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Volumn 6, Issue 2, 2002, Pages 251-260

Comparative study of some energetic and steric parameters of the wild type and mutants HIV-1 protease: A way to explain the viral resistance

Author keywords

Complex representation; Genetic code; Genomic signals; Genomics; Phase analysis; Sequence path; Unwrapped phase

Indexed keywords

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 0036550078     PISSN: 15821838     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1582-4934.2002.tb00192.x     Document Type: Article
Times cited : (8)

References (38)
  • 2
    • 0032537482 scopus 로고    scopus 로고
    • Resistance to HIV1 protease inhibitors: A comparison of enzyme inhibition and antiviral potency
    • Klabe R.M., Bacheler L.T., Ala P.J., Erickson-Viitanen S., Meek J.L., Resistance to HIV1 protease inhibitors: a comparison of enzyme inhibition and antiviral potency, Biochemistry, 37: 8735, 1998
    • (1998) Biochemistry , vol.37 , pp. 8735
    • Klabe, R.M.1    Bacheler, L.T.2    Ala, P.J.3    Erickson-Viitanen, S.4    Meek, J.L.5
  • 3
    • 20244373125 scopus 로고
    • X-ray analysis of HIV-1 proteinase at 2.7 Å resolution confirms structural homology among retroviral enzymes
    • Lappato R., Blundell T., Hemmings A., Overington J., Wilderspin A., X-ray analysis of HIV-1 proteinase at 2.7 Å resolution confirms structural homology among retroviral enzymes, Nature, 324: 299, 1989
    • (1989) Nature , vol.324 , pp. 299
    • Lappato, R.1    Blundell, T.2    Hemmings, A.3    Overington, J.4    Wilderspin, A.5
  • 4
    • 0024555898 scopus 로고
    • Three- Dimensional structure of aspartyl protease from Human Immunodeficiency Virus HIV-1
    • Navia M.A., Fitzgerald P.M., McKeever B.M., Leu C.T., Heimbach J.C., Three- dimensional structure of aspartyl protease from Human Immunodeficiency Virus HIV-1, Nature, 337: 615, 1989
    • (1989) Nature , vol.337 , pp. 615
    • Navia, M.A.1    Fitzgerald, P.M.2    McKeever, B.M.3    Leu, C.T.4    Heimbach, J.C.5
  • 5
    • 0024412506 scopus 로고
    • Conserved folding in retroviral protease: Crystal structure of a synthetic HIV-1 protease
    • Woldawer A., Miller M., Jaskolski M., Sathyanarayana B.K., Baldwin E., Conserved folding in retroviral protease: crystal structure of a synthetic HIV-1 protease, Science, 245: 611, 1989
    • (1989) Science , vol.245 , pp. 611
    • Woldawer, A.1    Miller, M.2    Jaskolski, M.3    Sathyanarayana, B.K.4    Baldwin, E.5
  • 6
    • 0031804609 scopus 로고    scopus 로고
    • Inhibitors of HIV1 protease: A major success of structure-assisted drug design
    • Wlodawer A., Vondrasek J., Inhibitors of HIV1 protease: a major success of structure-assisted drug design, Annu. Rev. Biophys. Struct., 27: 249, 1998
    • (1998) Annu. Rev. Biophys. Struct. , vol.27 , pp. 249
    • Wlodawer, A.1    Vondrasek, J.2
  • 7
    • 0033998647 scopus 로고    scopus 로고
    • Conformational flexibility of the catalytic Asp dyad in HIV-1 protease: An ab initio study on the free enzyme
    • Piana S., Carloni P., Conformational flexibility of the catalytic Asp dyad in HIV-1 protease: an ab initio study on the free enzyme, Proteins: Struct., Funct., and Genet., 39: 26, 2000
    • (2000) Proteins: Struct., Funct., and Genet. , vol.39 , pp. 26
    • Piana, S.1    Carloni, P.2
  • 8
    • 0034254518 scopus 로고    scopus 로고
    • Probing the S1/S1' substrate binding pocket geometry of HIV-1 protease with modified aspartic acid analogues
    • Short G.F., Laikhter L.A., Lodder M., Shayo Y., Arslan T., Hecht M.S., Probing the S1/S1' substrate binding pocket geometry of HIV-1 protease with modified aspartic acid analogues, Biochemstry, 39: 8768, 2000
    • (2000) Biochemstry , vol.39 , pp. 8768
    • Short, G.F.1    Laikhter, L.A.2    Lodder, M.3    Shayo, Y.4    Arslan, T.5    Hecht, M.S.6
  • 9
    • 0346225118 scopus 로고    scopus 로고
    • HIV-1 protease cleavage mechanism: A theoretical investigation based on classical MD simulation and reaction patch calculations using a hybrid QM/MM potential
    • Chatfiel D.C., Eurenius K.P., Brooks R.R., HIV-1 protease cleavage mechanism: a theoretical investigation based on classical MD simulation and reaction patch calculations using a hybrid QM/MM potential, Theochem. J. Mol. Struct., 423: 79, 1998
    • (1998) Theochem. J. Mol. Struct. , vol.423 , pp. 79
    • Chatfiel, D.C.1    Eurenius, K.P.2    Brooks, R.R.3
  • 10
    • 33746509624 scopus 로고    scopus 로고
    • Counteracting HIV1-protease drug resistance: Structural analysis of mutant protease complex with XV638 and SD146 cyclic urea amides with broad specifies
    • Ala P.J., Huston E.E., Klabe R.M., Jadhav K.P., Lam P.Y.S., Chang-Hwan C., Counteracting HIV1-protease drug resistance: structural analysis of mutant protease complex with XV638 and SD146 cyclic urea amides with broad specifies, Biochemistry, 36: 1573, 1998
    • (1998) Biochemistry , vol.36 , pp. 1573
    • Ala, P.J.1    Huston, E.E.2    Klabe, R.M.3    Jadhav, K.P.4    Lam, P.Y.S.5    Chang-Hwan, C.6
  • 11
    • 0032562224 scopus 로고    scopus 로고
    • Domain flexibility in retroviral proteases: Structural implication for drug resistant mutations
    • Rose R.B., Craick C.S., Stroud R.M., Domain flexibility in retroviral proteases: structural implication for drug resistant mutations, Biochemistry, 37: 2607, 1998
    • (1998) Biochemistry , vol.37 , pp. 2607
    • Rose, R.B.1    Craick, C.S.2    Stroud, R.M.3
  • 12
    • 0032567678 scopus 로고    scopus 로고
    • A computational study of the resistance of HIV-1 aspartic protease to the inhibitors ABT-538 and VX-478 and design of new analogues
    • Nair A.C., Miertus S., Tossi A., Romeo D., A computational study of the resistance of HIV-1 aspartic protease to the inhibitors ABT-538 and VX-478 and design of new analogues, Biochem. Biophys. Res. Commun., 242: 545, 1998
    • (1998) Biochem. Biophys. Res. Commun. , vol.242 , pp. 545
    • Nair, A.C.1    Miertus, S.2    Tossi, A.3    Romeo, D.4
  • 13
    • 0033862253 scopus 로고    scopus 로고
    • Structural and kinetic analyses of the protease from an amprenavir-resistant human immunodeficiency virus type 1 mutant rendered resistant to saquinavir and resensitised to amprenavir
    • Markland W, Rao BG, Parsons JD, Black J, Zuchowski L, Tisdale M., Structural and kinetic analyses of the protease from an amprenavir-resistant human immunodeficiency virus type 1 mutant rendered resistant to saquinavir and resensitised to amprenavir, J. Virol., 74: 4710, 2000
    • (2000) J. Virol. , vol.74 , pp. 4710
    • Markland, W.1    Rao, B.G.2    Parsons, J.D.3    Black, J.4    Zuchowski, L.5    Tisdale, M.6
  • 14
    • 0026438932 scopus 로고    scopus 로고
    • Molecular mechanism analysis of inhibitor binding to HIV1 protease
    • Sansom C.E., Wu J., Weber I.T., Molecular mechanism analysis of inhibitor binding to HIV1 protease, Protein. Eng., 5: 659, 2000
    • (2000) Protein. Eng. , vol.5 , pp. 659
    • Sansom, C.E.1    Wu, J.2    Weber, I.T.3
  • 15
    • 0032961895 scopus 로고    scopus 로고
    • The particle concept: Placing discrete water molecules during protein-ligand docking predictions
    • Rarey M., Kramer B., Lengauer T., The particle concept: placing discrete water molecules during protein-ligand docking predictions, Proteins, 34: 17, 1999
    • (1999) Proteins , vol.34 , pp. 17
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3
  • 16
    • 0026047763 scopus 로고
    • Determination of the relative binding free energies of pepetide inhibitors to the HIV-1 protease
    • Ferguson D.M., Radmer R.J., Kollman P.A., Determination of the relative binding free energies of pepetide inhibitors to the HIV-1 protease, J. Med Chem., 34: 2654, 1991
    • (1991) J. Med Chem. , vol.34 , pp. 2654
    • Ferguson, D.M.1    Radmer, R.J.2    Kollman, P.A.3
  • 17
    • 0032127391 scopus 로고    scopus 로고
    • Reaction path and free energy calculation of the tranzition between alternate conformations of HIV-1 protease
    • Rick S.W., Ericson J.W., Burt S.K., Reaction path and free energy calculation of the tranzition between alternate conformations of HIV-1 protease, Proteins: Struct. Funct. and Genet., 32: 7, 1998
    • (1998) Proteins: Struct. Funct. and Genet. , vol.32 , pp. 7
    • Rick, S.W.1    Ericson, J.W.2    Burt, S.K.3
  • 18
    • 0042139644 scopus 로고    scopus 로고
    • Comparison of generalized born and Poisson models: Energetic and dynamics of HIV protease
    • David L., Luo R., Gilson K.G., Comparison of generalized born and Poisson models: energetic and dynamics of HIV protease. J. Comp. Chem., 21: 295, 2000
    • (2000) J. Comp. Chem. , vol.21 , pp. 295
    • David, L.1    Luo, R.2    Gilson, K.G.3
  • 19
    • 0002133110 scopus 로고    scopus 로고
    • MBO(N)D: A multibody method for long-time molecular dynamics simulations
    • Chun M., MBO(N)D: A multibody method for long-time molecular dynamics simulations, J. Comp. Chem., 21: 159, 2000
    • (2000) J. Comp. Chem. , vol.21 , pp. 159
    • Chun, M.1
  • 20
    • 0027762073 scopus 로고
    • Three-dimensional QSAR of Human Immunodeficiency Virus (I) protease inhibitors. 1. A CoMFA study employing experimentally - Determined alignment rules
    • Waller L.C., Oprea T.I., Giolitti A., Marshall R.G., Three-dimensional QSAR of Human Immunodeficiency Virus (I) protease inhibitors. 1. A CoMFA study employing experimentally - determined alignment rules, J. Med. Chem., 36: 4152, 1993
    • (1993) J. Med. Chem. , vol.36 , pp. 4152
    • Waller, L.C.1    Oprea, T.I.2    Giolitti, A.3    Marshall, R.G.4
  • 21
    • 0028237444 scopus 로고
    • Three-dimensional QSAR of Human Immunodeficiency Virus (I) protease inhibitors. 2. Predictive power using limited exploration of alternate binding modes
    • Oprea T.I., Waller L.C., Marshall R.G., Three-dimensional QSAR of Human Immunodeficiency Virus (I) protease inhibitors. 2. Predictive power using limited exploration of alternate binding modes, J. Med. Chem., 37: 2206, 1994
    • (1994) J. Med. Chem. , vol.37 , pp. 2206
    • Oprea, T.I.1    Waller, L.C.2    Marshall, R.G.3
  • 22
    • 0031531210 scopus 로고    scopus 로고
    • Theoretical and practical aspects of three-dimensional qualitative structure-activity relationships
    • Oprea T.I., Waller L.C., Theoretical and practical aspects of three-dimensional qualitative structure-activity relationships, J. Comp. Chem., 11: 127, 1997
    • (1997) J. Comp. Chem. , vol.11 , pp. 127
    • Oprea, T.I.1    Waller, L.C.2
  • 23
    • 0033045015 scopus 로고    scopus 로고
    • Quantitative structure-active relationships of some HIV-protease inhibitors
    • Gupta S.P., Babu M.S., Kaw N., Quantitative structure-active relationships of some HIV-protease inhibitors, J. Enz. Inhib., 14: 109, 1999
    • (1999) J. Enz. Inhib. , vol.14 , pp. 109
    • Gupta, S.P.1    Babu, M.S.2    Kaw, N.3
  • 24
    • 0033491170 scopus 로고    scopus 로고
    • Quantitative structure-activity relationships studies on cyclic cyanoguanidine acting as HIV-1 protease inhibitors
    • Gupta S.P., Babu M.S., Garg R., Sowmya S., Quantitative structure-activity relationships studies on cyclic cyanoguanidine acting as HIV-1 protease inhibitors, Bioorganic and Medical Chemistry, 7: 407, 1999
    • (1999) Bioorganic and Medical Chemistry , vol.7 , pp. 407
    • Gupta, S.P.1    Babu, M.S.2    Garg, R.3    Sowmya, S.4
  • 25
    • 0033921869 scopus 로고    scopus 로고
    • Refinement of Catalyst hypotheses using simplex optimization
    • Norinder U., Refinement of Catalyst hypotheses using simplex optimization, J. Comp. Aided. Mol. Des., 14: 545, 2000
    • (2000) J. Comp. Aided. Mol. Des. , vol.14 , pp. 545
    • Norinder, U.1
  • 26
    • 0032574705 scopus 로고    scopus 로고
    • Molecular basis of resistance to HIV-1 protease inhibition: A plausible hypothesis
    • Luque I., Todd M.J., Gómez J., Semo N., Freire E., Molecular basis of resistance to HIV-1 protease inhibition: a plausible hypothesis, Biochemistry; 37: 5791, 1998
    • (1998) Biochemistry , vol.37 , pp. 5791
    • Luque, I.1    Todd, M.J.2    Gómez, J.3    Semo, N.4    Freire, E.5
  • 27
    • 0000538815 scopus 로고
    • Analytical molecular surface calculation
    • Connolly M.L., Analytical molecular surface calculation, J. Appl. Cryst., 16: 548, 1983
    • (1983) J. Appl. Cryst. , vol.16 , pp. 548
    • Connolly, M.L.1
  • 28
    • 84988112508 scopus 로고
    • An efficient Newton-like method for molecular mechanics energy minimization of large molecules
    • Ponder J.W., Richards F.M., An efficient Newton-like method for molecular mechanics energy minimization of large molecules, J. Comput. Chem., 8: 1016, 1987
    • (1987) J. Comput. Chem. , vol.8 , pp. 1016
    • Ponder, J.W.1    Richards, F.M.2
  • 29
    • 0002067212 scopus 로고    scopus 로고
    • Protein structure prediction using a combination of sequence homology and global energy minimization II. Energy functions
    • Dudek M., Ramnarayan K., Ponder J. W., Protein structure prediction using a combination of sequence homology and global energy minimization II. Energy functions, J. Comput. Chem., 19:548, 1998
    • (1998) J. Comput. Chem. , vol.19 , pp. 548
    • Dudek, M.1    Ramnarayan, K.2    Ponder, J.W.3
  • 30
    • 84986522918 scopus 로고
    • ICM - A new method for protein modeling and design. Applications to docking and structure prediction from the distorted native conformation
    • Abagyan R.A., Totrov, M.M., Kuznetsov D.N., ICM - a new method for protein modeling and design. Applications to docking and structure prediction from the distorted native conformation, J. Comp. Chem., 15: 488, 1994
    • (1994) J. Comp. Chem. , vol.15 , pp. 488
    • Abagyan, R.A.1    Totrov, M.M.2    Kuznetsov, D.N.3
  • 34
    • 33746565305 scopus 로고    scopus 로고
    • available from Hypercube, Inc. 1115 NW 4th Street, Gainesville, FL 32601 USA
    • HyperChem Computational Chemistry Manual (version 5) available from Hypercube, Inc. 1115 NW 4th Street, Gainesville, FL 32601 USA, 2001
    • (2001) HyperChem Computational Chemistry Manual (Version 5)
  • 37
    • 0037093067 scopus 로고    scopus 로고
    • Antitumorigenic effects of HIV protease inhibitor ritonavir: Inhibition of Kaposi sarcoma
    • Pati S., Pelser C.B., Dufraine J., Bryant J.L., Reitz M.S., Weichold F.F., Antitumorigenic effects of HIV protease inhibitor ritonavir: inhibition of Kaposi sarcoma, Blood, 99: 3771, 2002.
    • (2002) Blood , vol.99 , pp. 3771
    • Pati, S.1    Pelser, C.B.2    Dufraine, J.3    Bryant, J.L.4    Reitz, M.S.5    Weichold, F.F.6


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