References
Kollman, P., Free energy calculation: Applications to chemical and biochemical phenomena, Chem. Rev., 93 (1993) 2395–2417.
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.
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.
Doweyko, A.M., Three-dimensional pharmacophores from binding data, J. Med. Chem., 37 (1994) 1769–1778.
Meng, E.C., Kuntz, I.D., Abraham, D.J. and Kellogg, G.E., Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities, J. Comput.-Aided Mol. Design, 8 (1994) 299–306.
Nauchitel, V., Villaverde, M.C. and Sussman, F., Solvent accessibility as a predictive tool for the free-energy of inhibitor binding to the HIV-1 protease, Protein Science, 4 (1995) 1356–1364.
Wang, H. and Ben-Naim, A., A possible involvement of solvent-induced interactions in drug design, J. Med. Chem., 39 (1996) 1531–1539.
Wallqvist, A., Jernigan, R.L. and Covell, D.G., A preference-based free-energy parameterization of enzyme-inhibitor binding: Applications to HIV-1 protease inhibitor design, Protein Science, 4 (1995) 1881–1903.
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.
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.
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.
Meng, E.C. Shoichet, B.K. and Kuntz, I.D., Automated docking with grid-based energy evaluation, J. Comput. Chem., 13 (1992) 505.
Verlinde, C.L.M.J., Rudenko, G., and Wim, G.J.H., In search of new lead compounds for trypano-somiasis drug design: a protein structure-based linked-fragment approach, J., Comput.-Aided Mol. Design, 6 (1992) 131–147.
Rotstein, S.H. and Murcko, M.A., Groupbuild: A fragment-based method for de novo drug design, J. Med. Chem., 36 (1993) 1700–1710.
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.
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.
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.
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.
Vajda, S., Weng, Z., Rosenfeld, R. and DeLisi, C., Effect of conformational flexibility and solvation on receptor-ligand binding free energies, Biochemistry, 33 (1994) 13977–13988.
King, B.L., Vajda, S. and Delisi, C., Empirical free-energy as a target function in docking and design: Application to HIV-1 protease inhibitors, FEBS Lett., 384 (1996) 87–91.
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.
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.
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.
Kurinov, I.V. and Harrison, R.W., Prediction of New Serine Proteinase Inhibitors, Structural Biology, 1 (1994) 735–743.
Sansom, C.E., Wu, J. and Weber, I.T., Molecular mechanics analysis of inhibitor binding to HIV-1 protease, Protein Eng., 5 (1992) 659–667.
Weber, I.T., Harrison, R.W., Molecular mechanics calculations on HIV-1 protease with peptide-substrates correlate with experimental data, Protein Eng., 9 (1996) 679–690.
Miertus, S., Furlan, M., Tossi, A. and Romeo, D., Design of new inhibitors of HIV-1 aspartic protease, Chem. Phys., 204 (1996) 173–180.
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.
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.
Holloway, M.K., Wai, J.M., Halgren, T.A., Fitzgerald, P.M.D., Vacca, J.P., Dorsey, B.D., Levin, R. B., Thompson, W.J., Chen, L.J., Desolms, S.J., Gaffin, N., Ghosh, A.K., Giuliani, E.A., Graham, S.L., Guare, J.P., Hungate, R.W., Lyle, T.A., Sanders, W.M., Tucker, T.J., Wiggins, M., Wiscount, C.M., Woltersdorf, O.W., Young, S.D., Darke, P.L., and Zugay, J.A., A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site, J. Med. Chem., 38 (1995) 305–317.
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 agrochemicals, materials, and pharmaceuticals, ACS Symposium series 589, American Chemical Society, Washington, DC, 1995, pp. 36–50.
Thompson, W.J., Fitzgerald, P.M.D., Holloway, M.K., Emini, E.A., Darke, P.L., McKeever, B.M., Schleif, W.A., Quintero, J.C., Zugay, J.A., Tucker, T.J., Schwering, J.E., Homnick, C.F., Nunberg, J., Springer, J.P. and Huff, J.R., Synthesis and antiviral activity of a series of HIV-1 protease inhibitors with functionality tethered to the P1 or P1, phenyl sustituents: X-ray crystal structure assisted design, J. Med. Chem., 35 (1992) 1685–1701.
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.
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.
CHARMm version 21.1.7b.; available from Molecular Simulations, Inc., Burlington, MA, U.S.A.
Available from W. Clark Still, Department of Chemistry, Columbia University, New York, U.S.A.
Allinger, N.L., Conformational analysis. 130. MM2: A hydrocarbon force field utilizing V1 and V2 torsional terms, J. Am. Chem. Soc., 99 (1977) 8127.
Lam, P.Y.S., Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors, Science, 263 (1994) 380–384.
Thaisrivongs, S., Random and Rational: Lead Generation via Rational Drug Design and Combinatorial Chemistry, New York, 19–20 October 1994.
Vacca, J.P., Fitzgerald, P.M.D., Holloway, M.K., Hungate, R.W., Starbuck, K.E., Chen, L.J., Darke, P.L., Anderson, P.S., and Huff, J.R., Conformationally constrained HIV-1 protease inhibitors, Bioorg. Med. Chem. Lett., 4 (1994) 499–504.
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 10≠-aromatic system by a fused bis-tetrahydrofuran, J. Med. Chem., 37 (1994) 2506–2508.
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 (HIV) II protease complexed with L-735,524; An orally bioavailable inhibitor of the HIV protease, J. Biol. Chem., 269 (1994) 26344–26348.
Rights and permissions
About this article
Cite this article
Holloway, M.K. A priori prediction of ligand affinity by energy minimization. Perspectives in Drug Discovery and Design 9, 63–84 (1998). https://doi.org/10.1023/A:1027251719816
Issue Date:
DOI: https://doi.org/10.1023/A:1027251719816