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Volumn 15, Issue 4, 2011, Pages 979-987

Molecular dynamics directed CoMFA studies on carbocyclic neuraminidase inhibitors

Author keywords

Carbocyclic inhibitors; CoMFA; Molecular dynamics; Neuraminidase

Indexed keywords

SIALIDASE; SIALIDASE INHIBITOR; ZANAMIVIR;

EID: 84855250609     PISSN: 13811991     EISSN: 1573501X     Source Type: Journal    
DOI: 10.1007/s11030-011-9332-3     Document Type: Article
Times cited : (8)

References (34)
  • 1
    • 33751517736 scopus 로고    scopus 로고
    • Antiviral agents active against influenza A viruses
    • DOI 10.1038/nrd2175, PII NRD2175
    • De Clercq E (2006) Antiviral agents active against influenza A viruses. Nat Rev Drug Discov 5: 1015-1025. doi:10.1038/nrd2175 (Pubitemid 44835128)
    • (2006) Nature Reviews Drug Discovery , vol.5 , Issue.12 , pp. 1015-1025
    • De Clercq, E.1
  • 2
    • 0027930960 scopus 로고
    • Structure of influenza virus neuraminidase B/Lee/40 complexed with sialic acid and a dehydro analog at 1.8-A resolution: Implications for the catalytic mechanism
    • DOI 10.1021/bi00193a002
    • Janakiraman MN, White CL, Laver WG, Air GM, Luo M (1994) Structure of Influenza virus neuraminidase B/Lee/40 complexed with sialic acid and a dehydro analog at 1.8-. ANG. Resoluton: implications for the catalytic mechanism. Biochem 33: 8172-8179. doi:10.1021/bi00193a002 (Pubitemid 24241049)
    • (1994) Biochemistry , vol.33 , Issue.27 , pp. 8172-8179
    • Janakiraman, M.N.1    White, C.L.2    Laver, W.G.3    Air, G.M.4    Luo, M.5
  • 3
    • 0026755388 scopus 로고
    • Evidence for a sialosyl cation transition state complex in the reaction of sialidase from influenza virus
    • doi:10.1111/j. 1432-1033.1992.tb17055.x
    • Chong AKJ, Pegg MS, Taylor NR, Itzstein M (1992) Evidence for a sialosyl cation transition state complex in the reaction of sialidase from influenza virus. Eur J Biochem 207: 335-343. doi:10.1111/j. 1432-1033.1992.tb17055.x
    • (1992) Eur J Biochem , vol.207 , pp. 335-343
    • Chong, A.K.J.1    Pegg, M.S.2    Taylor, N.R.3    Itzstein, M.4
  • 4
    • 0028325249 scopus 로고
    • Molecular modeling studies on ligand binding to sialidase from influenza virus and the mechanism of catalysis
    • Taylor NR, ItzsteinM (1994) Molecular modeling studies on ligand binding to sialidase from influenza virus and the mechanism of catalysis. J Med Chem 37: 616-624. doi:10.1021/jm00031a011 (Pubitemid 24102181)
    • (1994) Journal of Medicinal Chemistry , vol.37 , Issue.5 , pp. 616-624
    • Taylor, N.R.1    Von Itzstein, M.2
  • 6
    • 0028013177 scopus 로고
    • Improved sensitivity of profile searches through the use of sequence weights and gap excision
    • Thompson JD, Higgins DG, Gibson TJ (1994) Improved sensitivity of profile searches through the use of sequence weights and gap excision. Comput Appl Biosci 10:19-29. doi:10.1093/bioinformatics/10.1.19 (Pubitemid 24066806)
    • (1994) Computer Applications in the Biosciences , vol.10 , Issue.1 , pp. 19-29
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 7
    • 55249083577 scopus 로고    scopus 로고
    • Structural characterization of the 1918 influenza virus H1N1 neuraminidase
    • DOI 10.1128/JVI.00959-08
    • Xu X, Zhu X, Dwek RA, Stevens J, Wilson IA (2008) Structural characterization of the 1918 influenza virus H1N1 neuraminidase. J Virol 82: 10493-10501. doi:10.1128/JVI.00959-08 (Pubitemid 352691147)
    • (2008) Journal of Virology , vol.82 , Issue.21 , pp. 10493-10501
    • Xu, X.1    Zhu, X.2    Dwek, R.A.3    Stevens, J.4    Wilson, I.A.5
  • 8
    • 0344595918 scopus 로고    scopus 로고
    • Methods for determining resistance to neuraminidase inhibitors
    • doi:10.1016/S0531-5131(01)00656-2
    • Tisdale M, Daly J, Gor D (2001) Methods for determining resistance to neuraminidase inhibitors. Int Congr Ser 1219: 879-886. doi:10.1016/S0531- 5131(01)00656-2
    • (2001) Int Congr ser , vol.1219 , pp. 879-886
    • Tisdale, M.1    Daly, J.2    Gor, D.3
  • 10
    • 56449084239 scopus 로고    scopus 로고
    • Design of multi-bindingsite inhibitors, ligand efficiency, and consensus screening of avian influenza H5N1 wild-type neuraminidase and of the oseltamivirresistantH274Y variant
    • doi:10. 1021/ci800242z
    • Garcia-Sosa AT, Sild S, Maran U (2008) Design of multi-bindingsite inhibitors, ligand efficiency, and consensus screening of avian influenza H5N1 wild-type neuraminidase and of the oseltamivirresistantH274Y variant. J Chem Inf Model 48: 2074-2080. doi:10. 1021/ci800242z
    • (2008) J Chem Inf Model , vol.48 , pp. 2074-2080
    • Garcia-Sosa, A.T.1    Sild, S.2    Maran, U.3
  • 11
    • 34548261773 scopus 로고    scopus 로고
    • Analogue inhibitors by modifying oseltamivir based on the crystal neuraminidase structure for treating drug-resistant H5N1 virus
    • DOI 10.1016/j.bbrc.2007.08.025, PII S0006291X07017317
    • Du QS, Wang SQ, Chou KC (2007) Analogue inhibitors by modifying oseltamivir based on the crystal neuraminidase structure for treating drug-resistant H5N1 virus. Biochem Biophys Res Commun 362: 525-531. doi:10.1016/j.bbrc.2007.08.025 (Pubitemid 47332441)
    • (2007) Biochemical and Biophysical Research Communications , vol.362 , Issue.2 , pp. 525-531
    • Du, Q.-S.1    Wang, S.-Q.2    Chou, K.-C.3
  • 13
    • 33748437791 scopus 로고    scopus 로고
    • The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design
    • DOI 10.1038/nature05114, PII NATURE05114
    • 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. Nat 443: 45-49. doi:10.1038/nature05114 (Pubitemid 44344043)
    • (2006) Nature , vol.443 , Issue.7107 , pp. 45-49
    • Russell, R.J.1    Haire, L.F.2    Stevens, D.J.3    Collins, P.J.4    Lin, Y.P.5    Blackburn, G.M.6    Hay, A.J.7    Gamblin, S.J.8    Skehel, J.J.9
  • 14
    • 0023751431 scopus 로고
    • Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins
    • doi:10.1021/ja00226a005
    • Cramer RD III, Patterson DE, Bunce JD (1988) Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J Am Chem Soc 110: 5959-5967. doi:10.1021/ja00226a005
    • (1988) J Am Chem Soc , vol.110 , pp. 5959-5967
    • Cramer Iii, R.D.1    Patterson, D.E.2    Bunce, J.D.3
  • 15
    • 0027762073 scopus 로고
    • Three-dimensional QSAR of human immunodeficiency virus (I) protease inhibitors. 1. A CoMFA study employing experimentally-determined alignment rules
    • Waller CL, Oprea TI, Giolitti A, Marshall GR (1993) Threedimensional QSAR of human immunodeficiency virus (I) protease inhibitors. 1. A CoMFA study employing experimentally-determined alignment rules. J Med Chem 36: 4152-4160. doi:10.1021/jm00078a003 (Pubitemid 24037924)
    • (1993) Journal of Medicinal Chemistry , vol.36 , Issue.26 , pp. 4152-4160
    • Waller, C.I.1    Oprea, T.I.2    Giolitti, A.3    Marshall, G.R.4
  • 16
    • 66149088374 scopus 로고    scopus 로고
    • Structure-based CoMFA as a predictive model-CYP2C9 inhibitors as a test case
    • doi:10. 1021/ci800313h
    • Yasuo K, Yamaotsu N, Gouda H, Tsujishita H, Hirono S (2009) Structure-based CoMFA as a predictive model-CYP2C9 inhibitors as a test case. J Chem Inf Model 49: 853-864. doi:10. 1021/ci800313h
    • (2009) J Chem Inf Model , vol.49 , pp. 853-864
    • Yasuo, K.1    Yamaotsu, N.2    Gouda, H.3    Tsujishita, H.4    Hirono, S.5
  • 19
    • 2942532422 scopus 로고    scopus 로고
    • Development and testing of a general amber force field
    • doi:10.1002/jcc.20035
    • Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 25: 1157-1174. doi:10.1002/jcc.20035
    • (2004) J Comput Chem , vol.25 , pp. 1157-1174
    • Wang, J.1    Wolf, R.M.2    Caldwell, J.W.3    Kollman, P.A.4    Case, D.A.5
  • 20
    • 33748538349 scopus 로고    scopus 로고
    • Automatic atom type and bond type perception in molecular mechanical calculations
    • DOI 10.1016/j.jmgm.2005.12.005, PII S1093326305001737
    • Wang J, Wang W, Kollman PA, Case DA (2006) Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graph Model 25: 247-260. doi:10.1016/j.jmgm.2005. 12.005 (Pubitemid 44363172)
    • (2006) Journal of Molecular Graphics and Modelling , vol.25 , Issue.2 , pp. 247-260
    • Wang, J.1    Wang, W.2    Kollman, P.A.3    Case, D.A.4
  • 21
    • 0141704162 scopus 로고    scopus 로고
    • Free energy landscape of protein folding in water: Explicit vs. implicit solvent
    • DOI 10.1002/prot.10483
    • Zhou R (2003) Free energy landscape of protein folding in water: explicit vs. implicit solvent. Proteins Struct Funct Genet 53: 148-161. doi:10.1002/prot.10483 (Pubitemid 37193811)
    • (2003) Proteins: Structure, Function and Genetics , vol.53 , Issue.2 , pp. 148-161
    • Zhou, R.1
  • 22
    • 9244224092 scopus 로고    scopus 로고
    • An efficient hybrid explicit/implicit solvent method for biomolecular simulations
    • doi:10.1002/jcc.20119
    • Lee MS, Salsbury FR Jr, Olson MA (2004) An efficient hybrid explicit/implicit solvent method for biomolecular simulations. J Comput Chem 25: 1967-1978. doi:10.1002/jcc.20119
    • (2004) J Comput Chem , vol.25 , pp. 1967-1978
    • Lee, M.S.1    Salsbury Jr., F.R.2    Olson, M.A.3
  • 23
    • 0029170114 scopus 로고
    • Molecular dynamics simulations on solvated biomolecular systems: The particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins
    • doi:10.1021/ja00119a045
    • Cheatham TE III, Miller JL, Fox T, Darden TA, Kollman PA (1995) Molecular dynamics simulations on solvated biomolecular systems: the particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins. J AmChem Soc 117: 4193-4194. doi:10.1021/ja00119a045
    • (1995) J AmChem Soc , vol.117 , pp. 4193-4194
    • Cheatham Iii, T.E.1    Miller, J.L.2    Fox, T.3    Darden, T.A.4    Kollman, P.A.5
  • 24
    • 0004016501 scopus 로고
    • Comparison of simple potential functions for simulating liquid water
    • doi:10.1063/1.445869
    • Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926. doi:10.1063/1.445869
    • (1983) J Chem Phys , vol.79 , pp. 926
    • Jorgensen, W.L.1    Chandrasekhar, J.2    Madura, J.D.3    Impey, R.W.4    Klein, M.L.5
  • 25
    • 0346996361 scopus 로고    scopus 로고
    • Investigation of Neuraminidase-Substrate Recognition Using Molecular Dynamics and Free Energy Calculations
    • DOI 10.1021/jm030060q
    • Masukawa KM, Kollman PA, Kuntz ID (2003) Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations. J Med Chem 46: 5628-5637. doi:10. 1021/jm030060q (Pubitemid 37543314)
    • (2003) Journal of Medicinal Chemistry , vol.46 , Issue.26 , pp. 5628-5637
    • Masukawa, K.M.1    Kollman, P.A.2    Kuntz, I.D.3
  • 28
    • 0028924311 scopus 로고
    • Three-dimensional quantitative structure- activity relationship (QSAR) of HIV integrase inhibitors: A comparativemolecular field analysis (CoMFA) study
    • doi:10.1021/jm00006a006
    • Raghavan K, Buolamwini JK, Fesen MR, Pommier Y, Kohn KW, Weinstein JN (1995) Three-dimensional quantitative structure- activity relationship (QSAR) of HIV integrase inhibitors: a comparativemolecular field analysis (CoMFA) study. J Med Chem 38: 890-897. doi:10.1021/jm00006a006
    • (1995) J Med Chem , vol.38 , pp. 890-897
    • Raghavan, K.1    Buolamwini, J.K.2    Fesen, M.R.3    Pommier, Y.4    Kohn, K.W.5    Weinstein, J.N.6
  • 29
    • 84988115618 scopus 로고
    • Validation of the general purpose Tripos 5.2 force field
    • doi:10.1002/jcc.540100804
    • Clark M, Cramer RD III, Van Opdenbosch N (1989) Validation of the general purpose Tripos 5.2 force field. J Comput Chem 10: 982-1012. doi:10.1002/jcc.540100804
    • (1989) J Comput Chem , vol.10 , pp. 982-1012
    • Clark, M.1    Cramer Iii, R.D.2    Van Opdenbosch, N.3
  • 30
    • 84987100711 scopus 로고
    • Crossvalidation, bootstrapping, and partial least squares compared with multiple regression in conventional QSAR studies
    • doi:10.1002/qsar.19880070105
    • Cramer RD III, Bunce JD, Patterson DE, Frank IE (1988) Crossvalidation, bootstrapping, and partial least squares compared with multiple regression in conventional QSAR studies. Quant Struct Act Relatsh 7: 18-25. doi:10.1002/qsar.19880070105
    • (1988) Quant Struct Act Relatsh , vol.7 , pp. 18-25
    • Cramer Iii, R.D.1    Bunce, J.D.2    Patterson, D.E.3    Frank, I.E.4
  • 31
    • 77954670462 scopus 로고    scopus 로고
    • A combined LS-SVM & MLR QSAR workflow for predicting the inhibition of CXCR3 receptor by quinazolinone analogs
    • doi:10.1007/s11030-009-9163-7
    • Afantitis A, Melagraki G, Sarimveis H, Koutentis PA, Igglessi-Markopoulou O, Kollias G (2009) A combined LS-SVM & MLR QSAR workflow for predicting the inhibition of CXCR3 receptor by quinazolinone analogs. Mol Divers 14: 225-235. doi:10.1007/s11030-009-9163-7
    • (2009) Mol Divers , vol.14 , pp. 225-235
    • Afantitis, A.1    Melagraki, G.2    Sarimveis, H.3    Koutentis, P.A.4    Igglessi-Markopoulou, O.5    Kollias, G.6
  • 33
    • 2142758637 scopus 로고    scopus 로고
    • 3D-QSAR studies of pyruvate dehydrogenase kinase inhibitors based on a divide and conquer strategy
    • DOI 10.1016/j.bmc.2004.03.019, PII S0968089604001956
    • Aboye TL, SobhiaME, Bharatam PV (2004) 3D-QSAR studies of pyruvate dehydrogenase kinase inhibitors based on a divide and conquer strategy* 1. Bioorg Med Chem 12: 2709-2715. doi:10. 1016/j.bmc.2004.03.019 (Pubitemid 38542795)
    • (2004) Bioorganic and Medicinal Chemistry , vol.12 , Issue.10 , pp. 2709-2715
    • Aboye, T.L.1    Sobhia, M.E.2    Bharatam, P.V.3
  • 34
    • 35548943518 scopus 로고    scopus 로고
    • QSAR analyses on avian influenza virus neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR
    • DOI 10.1007/s10822-006-9080-0
    • Zheng M, Yu K, Liu H, Luo X, Chen K, Zhu W, Jiang H (2006) QSAR analyses on avian influenza virus neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR. J Comput Aided Mol Des 20: 549-566. doi:10.1007/s10822-006-9080-0 (Pubitemid 44823891)
    • (2006) Journal of Computer-Aided Molecular Design , vol.20 , Issue.9 , pp. 549-566
    • Zheng, M.1    Yu, K.2    Liu, H.3    Luo, X.4    Chen, K.5    Zhu, W.6    Jiang, H.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.