메뉴 건너뛰기




Volumn 9, Issue , 1998, Pages 63-84

A Priori Prediction of Ligand Affinity by Energy Minimization

Author keywords

[No Author keywords available]

Indexed keywords


EID: 0001828363     PISSN: 09282866     EISSN: None     Source Type: Journal    
DOI: 10.1023/a:1027251719816     Document Type: Article
Times cited : (19)

References (42)
  • 1
    • 7044239742 scopus 로고
    • Free energy calculation: Applications to chemical and biochemical phenomena
    • Kollman, P., Free energy calculation: Applications to chemical and biochemical phenomena, Chem. Rev., 93 (1993) 2395-2417.
    • (1993) Chem. Rev. , vol.93 , pp. 2395-2417
    • Kollman, P.1
  • 2
    • 0028237444 scopus 로고
    • 3-dimensional quantitavie structure-activity relationship of human- immunodeficiency-virus-(I) protease inhibitors: 2. Predictive power using limited exploration of alternate binding modes
    • Oprea, T.I., Waller, C.L. and Marshall, G.R., 3-dimensional quantitavie structure-activity relationship of human-immunodeficiency-virus-(I) protease inhibitors: 2. Predictive power using limited exploration of alternate binding modes,. J. Med. Chem., 37 (1994) 2206-2215.
    • (1994) J. Med. Chem. , vol.37 , pp. 2206-2215
    • Oprea, T.I.1    Waller, C.L.2    Marshall, G.R.3
  • 3
    • 0027762073 scopus 로고
    • 3- dimensional QSAR of human-immunodeficiency-virus-(I) protease inhibitors: 1. A COMFA study employing experimentally-determined alignment rules
    • Waller, C.L., Oprea, T.I., Giolitti, A. and Marshall, G.R., 3-dimensional QSAR of human-immunodeficiency-virus-(I) protease inhibitors: 1. A COMFA study employing experimentally-determined alignment rules, J. Med. Chem., 36 (1993) 4152-4160.
    • (1993) J. Med. Chem. , vol.36 , pp. 4152-4160
    • Waller, C.L.1    Oprea, T.I.2    Giolitti, A.3    Marshall, G.R.4
  • 4
    • 0028362672 scopus 로고
    • Three-dimensional pharmacophores from binding data
    • Doweyko, A.M., Three-dimensional pharmacophores from binding data, J. Med. Chem., 37 (1994) 1769-1778.
    • (1994) J. Med. Chem. , vol.37 , pp. 1769-1778
    • Doweyko, A.M.1
  • 5
    • 0028455325 scopus 로고
    • Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities
    • Meng, E.C., Kuntz, I.D., Abraham, D.J. and Kellogg, O.E., Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities, J. Comput.-Aided Mol. Design, 8 (1994) 299-306.
    • (1994) J. Comput.-Aided Mol. Design , vol.8 , pp. 299-306
    • Meng, E.C.1    Kuntz, I.D.2    Abraham, D.J.3    Kellogg, O.E.4
  • 6
    • 0029020486 scopus 로고
    • Solvent accessibility as a predictive tool for the free-energy of inhibitor binding to the HlV-1 protease
    • Nauchitel, V., Villaverde, M.C. and Sussman, F., Solvent accessibility as a predictive tool for the free-energy of inhibitor binding to the HlV-1 protease, Protein Science, 4 (1995) 1356-1364.
    • (1995) Protein Science , vol.4 , pp. 1356-1364
    • Nauchitel, V.1    Villaverde, M.C.2    Sussman, F.3
  • 7
    • 0029989480 scopus 로고    scopus 로고
    • A possible involvement of solvent-induced interactions in drug design
    • Wang, H. and Ben-Naim, A., A possible involvement of solvent-induced interactions in drug design, J. Med. Chem., 39 (1996) 1531-1539.
    • (1996) J. Med. Chem. , vol.39 , pp. 1531-1539
    • Wang, H.1    Ben-Naim, A.2
  • 8
    • 0029119320 scopus 로고
    • A preference-based free-energy parameterization of enzyme-inhibitor binding: Applications to HlV-1 protease inhibitor design
    • Wallqvist, A., Jernigan, R.L. and Covell, D.G., A preference-based free-energy parameterization of enzyme-inhibitor binding: Applications to HlV-1 protease inhibitor design, Protein Science, 4 (1995) 1881-1903.
    • (1995) Protein Science , vol.4 , pp. 1881-1903
    • Wallqvist, A.1    Jernigan, R.L.2    Covell, D.G.3
  • 9
    • 0029798563 scopus 로고    scopus 로고
    • Docking enzyme-inhibitor complexes using a preference-based free-energy surface
    • Wallqvist, A. and Covell, D.G., Docking enzyme-inhibitor complexes using a preference-based free-energy surface, Proteins: Struct., Funct. Gene., 25 (1996) 403-419.
    • (1996) Proteins: Struct., Funct. Gene. , vol.25 , pp. 403-419
    • Wallqvist, A.1    Covell, D.G.2
  • 10
    • 0028881193 scopus 로고
    • Empirical free energy calculations of ligand-protein crystallographic complexes: I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity
    • Verkhivker, G., Appelt, K., Freer, S.T., and Villafranca, J.E., Empirical free energy calculations of ligand-protein crystallographic complexes: I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity, Protein Eng., 8 (1995) 677-691.
    • (1995) Protein Eng. , vol.8 , pp. 677-691
    • Verkhivker, G.1    Appelt, K.2    Freer, S.T.3    Villafranca, J.E.4
  • 11
    • 0030058373 scopus 로고    scopus 로고
    • A mean field model of ligand- protein interactions: Implications for the structural assessment of human immunodeficiency virus type I protease complexes and receptor-specific binding
    • Verkhivker, G.M. and Rejto, P.A., A mean field model of ligand-protein interactions: Implications for the structural assessment of human immunodeficiency virus type I protease complexes and receptor-specific binding, Proc. Natl. Acad. Sci. USA, 93 (1996) 60-64.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 60-64
    • Verkhivker, G.M.1    Rejto, P.A.2
  • 12
    • 84986432941 scopus 로고
    • Automated docking with grid-based energy evaluation
    • Meng, E.G. Shoichet, B.K. and Kuntz, I.D., Automated docking with grid-based energy evaluation, J Comput. Chem., 13 (1992) 505.
    • (1992) J Comput. Chem. , vol.13 , pp. 505
    • Meng, E.G.1    Shoichet, B.K.2    Kuntz, I.D.3
  • 13
    • 0026848170 scopus 로고
    • In search of new lead compounds for trypanosomiasis drug design: A protein structure-based linked-fragment approach
    • Verlinde, C.L.M.J., Rudenko, G., and Wim, G.J.H., In search of new lead compounds for trypanosomiasis drug design: a protein structure-based linked-fragment approach, J., Comput.-Aided Mol. Design, 6 (1992) 131-147.
    • (1992) J., Comput.-Aided Mol. Design , vol.6 , pp. 131-147
    • Verlinde, C.L.M.J.1    Rudenko, G.2    Wim, G.J.H.3
  • 14
    • 0027193713 scopus 로고
    • Groupbuild: A fragment-based method for de novo drug design
    • Rotstein, S.H. and Murcko, M. A., Groupbuild: A fragment-based method for de novo drug design, J. Med. Chem., 36 (1993) 1700-1710.
    • (1993) J. Med. Chem. , vol.36 , pp. 1700-1710
    • Rotstein, S.H.1    Murcko, M.A.2
  • 15
    • 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
    • Böhm, 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. Design, 8 (1994) 243-256.
    • (1994) J. Comput.-Aided Mol. Design , vol.8 , pp. 243-256
    • Böhm, H.-J.1
  • 16
    • 1542496902 scopus 로고
    • De novo design of highly diverse structures complementary to enzyme binding sites: Application to thermolysin
    • Reynolds, C.H., Holloway, M.K. and Cox, H.K., (Eds.) Computer-aided molecular design: Applications in agrochemicals, materials and pharmaceuticals, American Chemical Society, Washington, DC
    • Bohacek, R.S.; McMartin, C., De novo design of highly diverse structures complementary to enzyme binding sites: Application to thermolysin, In Reynolds, C.H., Holloway, M.K. and Cox, H.K., (Eds.) Computer-aided molecular design: Applications in agrochemicals, materials and pharmaceuticals, ACS Symposium series 589, American Chemical Society, Washington, DC, 1995, pp. 82-97.
    • (1995) ACS Symposium Series , vol.589 , pp. 82-97
    • Bohacek, R.S.1    McMartin, C.2
  • 17
    • 0029995624 scopus 로고    scopus 로고
    • VALIDATE: A new method for the receptor- based prediction of binding affinities of novel ligands
    • Head, R.D., Smythe, M.L., Oprea, T.I., Waller, C.L., Green, S.M. and Marshall, G.R., VALIDATE: A new method for the receptor-based prediction of binding affinities of novel ligands, J. Am. Chem. Soc., 118 (1996) 3959-3969.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 3959-3969
    • Head, R.D.1    Smythe, M.L.2    Oprea, T.I.3    Waller, C.L.4    Green, S.M.5    Marshall, G.R.6
  • 18
    • 0029000922 scopus 로고
    • Prediction of drug binding affinities by comparative binding energy analysis
    • Ortiz, A.R., Pisabarro, M.T., Gago, F. and Wade, R.C., Prediction of drug binding affinities by comparative binding energy analysis, J. Med. Chem., 38 (1995) 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
  • 19
    • 0028102849 scopus 로고
    • Effect of conformational flexibility and salvation on receptor-ligand binding free energies
    • Vajda, S., Weng, Z., Rosenfeld, R. and DeLisi, C., Effect of conformational flexibility and salvation on receptor-ligand binding free energies, Biochemistry, 33 (1994) 13977-13988.
    • (1994) Biochemistry , vol.33 , pp. 13977-13988
    • Vajda, S.1    Weng, Z.2    Rosenfeld, R.3    DeLisi, C.4
  • 20
    • 0029940017 scopus 로고    scopus 로고
    • Empirical free-energy as a target function in docking and design: Application to HlV-1 protease inhibitors
    • King, B.L., Vajda, S. and Delisi, C., Empirical free-energy as a target function in docking and design: Application to HlV-1 protease inhibitors, FEBS Lett., 384 (1996) 87-91.
    • (1996) FEBS Lett. , vol.384 , pp. 87-91
    • King, B.L.1    Vajda, S.2    Delisi, C.3
  • 21
    • 0028325249 scopus 로고
    • Molecular modeling studies on ligand-binding to sialidase from influenza virus and the mechanism of catalysis
    • Taylor, N.R. and von Itzstein, M., Molecular modeling studies on ligand-binding to sialidase from influenza virus and the mechanism of catalysis, J. Med. Chem., 37 (1994) 616-624.
    • (1994) J. Med. Chem. , vol.37 , pp. 616-624
    • Taylor, N.R.1    Von Itzstein, M.2
  • 22
    • 0029003606 scopus 로고
    • Aldose reductase as a target for drug design-Molecular modeling calculations on the binding of acyclic sugar substrates to the enzyme
    • De Winter, H.L., and von Itzstein, M., Aldose reductase as a target for drug design-Molecular modeling calculations on the binding of acyclic sugar substrates to the enzyme, Biochemistry, 34 (1995) 8299-8308.
    • (1995) Biochemistry , vol.34 , pp. 8299-8308
    • De Winter, H.L.1    Von Itzstein, M.2
  • 23
    • 0001452822 scopus 로고
    • Correlation of binding affinities with nonbonded interaction energies of thrombin-inhibitor complexes
    • Grootenhuis, P.D.J. and van Galen, P.J.M., Correlation of binding affinities with nonbonded interaction energies of thrombin-inhibitor complexes, Acta Cryst., D51 (1995) 560-566.
    • (1995) Acta Cryst. , vol.D51 , pp. 560-566
    • Grootenhuis, P.D.J.1    Van Galen, P.J.M.2
  • 24
    • 0028519286 scopus 로고
    • Prediction of New Serine Proteinase Inhibitors
    • Kurinov, I.V. and Harrison, R. W., Prediction of New Serine Proteinase Inhibitors, Structural Biology, 1 (1994) 735-743.
    • (1994) Structural Biology , vol.1 , pp. 735-743
    • Kurinov, I.V.1    Harrison, R.W.2
  • 25
    • 0026438932 scopus 로고
    • Molecular mechanics analysis of inhibitor binding to HlV-1 protease
    • Sansom, C.E., Wu, J. and Weber, I.T., Molecular mechanics analysis of inhibitor binding to HlV-1 protease, Protein Eng., 5 (1992) 659-667.
    • (1992) Protein Eng. , vol.5 , pp. 659-667
    • Sansom, C.E.1    Wu, J.2    Weber, I.T.3
  • 26
    • 0029790550 scopus 로고    scopus 로고
    • Molecular mechanics calculations on HIV-1 prolease with peptide-substrates correlate with experimental data
    • Weber, I.T., Harrison, R.W., Molecular mechanics calculations on HIV-1 prolease with peptide-substrates correlate with experimental data, Protein Eng., 9 (1996) 679-690.
    • (1996) Protein Eng. , vol.9 , pp. 679-690
    • Weber, I.T.1    Harrison, R.W.2
  • 27
    • 0030533267 scopus 로고    scopus 로고
    • Design of new inhibitors of HIV-1 aspartic protease
    • Miertus, S., Furlan. M., Tossi, A. and Romeo, D., Design of new inhibitors of HIV-1 aspartic protease, Chem. Phys., 204 (1996) 173-180.
    • (1996) Chem. Phys. , vol.204 , pp. 173-180
    • Miertus, S.1    Furlan, M.2    Tossi, A.3    Romeo, D.4
  • 28
    • 1542706596 scopus 로고    scopus 로고
    • Efficient inhibition of HIV-1 aspartic protease by synthetic, computer designed peptide mimetics
    • Tossi, A., Furlan, M., Antcheva, N., Romeo, D. and Miertus, S., Efficient inhibition of HIV-1 aspartic protease by synthetic, computer designed peptide mimetics. Minerva Biotec., 8 (1996) 165-171.
    • (1996) Minerva Biotec. , vol.8 , pp. 165-171
    • Tossi, A.1    Furlan, M.2    Antcheva, N.3    Romeo, D.4    Miertus, S.5
  • 29
    • 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 I protease
    • Viswanadhan, V.N., Reddy, M.R., Wlodawer, A., Varney. M.D. and 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 I protease, J. Med. Chem., 39 (1996) 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
  • 31
    • 0039837427 scopus 로고
    • Structure-based design of human immunodeficiency virus-1 protease inhibitors: Correlating calculated energy with activity
    • Reynolds, C.H., Holloway, M.K., and Cox, H.K. (Eds.) Computer-aided molecular design: Applications in agrochernicals, materials, and pharmaceuticals, American Chemical Society, Washington, DC
    • Holloway, M.K. and Wai, J.M., Structure-based design of human immunodeficiency virus-1 protease inhibitors: Correlating calculated energy with activity, In Reynolds, C.H., Holloway, M.K., and Cox, H.K. (Eds.) Computer-aided molecular design: Applications in agrochernicals, materials, and pharmaceuticals, ACS Symposium series 589, American Chemical Society, Washington, DC, 1995, pp. 36-50.
    • (1995) ACS Symposium Series , vol.589 , pp. 36-50
    • Holloway, M.K.1    Wai, J.M.2
  • 33
    • 0021762055 scopus 로고
    • Effect of pH on the activities of Penicillopepsin and Rhizopus pepsin and a proposal for the productive substrate binding mode in Penicillopepsin
    • Hofmann, T., Hodges, R.S. and James, M.N.G., Effect of pH on the activities of Penicillopepsin and Rhizopus pepsin and a proposal for the productive substrate binding mode in Penicillopepsin, Biochemistry, 23 (1984) 635-643.
    • (1984) Biochemistry , vol.23 , pp. 635-643
    • Hofmann, T.1    Hodges, R.S.2    James, M.N.G.3
  • 34
    • 0026005186 scopus 로고
    • Human immunodeficiency virus-1 protease: 2. Use of pH rate studies and solvent kinetic isotope effects to elucidate details of chemical mechanism
    • Hyland, L.J., Tomaszek, T.A., Jr. and Meek, T.D., Human immunodeficiency virus-1 protease: 2. Use of pH rate studies and solvent kinetic isotope effects to elucidate details of chemical mechanism, Biochemistry, 30 (1991) 8454-8463.
    • (1991) Biochemistry , vol.30 , pp. 8454-8463
    • Hyland, L.J.1    Tomaszek Jr., T.A.2    Meek, T.D.3
  • 35
    • 1542601613 scopus 로고    scopus 로고
    • available from Molecular Simulations, Inc., Burlington, MA, U.S.A.
    • CHARMm version 21.1.7b.; available from Molecular Simulations, Inc., Burlington, MA, U.S.A.
    • CHARMm Version 21.1.7b
  • 36
    • 1542392018 scopus 로고    scopus 로고
    • Available from W. Clark Still, Department of Chemistry, Columbia University, New York, U.S.A..
    • Available from W. Clark Still, Department of Chemistry, Columbia University, New York, U.S.A..
  • 38
    • 0028057975 scopus 로고
    • Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors
    • Lam, P.Y.S., Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors, Science, 263 (1994) 380-384.
    • (1994) Science , vol.263 , pp. 380-384
    • Lam, P.Y.S.1
  • 41
    • 0028017685 scopus 로고
    • Structure- based design of HIV-1 protease inhibitors: Replacement of two amides and a 10Π-aromatic system by a fused bis-tetrahydrofuran
    • Ghosh, A.K., Thompson, W.J., Fitzgerald, P.M.D., Culberson, J.C., Axel, M.G., McKee, S.P., Huff, J.R. and Anderson, P.S., Structure-based design of HIV-1 protease inhibitors: Replacement of two amides and a 10Π-aromatic system by a fused bis-tetrahydrofuran, J. Med. Chem., 37 (1994) 2506-2508.
    • (1994) J. Med. Chem. , vol.37 , pp. 2506-2508
    • Ghosh, A.K.1    Thompson, W.J.2    Fitzgerald, P.M.D.3    Culberson, J.C.4    Axel, M.G.5    McKee, S.P.6    Huff, J.R.7    Anderson, P.S.8
  • 42
    • 0027943157 scopus 로고
    • Crystal structure at 1.9-A resolution of human immunodeficiency virus (HlV) II protease complexed with L-735,524; An orally bioavailable inhibitor of the HIV protease
    • Chen, Z., Li, Y., Chen, E., Hall, D.L., Darke, P.L, Culberson, J.C., Shafer, J. and Kuo, L.C., Crystal structure at 1.9-A resolution of human immunodeficiency virus (HlV) II protease complexed with L-735,524; An orally bioavailable inhibitor of the HIV protease, J. Biol. Chem., 269 (1994) 26344-26348.
    • (1994) J. Biol. Chem. , vol.269 , pp. 26344-26348
    • Chen, Z.1    Li, Y.2    Chen, E.3    Hall, D.L.4    Darke, P.L.5    Culberson, J.C.6    Shafer, J.7    Kuo, L.C.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.