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Volumn 41, Issue 6, 1998, Pages 836-852

Comparative binding energy analysis of HIV-1 protease inhibitors: Incorporation of solvent effects and validation as a powerful tool in receptor-based drug design

Author keywords

[No Author keywords available]

Indexed keywords

PROTEINASE INHIBITOR; RECEPTOR; SOLVENT;

EID: 0032510317     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm970535b     Document Type: Article
Times cited : (122)

References (60)
  • 1
    • 0028297112 scopus 로고
    • Application of the Three-Dimensional Structures of Protein Target Molecules in Structure-Based Drug Design
    • (a) Gréer, J.; Erickson, J. W.; Baldwin, J. J.; Varney, M. D. Application of the Three-Dimensional Structures of Protein Target Molecules in Structure-Based Drug Design. J. Med, Chem. 1994, 37, 1035-1054.
    • (1994) J. Med, Chem. , vol.37 , pp. 1035-1054
    • Gréer, J.1    Erickson, J.W.2    Baldwin, J.J.3    Varney, M.D.4
  • 3
    • 0031189711 scopus 로고    scopus 로고
    • Molecular Recognition of Protein-Ligand Complexes: Applications to Drug Design
    • Babine, R. E.; Bender, S. L. Molecular Recognition of Protein-Ligand Complexes: Applications to Drug Design. Chem. Rev. 1997, 97, 1359-1472.
    • (1997) Chem. Rev. , vol.97 , pp. 1359-1472
    • Babine, R.E.1    Bender, S.L.2
  • 4
    • 0029623184 scopus 로고
    • Computational Methods to Predict Binding Free Energy in Ligand-Receptor Complexes
    • Ajay; Murcko, M. A. Computational Methods to Predict Binding Free Energy in Ligand-Receptor Complexes. J. Med. Chem. 1995, 38, 4953-4967.
    • (1995) J. Med. Chem. , vol.38 , pp. 4953-4967
    • Ajay1    Murcko, M.A.2
  • 5
    • 0031058541 scopus 로고    scopus 로고
    • The Statistical-Thermodynamic Basis for Computation of Binding Affinities: A Critical Review
    • Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. The Statistical-Thermodynamic Basis for Computation of Binding Affinities: A Critical Review. Biophys. J. 1997, 72,1047-1069.
    • (1997) Biophys. J. , pp. 1047-1069
    • Gilson, M.K.1    Given, J.A.2    Bush, B.L.3    McCammon, J.A.4
  • 6
    • 0027054352 scopus 로고
    • Partitioning of Free Energy Contributions in the Estimation of Binding Constants: Residual Motions and Consequences for Amide-Amide Hydrogen Bond Strengths
    • (a) Searle, M. S.; Williams, D. H.; Gerhard, U. Partitioning of Free Energy Contributions in the Estimation of Binding Constants: Residual Motions and Consequences for Amide-Amide Hydrogen Bond Strengths. J. Am. Chem. Soc. 1992,114,10697-10704.
    • (1992) J. Am. Chem. Soc. , pp. 10697-10704
    • Searle, M.S.1    Williams, D.H.2    Gerhard, U.3
  • 7
    • 0029940017 scopus 로고    scopus 로고
    • Empirical Free Energy as a Target Function in Docking and Design: Application to HIV-1 Protease Inhibitors
    • (b) King, B. L.; Vajda, S.; DeLisi, C. Empirical Free Energy as a Target Function in Docking and Design: Application to HIV-1 Protease Inhibitors. FEES Lett. 1996, 384, 87-91.
    • (1996) FEES Lett. , vol.384 , pp. 87-91
    • King, B.L.1    Vajda, S.2    Delisi, C.3
  • 8
    • 0029933286 scopus 로고    scopus 로고
    • Prediction of Protein Complexes Using Empirical Free Energy Functions
    • Weng, Z. S.; Vajda, S.; DeLisi, C. Prediction of Protein Complexes Using Empirical Free Energy Functions. Protein Sei. 1996, 5, 614-626.
    • (1996) Protein Sei. , vol.5 , pp. 614-626
    • Weng, Z.S.1    Vajda, S.2    Delisi, C.3
  • 9
    • 0030474049 scopus 로고    scopus 로고
    • Vhat Can We Learn from Molecular Recognition in Protein-Ligand Complexes for the Design of New Drugs?
    • Böhm, H.-J.; Keble, G. \Vhat Can We Learn from Molecular Recognition in Protein-Ligand Complexes for the Design of New Drugs? Angew. Chem., Int. Ed. Engl. 1996, 35, 2588-2614.
    • (1996) Angew. Chem., Int. Ed. Engl. , vol.35 , pp. 2588-2614
    • Böhm, H.-J.1
  • 10
    • 0028861437 scopus 로고
    • Elusive Affinities
    • (e) Janin, J. Elusive Affinities. Proteins 1995, 21, 30-39.
    • (1995) Proteins , vol.21 , pp. 30-39
    • Janin, J.1
  • 11
    • 0030255303 scopus 로고    scopus 로고
    • Scoring Noncovalent Protein-Ligand Interactions: A Continuous Differentiable Function Tuned to Compute Binding Affinities
    • (f) Jain, A. N. Scoring Noncovalent Protein-Ligand Interactions: A Continuous Differentiable Function Tuned to Compute Binding Affinities. J. Comput.-Aidcd Mol. Design 1996, 10,427-440.
    • (1996) J. Comput.-Aidcd Mol. Design , pp. 427-440
    • Jain, A.N.1
  • 12
    • 0031547977 scopus 로고    scopus 로고
    • Empirical free Energy Calculations: A Blind Test and . Further Improvements to the Method
    • (g) Novotny, J,; Bruccoleri, R. E.; Davis, M.; Sharp, K. A. Empirical free Energy Calculations: A Blind Test and . Further Improvements to the Method. J. Mol. Biol. 1997, 268, 401-411.
    • (1997) J. Mol. Biol. , vol.268 , pp. 401-411
    • Novotny, J.1    Bruccoleri, R.E.2    Davis, M.3    Sharp, K.A.4
  • 13
    • 0024553083 scopus 로고
    • The Binding of Benzenesulfonamides to Carbonic Anhydrase Enzyme. a Molecular Mechanics Study and Quantitative Structure-Activity Relationships
    • Menziani, M. C.; De Benedetti, P. G.; Gago, F.; Richards, W. G. The Binding of Benzenesulfonamides to Carbonic Anhydrase Enzyme. A Molecular Mechanics Study and Quantitative Structure-Activity Relationships J. Med. Chem. 1989,32, 951-956.
    • (1989) J. Med. Chem. , vol.32 , pp. 951-956
    • Menziani, M.C.1    De Benedetti, P.G.2    Gago, F.3    Richards, W.G.4
  • 15
    • 0039837427 scopus 로고
    • Structure-Based Design of Human Immunodeficiency Virus-1 Protease Inhibitors
    • Reynolds, C. H., Holloway, M. K., Cox, H. K., Eds.; American Chemical Society: Washington
    • (b) Holloway, M. K.; Wai, J. M. Structure-Based Design of Human Immunodeficiency Virus-1 Protease Inhibitors. In Computer-Aided Molecular Design. Applications in Agrochemicals, Materials, and Pharmaceuticals; Reynolds, C. H., Holloway, M. K., Cox, H. K., Eds.; American Chemical Society: Washington, 1995; pp 36-50.
    • (1995) Computer-Aided Molecular Design. Applications in Agrochemicals, Materials, and Pharmaceuticals , pp. 36-50
    • Holloway, M.K.1    Wai, J.M.2
  • 16
    • 0001452822 scopus 로고
    • Correlation of Binding Affinities with Non-Bonded Interaction Energies of ThrombinInhibitor Complexes
    • Grootenhuis, P. D. J.; van Galen, P. J. M. Correlation of Binding Affinities with Non-Bonded Interaction Energies of ThrombinInhibitor Complexes. Ada Crystallogr. 1995, D51, 560-566.
    • (1995) Ada Crystallogr. , vol.D51 , pp. 560-566
    • Grootenhuis, P.D.J.1    Van Galen, P.J.M.2
  • 17
    • 0346029042 scopus 로고
    • Calculation of Relative Binding Affinities of Purine Nucleoside Phosphorylase Inhibitors
    • Carson, M.; Yang, Z.; Babu, Y. S.; Montgomery, J. A. Calculation of Relative Binding Affinities of Purine Nucleoside Phosphorylase Inhibitors. Ada Crystallogr. 1995, 057, 536-540.
    • (1995) Ada Crystallogr. , vol.57 , pp. 536-540
    • Carson, M.1    Yang, Z.2    Babu, Y.S.3    Montgomery, J.A.4
  • 18
    • 13344282748 scopus 로고    scopus 로고
    • An Approach to Rapid Estimation of Relative Binding Affinities of Enzyme Inhibitors: Application to Peptidomimetic Inhibitors of the Human Immunodeficiency Virus Type 1 Protease
    • Viswanadhan, V. N.; Reddy, M. R.; Wlodawer, A.; Varney, M. D.; Weinstein, J. N. An Approach to Rapid Estimation of Relative Binding Affinities of Enzyme Inhibitors: Application to Peptidomimetic Inhibitors of the Human Immunodeficiency Virus Type 1 Protease. J. Med. Chem. 1996,39, 705-712.
    • (1996) J. Med. Chem. , vol.39 , pp. 705-712
    • Viswanadhan, V.N.1    Reddy, M.R.2    Wlodawer, A.3    Varney, M.D.4    Weinstein, J.N.5
  • 19
    • 0031469618 scopus 로고    scopus 로고
    • Assessment of Solvation Effects on Calculated Binding Affinity Differences: Trypsin Inhibition by Flavonoids as a Model System for Congeneric Series
    • Checa, A.; Ortiz, A. R.; de Pascual-Teresa, B.; Gago, F. Assessment of Solvation Effects on Calculated Binding Affinity Differences: Trypsin Inhibition by Flavonoids as a Model System for Congeneric Series. J. Med. Chem. 1997, 40, 4136-4145.
    • (1997) J. Med. Chem. , vol.40 , pp. 4136-4145
    • Checa, A.1    Ortiz, A.R.2    De Pascual-Teresa, B.3    Gago, F.4
  • 21
    • 7044239742 scopus 로고
    • Free Energy Calculations: Applications to Chemical and Biochemical Phenomena
    • (b) Kollman, P. Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. Chem. Rev. 1993, 93, 2395-2417.
    • (1993) Chem. Rev. , vol.93 , pp. 2395-2417
    • Kollman, P.1
  • 22
    • 0031012579 scopus 로고    scopus 로고
    • Enzyme-Inhibitor Association Thermodynamics: Explicit and Continuum Solvent Studies
    • Resat, H.; Marrone, T. J.; McCammon, J. A. Enzyme-Inhibitor Association Thermodynamics: Explicit and Continuum Solvent Studies. Biophys. J. 1997, 72, 522-532.
    • (1997) Biophys. J. , vol.72 , pp. 522-532
    • Resat, H.1    Marrone, T.J.2    McCammon, J.A.3
  • 23
    • 0028155689 scopus 로고
    • Åqvist, J.; Medina, C.; Samuelsson, J.-E. A New Method for Predicting Binding Affinity in Computer-Aided Drug Design. Protein Eng. 1994, 7, 385-391.
    • (1994) Protein Eng. , vol.7 , pp. 385-391
    • Åqvist, J.1    Medina, C.2
  • 24
    • 0030906731 scopus 로고    scopus 로고
    • Binding Affinities for Sulfonamide Inhibitors with Human Thrombin Using Monte Carlo Simulations with a Linear Response Method
    • Jones-Hertzog, D. K.; Jorgensen, W. L. Binding Affinities for Sulfonamide Inhibitors with Human Thrombin Using Monte Carlo Simulations with a Linear Response Method. J. Med. Chem. 1997, 40, 1539-1549.
    • (1997) J. Med. Chem. , vol.40 , pp. 1539-1549
    • Jones-Hertzog, D.K.1    Jorgensen, W.L.2
  • 25
    • 0028349919 scopus 로고
    • Calculation of Relative Differences in the Binding Free Energies of HIV1 Protease Inhibitors: A Thermodynamic Cycle Perturbation Approach
    • Reddy, M. R.; Varney, M. D.; Kalish, V.; Viswanadhan, V. N.; Appell, 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
    • Reddy, M.R.1    Varney, M.D.2    Kalish, V.3    Viswanadhan, V.N.4    Appell, K.5
  • 26
    • 0029000922 scopus 로고
    • Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis
    • (a) Ortiz, A. R.; Pisabarro, M. T.; Gago, F.; Wade, R. C. Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis. J. Med. Chem. 1995,38, 2681-2691.
    • (1995) J. Med. Chem. , vol.38 , pp. 2681-2691
    • Ortiz, A.R.1    Pisabarro, M.T.2    Gago, F.3    Wade, R.C.4
  • 28
    • 0002309097 scopus 로고
    • PLS-Partial LeastSquares Projections to Latent Structures
    • Kubinyi, H., Ed.; ESCOM Science Publishers B.V.: Leiden
    • (a) Wold, S.; Johansson, E.; Cocchi, M. PLS-Partial LeastSquares Projections to Latent Structures. In 3D QSAR in Drug Design. Theory, Methods and Applications; Kubinyi, H., Ed.; ESCOM Science Publishers B.V.: Leiden, 1993; pp 523-550.
    • (1993) 3D QSAR in Drug Design. Theory, Methods and Applications , pp. 523-550
    • Wold, S.1    Johansson, E.2    Cocchi, M.3
  • 29
    • 34250078600 scopus 로고
    • Partial Least Squares (PLS): Its Strengths and Limitations
    • (b) Cramer, R. D., III. Partial Least Squares (PLS): Its Strengths and Limitations. Perspect. Drug Discovery Design 1993,1,269-278.
    • (1993) Perspect. Drug Discovery Design , vol.1 , pp. 269-278
    • Cramer III, R.D.1
  • 30
    • 0344778061 scopus 로고
    • Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics
    • Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. J. Am. Chem. Soc. 1990, 112, 6127-6129.
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 6127-6129
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hendrickson, T.4
  • 32
    • 84986492477 scopus 로고
    • Atomic Charges Derived from Semiempirical Methods
    • Besler, B. H.; Merz, K. M.; Kollman, P. A. Atomic Charges Derived from Semiempirical Methods. J. Comput. Chem. 1990, 77, 431-439.
    • (1990) J. Comput. Chem. , vol.77 , pp. 431-439
    • Besler, B.H.1    Merz, K.M.2    Kollman, P.A.3
  • 34
    • 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, 543-585.
    • (1993) Annu. Rev. Biochem. , vol.62 , pp. 543-585
    • Wlodawer, A.1    Erickson, J.W.2
  • 35
    • 0029757151 scopus 로고    scopus 로고
    • Solution NMR Evidence that the HIV-1 Protease Catalytic Aspartyl Groups Have Different lonization States in the Complex Formed with the Asymmetric Drug KNI-272
    • Wang, Y.-X.; Freedberg, D. I.; Yamazaki, T.; Wingfield, P. T.; Stahl, S. J.; Kaufman, J. D.; Kiso, Y.; Torchia, D. A. Solution NMR Evidence That the HIV-1 Protease Catalytic Aspartyl Groups Have Different lonization States in the Complex Formed with the Asymmetric Drug KNI-272. Biochemistry 1996, 35, 9945-9950.
    • (1996) Biochemistry , vol.35 , pp. 9945-9950
    • Wang, Y.-X.1    Freedberg, D.I.2    Yamazaki, T.3    Wingfield, P.T.4    Stahl, S.J.5    Kaufman, J.D.6    Kiso, Y.7    Torchia, D.A.8
  • 36
    • 0003583852 scopus 로고
    • 9685 Scranton Road, San Diego, CA 92121-3752.
    • Insight II, release 95.0 (1995), Biosym/Molecular Simulations, 9685 Scranton Road, San Diego, CA 92121-3752.
    • (1995) Biosym/Molecular Simulations
  • 37
    • 0004193646 scopus 로고
    • Fujitsu Ltd., Tokyo, Japan.
    • Stewart, J. J. P. MOPAC 93 (1993), Fujitsu Ltd., Tokyo, Japan.
    • (1993) MOPAC 93
  • 40
    • 84986486656 scopus 로고
    • Rapid Finite Difference Algorithm, Utilizing Successive Over-Relaxation to Solve the PoissonBoltzmann Equation
    • Nicholls, A.; Honig, B. A Rapid Finite Difference Algorithm, Utilizing Successive Over-Relaxation to Solve the PoissonBoltzmann Equation. J. Comput. Chem. 1991, 72, 435-445.
    • (1991) J. Comput. Chem. , vol.72 , pp. 435-445
    • Nicholls, A.1    Honig, B.A.2
  • 42
    • 84988087911 scopus 로고
    • Calculating the Electrostatic Potential of Molecules in Solution: Method and
    • (a) Gilson, M. K.; Sharp, K. A.; Honig, B. H. Calculating the Electrostatic Potential of Molecules in Solution: Method and Error Assessment. J. Comput. Chem. 1987, 9, 327-335.
    • (1987) J. Comput. Chem. , vol.9 , pp. 327-335
    • Gilson, M.K.1    Sharp, K.A.2    Honig, B.H.3    Assessment, E.4
  • 43
    • 0023779259 scopus 로고
    • Calculation of the Total Electrostatic Energy of a Macromolecular System: Solvation Energies, Binding Energies, and Conformational Analysis
    • (b) Gilson, M. K.; Honig, B. Calculation of the Total Electrostatic Energy of a Macromolecular System: Solvation Energies, Binding Energies, and Conformational Analysis. Proteins 1988, 4, 7-18.
    • (1988) Proteins , vol.4 , pp. 7-18
    • Gilson, M.K.1    Honig, B.2
  • 44
    • 0029019869 scopus 로고
    • A Continuum Model for Protein-Protein Interactions: Application to the Docking Problem
    • Jackson, R. M.; Sternberg, M. J. E. A Continuum Model for Protein-Protein Interactions: Application to the Docking Problem. J. Mol. Biol. 1995, 250, 258-275.
    • (1995) J. Mol. Biol. , vol.250 , pp. 258-275
    • Jackson, R.M.1    Sternberg, M.J.E.2
  • 45
    • 0030892498 scopus 로고    scopus 로고
    • Reliability of CoMFA Models: Effects of Data Scaling and Variable Selection Using a Set of Human Synovial Fluid Phospholipase A2 Inhibitors
    • Ortiz, A. R., Pastor, M., Palomer, A., Cruciani, G., Gago, F., Wade, R. C. Reliability of CoMFA Models: Effects of Data Scaling and Variable Selection Using a Set of Human Synovial Fluid Phospholipase A2 Inhibitors. J. Med. Chem. 1997, 40, 1136-1148.
    • (1997) J. Med. Chem. , vol.40 , pp. 1136-1148
    • Ortiz, A.R.1    Pastor, M.2    Palomer, A.3    Cruciani, G.4    Gago, F.5    Wade, R.C.6
  • 47
    • 0000538815 scopus 로고
    • Analytical Molecular Surface Calculation
    • Connolly, M. L. Analytical Molecular Surface Calculation J. Appl Crystalogrl. 1983, 16, 548-558.
    • (1983) J. Appl Crystalogrl. , vol.16 , pp. 548-558
    • Connolly, M.L.1
  • 48
    • 0022964504 scopus 로고
    • Focusing of Electric Fields in the Active Site of Cu-Zn Superoxide Dismutase: Effects of Ionic Strength and
    • Happer, I.; Hagstrom, R.; Fine, R.; Sharp, K; Honig, B. Focusing of Electric Fields in the Active Site of Cu-Zn Superoxide Dismutase: Effects of Ionic Strength and Amino-acid Modification. Proteins 1986, 1, 47-59.
    • (1986) Proteins , vol.1 , pp. 47-59
    • Happer, I.1    Hagstrom, R.2    Fine, R.3    Sharp, K.4    Honig, B.5    Modification, A.-A.6
  • 50
    • 33847423502 scopus 로고    scopus 로고
    • Multivariate Infometric Analysis, Viale dei Castagni 16, Perugia, Italy.
    • GOLPE, version 3.0 (1996), Multivariate Infometric Analysis, Viale dei Castagni 16, Perugia, Italy.
    • Version 3.0 (1996)
  • 52
    • 33847445472 scopus 로고    scopus 로고
    • In preparation.
    • (38) Cuevas, C.; Pérez, C.; Pastor, M.; Gago, F. In preparation.
    • , vol.38
  • 54
    • 0028986487 scopus 로고
    • Targe.ting HIV-1 Protease: A Test of Drug Design Methodologies
    • West, M. L.; Fairlie, D. P. Targe.ting HIV-1 Protease: A Test of Drug Design Methodologies. Trends Pharmacol. Sei. 1995, 16, 67-75.
    • (1995) Trends Pharmacol. Sei. , vol.16 , pp. 67-75
    • West, M.L.1    Fairlie, D.P.2
  • 55
    • 0030905238 scopus 로고    scopus 로고
    • Structure-Based Thermodynamic Analysis of HIV-1 Protease Inhibitors
    • Bardi, J. S.; Luque, L; Freire, E. Structure-Based Thermodynamic Analysis of HIV-1 Protease Inhibitors. Biochemistry 1997, 36, 6588-6596.
    • (1997) Biochemistry , vol.36 , pp. 6588-6596
    • Bardi, J.S.1    Luque, L.2    Freire, E.3
  • 57
    • 0030176923 scopus 로고    scopus 로고
    • The Energetics of Ligand Binding at Catecholamine Receptors
    • Strange, P. G. The Energetics of Ligand Binding at Catecholamine Receptors. Trends Pharmacol. Sei. 1996, 17, 238-244.
    • (1996) Trends Pharmacol. Sei. , vol.17 , pp. 238-244
    • Strange, P.G.1
  • 59
    • 0029775232 scopus 로고    scopus 로고
    • Crystal Structures of Complexes of a Peptidic Inhibitor with Wild-Type and Two Mutant HIV-1 Proteases
    • (b) Hong, L.; Treharne, A.; Hartsuck, J. A.; Foundling, S.; Tang, J. Crystal Structures of Complexes of a Peptidic Inhibitor with Wild-Type and Two Mutant HIV-1 Proteases. Biochemistry 1996, 35, 10627-10633.
    • (1996) Biochemistry , vol.35 , pp. 10627-10633
    • Hong, L.1    Treharne, A.2    Hartsuck, J.A.3    Foundling, S.4    Tang, J.5


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