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Volumn 39, Issue 3, 1996, Pages 705-712

An approach to rapid estimation of relative binding affinities of enzyme inhibitors: Application to peptidomimetic inhibitors of the human immunodeficiency virus type 1 protease

Author keywords

[No Author keywords available]

Indexed keywords

PROTEINASE; VIRUS ENZYME;

EID: 13344282748     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm940778t     Document Type: Article
Times cited : (41)

References (59)
  • 1
    • 0001903028 scopus 로고
    • The Complexities of AIDS: An Assessment of the HIV Protease as a Therapeutic Target
    • Tomaselli, A G.; Howe, J W.; Sawyer, T. K.; Wlodawer, A.; Heinrickson, R. L. The Complexities of AIDS: An Assessment of the HIV Protease as a Therapeutic Target. Chim. Oggi 1991, 9, 6-27.
    • (1991) Chim. Oggi , vol.9 , pp. 6-27
    • Tomaselli, A.G.1    Howe, J.W.2    Sawyer, T.K.3    Wlodawer, A.4    Heinrickson, R.L.5
  • 2
    • 0027218692 scopus 로고
    • Structure-Based Inhibitors of HIV-1 Protease
    • Wlodawer, A.; Erickson, J. W. Structure-Based Inhibitors of HIV-1 Protease. Annu. Rev. Biochem. 1993, 62, 543-85.
    • (1993) Annu. Rev. Biochem. , vol.62 , pp. 543-585
    • Wlodawer, A.1    Erickson, J.W.2
  • 3
    • 16044375105 scopus 로고
    • Crystal Structures of HIV-1 Protease Complexes
    • Appelt, K. Crystal Structures of HIV-1 Protease Complexes. Perspect. Drug Discovery Des. 1993, 1, 23-48.
    • (1993) Perspect. Drug Discovery Des. , vol.1 , pp. 23-48
    • Appelt, K.1
  • 11
    • 0023663097 scopus 로고
    • Computer-Aided Molecular Design
    • McCammon, J. A. Computer-Aided Molecular Design. Science 1987, 238, 486-491.
    • (1987) Science , vol.238 , pp. 486-491
    • McCammon, J.A.1
  • 12
    • 0026730489 scopus 로고
    • Structure-Based Strategies for Drug Design and Discovery
    • Kuntz, I. D. Structure-Based Strategies for Drug Design and Discovery. Science 1992, 257, 1078-1082.
    • (1992) Science , vol.257 , pp. 1078-1082
    • Kuntz, I.D.1
  • 15
    • 0027082243 scopus 로고
    • Calculation of Solvation and Binding Free Energy Differences for Folate-Based Inhibitors of the Enzyme Thymidylate Synthase
    • Rami Reddy, M.; Bacquet, R. J.; Zichi, D.; Mathews, D. A.; Welsh, K. M.; Jones, T. R.; Freer, S. Calculation of Solvation and Binding Free Energy Differences for Folate-Based Inhibitors of the Enzyme Thymidylate Synthase. J. Am. Chem. Soc. 1992, 114, 10117-10122.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 10117-10122
    • Rami Reddy, M.1    Bacquet, R.J.2    Zichi, D.3    Mathews, D.A.4    Welsh, K.M.5    Jones, T.R.6    Freer, S.7
  • 16
    • 0026503819 scopus 로고
    • Application of Free Energy Simulations to the Binding of a Transition State Analogue Inhibitor to HIV Protease
    • Tropshaw, A. J.; Hermans, J. Application of Free Energy Simulations to the Binding of a Transition State Analogue Inhibitor to HIV Protease. Protein Eng. 1992, 5, 29-33.
    • (1992) Protein Eng. , vol.5 , pp. 29-33
    • Tropshaw, A.J.1    Hermans, J.2
  • 17
    • 0026717932 scopus 로고
    • Free Energy Perturbation Studies on Inhibitor Binding to HIV-1 Proteinase
    • Rao, B. G.; Tilton, R. F.; Singh, U. C. Free Energy Perturbation Studies on Inhibitor Binding to HIV-1 Proteinase. J. Am. Chem. Soc. 1992, 114, 4447-4452.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 4447-4452
    • Rao, B.G.1    Tilton, R.F.2    Singh, U.C.3
  • 18
    • 36849122972 scopus 로고
    • High Temperature Equation of State by a Perturbation Method. I. Non-polar Gases
    • Zwanzig, R. W. High Temperature Equation of State by a Perturbation Method. I. Non-polar Gases. J. Chem Phys. 1954, 22, 1420-1426.
    • (1954) J. Chem Phys. , vol.22 , pp. 1420-1426
    • Zwanzig, R.W.1
  • 19
    • 0008796956 scopus 로고
    • Molecular Dynamics/Free Energy Perturbation Study on the Relative Affinities of the Binding of Reduced and Oxidized NADP to Dihydrofolate Reductase
    • Cummins, P. L.; Ramnarayan, K.; Singh, U. C.; Gready, J. E. Molecular Dynamics/Free Energy Perturbation Study on the Relative Affinities of the Binding of Reduced and Oxidized NADP to Dihydrofolate Reductase. J. Am. Chem. Soc. 1991, 113, 8247-8256.
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 8247-8256
    • Cummins, P.L.1    Ramnarayan, K.2    Singh, U.C.3    Gready, J.E.4
  • 20
    • 0026047763 scopus 로고
    • Determination of the Relative Binding Free Energies of Peptide Inhibitors to the HIV-1 protease
    • Ferguson, D. M.; Radmer, R. J.; Kollman, P. A. Determination of the Relative Binding Free Energies of Peptide Inhibitors to the HIV-1 protease. J. Med. Chem. 1991, 34, 2654-2659.
    • (1991) J. Med. Chem. , vol.34 , pp. 2654-2659
    • Ferguson, D.M.1    Radmer, R.J.2    Kollman, P.A.3
  • 21
    • 0024365336 scopus 로고
    • Hidden Thermodynamics of Mutant Proteins: A Molecular Dynamics Analysis
    • Gao, J.; Kuczera, K.; Tidor, B.; Karplus, M. Hidden Thermodynamics of Mutant Proteins: A Molecular Dynamics Analysis. Science 1989, 244, 1069-1072.
    • (1989) Science , vol.244 , pp. 1069-1072
    • Gao, J.1    Kuczera, K.2    Tidor, B.3    Karplus, M.4
  • 22
    • 0025720738 scopus 로고
    • Relative Free Energy Differences in the Binding Free Energies of Human Immunodeficiency Virus 1 Protease Inhibitors: A Thermodynamic Cycle Perturbation Approach
    • Rami Reddy, M.; Viswanadhan, V N., Weinstein, J. N. Relative Free Energy Differences in the Binding Free Energies of Human Immunodeficiency Virus 1 Protease Inhibitors: A Thermodynamic Cycle Perturbation Approach Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 10287-10291.
    • (1991) Proc. Natl. Acad. Sci. U.S.A. , vol.88 , pp. 10287-10291
    • Rami Reddy, M.1    Viswanadhan, V.N.2    Weinstein, J.N.3
  • 23
    • 0028349919 scopus 로고
    • Calculation of Relative Differences in the Binding Free Energies of HIV1 Protease Inhibitors: A Thermodynamic Cycle Perturbation Approach
    • Rami Reddy, M.; Varney, M. D.; Kalish, V.; Viswanadhan, V. N.; Appelt, K. Calculation of Relative Differences in the Binding Free Energies of HIV1 Protease Inhibitors: A Thermodynamic Cycle Perturbation Approach. J. Med. Chem. 1994, 37, 1145-1152.
    • (1994) J. Med. Chem. , vol.37 , pp. 1145-1152
    • Rami Reddy, M.1    Varney, M.D.2    Kalish, V.3    Viswanadhan, V.N.4    Appelt, K.5
  • 24
    • 0027613969 scopus 로고
    • An approximate but efficient method to calculate free energy trends by computer simulation: Application to dihydrofolate reductase-inhibitor complexes
    • Gerber, P. R.; Mark, A. E.; van Gunsteren, W. F. An approximate but efficient method to calculate free energy trends by computer simulation: Application to dihydrofolate reductase-inhibitor complexes. J. Comput.-Aided Mol. Des. 1993, 7, 305-323.
    • (1993) J. Comput.-Aided Mol. Des. , vol.7 , pp. 305-323
    • Gerber, P.R.1    Mark, A.E.2    Van Gunsteren, W.F.3
  • 26
    • 0024716284 scopus 로고
    • Atomic Physicochemical Parameters for Three Dimensional Structure Directed Quantitative Structure-Activity Relationships. IV. Additional Parameters for Hydrophobic and Dispersive Interactions and Their Application for an Automated Superposition of Certain Naturally Occurring Nucleoside Antibiotics
    • Viswanadhan, V. N.; Ghose, A. K.; Revankar, G. R.; Robins, R. K. Atomic Physicochemical Parameters for Three Dimensional Structure Directed Quantitative Structure-Activity Relationships. IV. Additional Parameters for Hydrophobic and Dispersive Interactions and Their Application for an Automated Superposition of Certain Naturally Occurring Nucleoside Antibiotics. J. Chem. Inf. Comput. Sci. 1989, 29, 163-172.
    • (1989) J. Chem. Inf. Comput. Sci. , vol.29 , pp. 163-172
    • Viswanadhan, V.N.1    Ghose, A.K.2    Revankar, G.R.3    Robins, R.K.4
  • 27
    • 0027762073 scopus 로고
    • Three-Dimensional QSAR of Human Immunodeficiency Virus (I) Protease Inhibitors. 1. a CoMFA Study Employing Experimentally-Determined Alignment Rules
    • Waller, C.; Oprea, T. I.; Giolitti, A.; Marshall, G. R. Three-Dimensional QSAR of Human Immunodeficiency Virus (I) Protease Inhibitors. 1. A CoMFA Study Employing Experimentally-Determined Alignment Rules. J. Med. Chem. 1993, 36, 4152-4160.
    • (1993) J. Med. Chem. , vol.36 , pp. 4152-4160
    • Waller, C.1    Oprea, T.I.2    Giolitti, A.3    Marshall, G.R.4
  • 28
    • 0026080846 scopus 로고
    • Allosteric Modifiers of Hemoglobin 2. Crystallographically Determined Binding Sites and Hydrophobic Binding/Interaction Analysis of Novel Hemoglobin Oxygen Effectors
    • Wireko, F. C.; Kellogg, G. E.; Abraham, D. J. Allosteric Modifiers of Hemoglobin 2. Crystallographically Determined Binding Sites and Hydrophobic Binding/Interaction Analysis of Novel Hemoglobin Oxygen Effectors. J. Med. Chem. 1991, 34, 758-767.
    • (1991) J. Med. Chem. , vol.34 , pp. 758-767
    • Wireko, F.C.1    Kellogg, G.E.2    Abraham, D.J.3
  • 29
    • 0028454828 scopus 로고
    • The development of a simple empirical scoring function to estimate the binding constant for a protein ligand complex of known three-dimensional structure
    • (a) Bohm, H.-J. The development of a simple empirical scoring function to estimate the binding constant for a protein ligand complex of known three-dimensional structure. J. Comput.-Aided Mol. Des. 1994, 8, 243-256.
    • (1994) J. Comput.-Aided Mol. Des. , vol.8 , pp. 243-256
    • Bohm, H.-J.1
  • 30
    • 13344286524 scopus 로고    scopus 로고
    • A scoring function, 'VALIDATE', has been reported in the while this report was in progress
    • (b) A scoring function, 'VALIDATE', has been reported in the ACS meetings (by R. D. Head and G. R. Marshall) while this report was in progress.
    • ACS Meetings
    • Head, R.D.1    Marshall, G.R.2
  • 31
    • 0024239036 scopus 로고
    • A Free Energy Perturbation Study of the Binding of Methotrexate to Mutants of Dihydrofolate Reductase
    • Singh, U. C.; Benkovic, S. J. A Free Energy Perturbation Study of the Binding of Methotrexate to Mutants of Dihydrofolate Reductase. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 9519-9523.
    • (1988) Proc. Natl. Acad. Sci. U.S.A. , vol.85 , pp. 9519-9523
    • Singh, U.C.1    Benkovic, S.J.2
  • 32
    • 0025319621 scopus 로고
    • Calculation of the Relative Binding Free Energy of 2′GMP and 2′AMP to Ribonuclease T1 Using Molecular Dynamics/Free Energy Perturbation Approaches
    • Hirono, S.; Kollman, P. A. Calculation of the Relative Binding Free Energy of 2′GMP and 2′AMP to Ribonuclease T1 Using Molecular Dynamics/Free Energy Perturbation Approaches. J. Mol. Biol. 1990, 212, 197-209.
    • (1990) J. Mol. Biol. , vol.212 , pp. 197-209
    • Hirono, S.1    Kollman, P.A.2
  • 33
    • 0024166782 scopus 로고
    • Estimating and Representing Hydrophobicity Potential
    • Fauchere, J.-L.; Quarendon, P.; Kaetterer, L. Estimating and Representing Hydrophobicity Potential J. Mol. Graph. 1988, 6, 203-206.
    • (1988) J. Mol. Graph. , vol.6 , pp. 203-206
    • Fauchere, J.-L.1    Quarendon, P.2    Kaetterer, L.3
  • 34
    • 0022596727 scopus 로고
    • Solvation energy in protein folding and binding
    • Eisenberg, D.; McLachlan, A. D. Solvation energy in protein folding and binding. Nature (London) 1986, 379, 199-203.
    • (1986) Nature (London) , vol.379 , pp. 199-203
    • Eisenberg, D.1    McLachlan, A.D.2
  • 35
    • 0023338543 scopus 로고
    • Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides
    • Ooi, T.; Oobatake, M.; Nemethy, G.; Scheraga, H. A. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 3086-3090.
    • (1987) Proc. Natl. Acad. Sci. U.S.A. , vol.84 , pp. 3086-3090
    • Ooi, T.1    Oobatake, M.2    Nemethy, G.3    Scheraga, H.A.4
  • 36
    • 0023779057 scopus 로고
    • Effects of hydrated water on protein unfolding
    • Ooi, T.; Oobatake, M. Effects of hydrated water on protein unfolding. J. Biochem. 1988, 103, 114-120.
    • (1988) J. Biochem. , vol.103 , pp. 114-120
    • Ooi, T.1    Oobatake, M.2
  • 37
    • 0027080909 scopus 로고
    • Atomic solvation Parameters applied to molecular dynamics of proteins in solution
    • Wesson, L.; Eisenberg, D. Atomic solvation Parameters applied to molecular dynamics of proteins in solution. Protein Sci. 1992, 1, 227-235.
    • (1992) Protein Sci. , vol.1 , pp. 227-235
    • Wesson, L.1    Eisenberg, D.2
  • 40
    • 0025225682 scopus 로고
    • X-ray Crystallographic Structure of a Complex between a Synthetic Protease of Human Immunodeficiency Virus 1 and a Substrate Based Hydroxyl Ethylamine Inhibitor
    • Swain, A. L.; Miller, M.; Green, J.; Rich, D. H.; Schneider, J.; Kent, S. B. H.; Wlodawer, A. X-ray Crystallographic Structure of a Complex Between a Synthetic Protease of Human Immunodeficiency Virus 1 and a Substrate Based Hydroxyl Ethylamine Inhibitor. Proc. Natl Acad. Sci. U S.A. 1990, 87, 8805-8809.
    • (1990) Proc. Natl Acad. Sci. U S.A. , vol.87 , pp. 8805-8809
    • Swain, A.L.1    Miller, M.2    Green, J.3    Rich, D.H.4    Schneider, J.5    Kent, S.B.H.6    Wlodawer, A.7
  • 41
    • 13344280521 scopus 로고    scopus 로고
    • Modeling was conducted using QUANTA program from Molecular Simulations Inc., Burlington, MA, 1991
    • Modeling was conducted using QUANTA program from Molecular Simulations Inc., Burlington, MA, 1991.
  • 43
    • 84988098098 scopus 로고
    • Atomic Charges Derived from Electrostatic Potentials: A Detailed Study
    • Chirlian, L. E.; Francl, M. M. Atomic Charges Derived from Electrostatic Potentials: A Detailed Study. J. Comput. Chem. 1987, 8, 894-905.
    • (1987) J. Comput. Chem. , vol.8 , pp. 894-905
    • Chirlian, L.E.1    Francl, M.M.2
  • 45
    • 45149145779 scopus 로고
    • The Dielectric Constant of SPC/E Water
    • Reddy, M. R.; Berkowitz, M. L. The Dielectric Constant of SPC/E Water. Chem. Phys. Lett. 1989, 155, 173-176.
    • (1989) Chem. Phys. Lett. , vol.155 , pp. 173-176
    • Reddy, M.R.1    Berkowitz, M.L.2
  • 47
    • 0025774665 scopus 로고
    • Effect of Hydroxyl Group Configuration in Hydroxyethyl Amine Dipeptide Isosteres on HIV Protease Inhibition. Evidence for Multiple Binding Modes
    • Rich, D. H.; Sun, C.-Q.; ara Prasad, J. V. N.; Pathiasseril, A.; Total, M. V.; Marshall, G. R.; Clare, M.; Mueller, R. A.; Houseman, K. Effect of Hydroxyl Group Configuration in Hydroxyethyl Amine Dipeptide Isosteres on HIV Protease Inhibition. Evidence for Multiple Binding Modes. J. Med. Chem. 1991, 34, 1222-1225.
    • (1991) J. Med. Chem. , vol.34 , pp. 1222-1225
    • Rich, D.H.1    Sun, C.-Q.2    Ara Prasad, J.V.N.3    Pathiasseril, A.4    Total, M.V.5    Marshall, G.R.6    Clare, M.7    Mueller, R.A.8    Houseman, K.9
  • 48
    • 0024174413 scopus 로고
    • 3D Molecular lipophilicity potential profiles: A new tool in molecular modeling
    • Furet, P.; Sele, A.; Cohen, N. C. 3D Molecular lipophilicity potential profiles: A new tool in molecular modeling. J. Mol. Graph. 1988, 6, 182-189.
    • (1988) J. Mol. Graph. , vol.6 , pp. 182-189
    • Furet, P.1    Sele, A.2    Cohen, N.C.3
  • 49
    • 0015222647 scopus 로고
    • The interpretation of protein structures. Estimation of static accessibility
    • Lee, B. K.; Richards, F. M. The interpretation of protein structures. Estimation of static accessibility. J. Mol. Biol. 1971, 55, 379-400.
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.K.1    Richards, F.M.2
  • 50
    • 0021107965 scopus 로고
    • Solvent-Accessible Surfaces of Proteins and Nucleic Acids
    • Connolly, M. J. Solvent-Accessible Surfaces of Proteins and Nucleic Acids. Science 1983, 221, 709-713.
    • (1983) Science , vol.221 , pp. 709-713
    • Connolly, M.J.1
  • 51
    • 24544469216 scopus 로고
    • oct from Structures
    • oct from Structures. Chem. Rev. 1993, 93, 1281-1306.
    • (1993) Chem. Rev. , vol.93 , pp. 1281-1306
    • Leo, A.J.1
  • 52
    • 0001059812 scopus 로고
    • Quantitative Structure-Activity Relationships and the Unnamed Science
    • Hansch, C. Quantitative Structure-Activity Relationships and the Unnamed Science. Acc. Chem. Res. 1993, 26, 147-153.
    • (1993) Acc. Chem. Res. , vol.26 , pp. 147-153
    • Hansch, C.1
  • 53
    • 0025286882 scopus 로고
    • Mapping the Binding Site of the Nucleoside Transporter Protein: A 3D-QSAR Study
    • Viswanadhan, V. N.; Ghose, A. K.; Weinstein, J. N. Mapping the Binding Site of the Nucleoside Transporter Protein: A 3D-QSAR Study. Biochim. Biophys. Acta 1991, 1039, 356-366.
    • (1991) Biochim. Biophys. Acta , vol.1039 , pp. 356-366
    • Viswanadhan, V.N.1    Ghose, A.K.2    Weinstein, J.N.3
  • 54
    • 0016352763 scopus 로고
    • Hydrophobic bonding and accessible surface area in proteins
    • Chothia, C. Hydrophobic bonding and accessible surface area in proteins. Nature (London) 1974, 248, 338-339.
    • (1974) Nature (London) , vol.248 , pp. 338-339
    • Chothia, C.1
  • 55
    • 0027432959 scopus 로고
    • Surface Area Included in Energy Refinement of Proteins
    • von Freyberg, B.; Richmond, T. J.; Braun, W. Surface Area Included in Energy Refinement of Proteins. J. Mol. Biol. 1993, 233, 275-292.
    • (1993) J. Mol. Biol. , vol.233 , pp. 275-292
    • Von Freyberg, B.1    Richmond, T.J.2    Braun, W.3
  • 56
    • 0041548461 scopus 로고
    • Daylight Chemical Information Systems: Irvine, CA
    • Leo, A. J.; Weininger, D. CLOGP, Daylight Chemical Information Systems: Irvine, CA, 1991.
    • (1991) CLOGP
    • Leo, A.J.1    Weininger, D.2
  • 57
    • 0000486708 scopus 로고
    • Assessment of Methods Used for Predicting Lipophilicity: Application to Nucleosides and Nucleoside Bases
    • Viswanadhan, V. N.; Rami Reddy, M.; Bacquet, R. J.; Erion, M. D. Assessment of Methods Used for Predicting Lipophilicity: Application to Nucleosides and Nucleoside Bases. J. Comput. Chem. 1993, 14, 1019-1026.
    • (1993) J. Comput. Chem. , vol.14 , pp. 1019-1026
    • Viswanadhan, V.N.1    Rami Reddy, M.2    Bacquet, R.J.3    Erion, M.D.4
  • 59
    • 0027978699 scopus 로고
    • 3D-QSAR of Human Immunodeficiency Virus (I) Protease Inhibitors III. Interpretation of CoMFA Results
    • Oprea, T. I.; Waller, C. L.; Marshall, G. R. 3D-QSAR of Human Immunodeficiency Virus (I) Protease Inhibitors III. Interpretation of CoMFA Results. Drug Des Discovery 1994, 12, 29-51.
    • (1994) Drug des Discovery , vol.12 , pp. 29-51
    • Oprea, T.I.1    Waller, C.L.2    Marshall, G.R.3


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