Comparative Binding Energy Analysis

Perspectives in Drug Discovery and Design

Volumn 9--11, Issue , 1998, Pages 19-34

  Wade, Rebecca C ^a   Ortiz, Angel R ^b   Gago, Federico ^c  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

^c UNIVERSITY OF ALCALÁ   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0002207845     PISSN: 09282866     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (32)

1. Kubinyi, H., QSAR: Hansch analysis and related approaches, VCH, Weinheim, 1993.
2. Kubinyi, H. (Ed.), 3D-QSAR in drug design: Theory, methods and applications, ESCOM, Leiden, 1993.
3. Kuntz, I.D., Structure-based Strategies for drug design and discovery, Science 257 (1992) 1078-1082.
4. Blundell, T.L., Structure-based drug design, Nature, 384 Suppl. (1996) 23-26.
5. Greer, J., Erickson, J.W., Baldwin, J.J. and Varney, M.D., Application of the three-dimensional structures of protein target molecules in structure-based drug design, J. Med. Chem., 37 (1994) 1035-1054.
6. Hogan, J.C., Directed combinatorial chemistry, Nature, 384 Suppl. (1996) 17-19.
7. 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.
8. 2 Inhibitors, In QSAR and molecular modelling: Concepts, computational tools and biological applications, Sanz, F., Giraldo, J. and Manaut, F. (Eds.) J.R. Prous, Barcelona, 1995, pp. 439-443.
9. Cramer, III. R.D., Patterson, D.E. and Bunce, J.D., Comparative molecular field analysis (CoMFA): 1. Effect of shape on binding of steroids to carrier proteins, J. Am. Chem. Soc., 110 (1988) 5959-5967.
10. Straatsma, T.P. and McCammon, J.A., Computational alchemy, Ann. Rev. Phys. Chem., 43 (1992) 407-435.
11. Kollman, P., Free energy calculations: Applications to chemical and biochemical phenomena, Chem. Rev., 93 (1993) 2395-2417.
12. Blaney, J.M., Weiner, P.K., Dearing, A., Kollman, P.A., Jorgensen, E.C., Oatley, S.J., Burridge, J.M. and Blake, C.C.F., Molecular mechanics simulation of protein-ligand interactions: Binding of thyroid hormone analogues to prealbumin, J. Am. Chem. Soc., 104 (1982) 6424-6434.
13. Menziani, M.C., De Benedetti, P.G., Gago, F. and Richards, W.G., The binding of benzene sulfonamides to carbonic anhydrase enzyme: A molecular mechanics study and quantitative structure-activity relationship, J. Med. Chem., 32 (1989) 951-956.
14. 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.
15. Grootenhuis, P.D.J. and van Galen, P.J.M., Correlation of binding affinities with non-bonded interaction energies of thrombin-inhibitor complexes, Acta Cryst., D51 (1995) 560-566.
16. Åqvist, J., Medina, C. and Samuelsson, J.E., A new method for predicting binding afftinity in computer-aided drug design, Prot. Eng., 7 (1994) 385-391.
17. 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.
18. 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.
19. Ortiz, A.R., Pastor, M., Palomer, A., Cruciani, G., Gago, F. and Wade, R.C., Reliability of comparative molecular field analysis models: Effects of data scaling and variable selection using a set of human synovial phospholipase A2 inhibitors, J. Med. Chem. (1997) 40, 1136-1148.
20. Honig, B. and Nicholls, A., Classical electrostatics in biology and chemistry. Science, 268 (1995) 1144-1149.
21. Wold, S., PLS-partial least squares projections to latent structures, In 3D-QSAR in drug design: Theory, methods and applications, Kubinyi, H. (Ed.), ESCOM, Leiden, 1993, pp. 523-550.
22. Baroni, M., Constantino, G., Cruciani, G., Riganelli, D., Valigi, R. and Clementi, S., Generating optimal linear PLS estimations (GOLPE): An advanced chemometric tool for handling 3DQSAR problems, Quant. Struct.-Act. Relat., 12 (1993) 9-20.
23. 2, Nat. Struct. Biol., 2 (1995) 458-465.
24. Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K.M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W. and Kollman, P.A., A second generation force field for the simulation of proteins, nucleic acids, and organic molecules, J. Am. Chem. Soc., 117 (1995) 5179-5197.
25. Gilson, M.K., Sharp, K.A. and Honig, B.H., Calculating the electrostatic potential of molecules in solution: Method and error assessment, J. Comput. Chem., 9 (1987) 327-335.
26. 2, J. Med. Chem., 37 (1995) 4118-4129.
27. Ajay and Murcko, M.A., Computational methods to predict binding free energy in ligand-receptor complexes, J. Med. Chem., 38 (1995) 4953-4967.
28. Gilson, M.K., Given, J.A., Bush, B.L. and McCammon, J.A., The statistical thermodynamic basis for computation of binding affinities: a critical review, Biophys. J., 72 (1997) 1047-1069.
29. Lybrand, T.P., Ligand-protein docking and rational drug design, Curr. Op. Str. Biol. 5 (1995) 224-228.
30. Checa, A., Ortiz, A.R., de Pascual Teresa, B. and Gago, F., Assessment of solvation effects on calculated binding affinity differences: Trypsin inhibition by flavonoids as a model system for congeneric series. Med. Chem., in press.
31. Mattos, C. and Ringe, D., Multiple binding modes, In 3D QSAR in Drug design: Theory, methods and applications, Kubinyi, H., (Ed.) ESCOM, Leiden, 1993, pp. 226-254.
32. Kraulis, P. J., MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures, J. Appl. Crystallog., 24 (1991) 946-950.