로고
    • Decomposition of the solvation free energies of deoxyribonucleoside triphosphates using the free energy perturbation method
    • Bren, U.; Martínek, V.; Florián, J. Decomposition of the solvation free energies of deoxyribonucleoside triphosphates using the free energy perturbation method J. Phys. Chem. B 2006, 110, 12782-12788
    • (2006) J. Phys. Chem. B , vol.110 , pp. 12782-12788
    • Bren, U.1    Martínek, V.2    Florián, J.3
  • 93
    • 33947495228 scopus 로고    scopus 로고
    • Do all pieces make a whole? Thiele cumulants and the free energy decomposition
    • Bren, M.; Florián, J.; Mavri, J.; Bren, U. Do all pieces make a whole? Thiele cumulants and the free energy decomposition Theor. Chem. Acc. 2007, 117, 535-540
    • (2007) Theor. Chem. Acc. , vol.117 , pp. 535-540
    • Bren, M.1    Florián, J.2    Mavri, J.3    Bren, U.4
  • 94
    • 84860635411 scopus 로고    scopus 로고
    • Characterization of Domain-peptide Interaction Interface: Prediction of SH3 Domain-Mediated Protein-protein Interaction Network in Yeast by Generic Structure-Based Models
    • Hou, T.; Li, N.; Li, Y.; Wang, W. Characterization of Domain-peptide Interaction Interface: Prediction of SH3 Domain-Mediated Protein-protein Interaction Network in Yeast by Generic Structure-Based Models J. Proteome Res. 2012, 11, 2982
    • (2012) J. Proteome Res. , vol.11 , pp. 2982
    • Hou, T.1    Li, N.2    Li, Y.3    Wang, W.4
  • 95
    • 0043245780 scopus 로고    scopus 로고
    • Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes
    • Gohlke, H.; Kiel, C.; Case, D. A. Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes J. Mol. Biol. 2003, 330, 891-913
    • (2003) J. Mol. Biol. , vol.330 , pp. 891-913
    • Gohlke, H.1    Kiel, C.2    Case, D.A.3
  • 96
    • 39049111013 scopus 로고    scopus 로고
    • Characterization of domain-peptide interaction interface: A case study on the amphiphysin-1 SH3 domain
    • Hou, T.; Zhang, W.; Case, D. A.; Wang, W. Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain J. Mol. Biol. 2008, 376, 1201-1214
    • (2008) J. Mol. Biol. , vol.376 , pp. 1201-1214
    • Hou, T.1    Zhang, W.2    Case, D.A.3    Wang, W.4
  • 98
    • 79959405623 scopus 로고    scopus 로고
    • Prediction of peptides binding to the PKA RII alpha subunit using a hierarchical strategy
    • Hou, T. J.; Li, Y. Y.; Wang, W. Prediction of peptides binding to the PKA RII alpha subunit using a hierarchical strategy Bioinformatics 2011, 27, 1814-1821
    • (2011) Bioinformatics , vol.27 , pp. 1814-1821
    • Hou, T.J.1    Li, Y.Y.2    Wang, W.3
  • 99
    • 20644449471 scopus 로고    scopus 로고
    • Modification of the generalized Born model suitable for macromolecules
    • Onufriev, A.; Bashford, D.; David, A. Modification of the generalized Born model suitable for macromolecules J. Phys. Chem. B 2000, 104, 3712-3720
    • (2000) J. Phys. Chem. B , vol.104 , pp. 3712-3720
    • Onufriev, A.1    Bashford, D.2    David, A.3
  • 100
    • 0020633096 scopus 로고
    • Structure of the catalytic and antigenic sites in influenza virus neuraminidase
    • Colman, P. M.; Varghese, J. N.; Laver, W. G. Structure of the catalytic and antigenic sites in influenza virus neuraminidase Nature 1983, 303, 41-44
    • (1983) Nature , vol.303 , pp. 41-44
    • Colman, P.M.1    Varghese, J.N.2    Laver, W.G.3
  • 102
    • 78049425866 scopus 로고    scopus 로고
    • Molecular dynamics simulations suggest that electrostatic funnel directs binding of Tamiflu to influenza N1 neuraminidases
    • Le, L.; Lee, E. H.; Hardy, D. J.; Truong, T. N.; Schulten, K. Molecular dynamics simulations suggest that electrostatic funnel directs binding of Tamiflu to influenza N1 neuraminidases Plos Comput. Biol. 2010, 6, e1000939
    • (2010) Plos Comput. Biol. , vol.6 , pp. 1000939
    • Le, L.1    Lee, E.H.2    Hardy, D.J.3    Truong, T.N.4    Schulten, K.5
  • 103
    • 29144433925 scopus 로고    scopus 로고
    • Oseltamivir resistance-disabling our influenza defenses
    • Moscona, A. Oseltamivir resistance-disabling our influenza defenses N. Engl. J. Med. 2005, 353, 2633-2636
    • (2005) N. Engl. J. Med. , vol.353 , pp. 2633-2636
    • Moscona, A.1
  • 105
    • 79851471047 scopus 로고    scopus 로고
    • Generation and Characterization of Recombinant Pandemic Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors
    • Pizzorno, A.; Bouhy, X.; Abed, Y.; Boivin, G. Generation and Characterization of Recombinant Pandemic Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors J. Infect. Dis. 2011, 203, 25-31
    • (2011) J. Infect. Dis. , vol.203 , pp. 25-31
    • Pizzorno, A.1    Bouhy, X.2    Abed, Y.3    Boivin, G.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.