Prediction of ligand-receptor binding thermodynamics by free energy force field (FEFF) 3D-QSAR analysis: Application to a set of peptidometic renin inhibitors

Journal of Chemical Information and Computer Sciences

Volumn 37, Issue 4, 1997, Pages 792-811

  Tokarski, J S ^a,b   Hopfinger, A J ^a  

^a UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^b Chem21 Group Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARTIC ACID; CELL SURFACE RECEPTOR; LIGAND; OLIGOPEPTIDE; RENIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; DRUG ANTAGONISM; DRUG DESIGN; METABOLISM; PROTEIN CONFORMATION; STRUCTURE ACTIVITY RELATION; THERMODYNAMICS;

AMINO ACID SEQUENCE; ASPARTIC ACID; BINDING SITES; COMPUTER SIMULATION; DRUG DESIGN; LIGANDS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR STRUCTURE; OLIGOPEPTIDES; PROTEIN CONFORMATION; RECEPTORS, CELL SURFACE; RENIN; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS;

EID: 0031180937     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci970006g     Document Type: Article

References (36)

1. Hopfinger, A. J.; Nakata, Y.; Max, N. In Intermolecular Forces; Pullman, B., Ed.; Reidel-Dordrecht: Netherlands, 1981; p 431.
2. 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.
3. Hopfinger, A. J. A QSAR Investigation of Dihydrofolate Reductase Inhibition by Baker Triazines Based Upon Molecular Shape Analysis. J. Am. Chem. Soc. 1980, 102, 7196-7206.
4. Chervenak, M. C.; Toone, E. J. A Direct Measure of the Contribution of Solvent Reorganization to the Enthalpy of Ligand Binding. J. Am. Chem. Soc. 1994, 116, 10533-10539.
5. Sialecki, A. R.; Hayakawa, K.; Fujinaga, M.; Murphy, M.; Fraser, M.; Muir, A. Carilli, C.; Lewicki, J. A.; Baxter, J. D.; James, M. N. G. Structure of Recombinant Human Renin, a Target for Cardiovascular-Active Drugs, at 2.5 Å Resolution. Science 1989, 243, 1346-1351.
6. Rahuel, J.; Priestle, J. P.; Grütter, M. G. The Crystal Structures of Recombinant Glycosylated Human Renin Alone and in Complex with a Transition State Analog Inhibitor. J. Struct. Biol. 1991, 107, 227-236.
7. Dhanaraj, V.; Dealwis, C. G.; Frazao, C.; Badasso, M.; Sibanda, B. L.; Tickle, I. J.; Cooper. J. B.; Driessen, H. P. C.; Newman, M.; Aguilar, C.; Wood, S. P.; Blundell, T. L.; Hobart, P. M.; Geoghegan, K. F.; Ammirati, M. J.; Danley, D. E.; O'Connor, B. A.; Hoover, D. J. X-ray Analyses of Peptide-Inhibitor Complexes Define the Structural Basis of Specificity for Human and Mouse Renins. Nature 1992, 357, 466-472.
8. Epps, D. E.; Cheney, J.; Schostarez, H.; Sawyer, T. K.; Prairie, M.; Krueger, W. C.; Mandel, F. Thermodynamics of the Interaction of Inhibitors with the Binding Site of Recombinant Human Renin. J. Med. Chem. 1990, 33, 2080-2086.
9. Bernstein, F. C.; Koetzle, T. F.; Williams, G. J. B.; Meyer, E. F.; Brice, M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M. The Protetin Databank, a Computer Based Archival File for Macromolecular Structures. J. Mol. Biol. 1977, 112, 535-542.
10. Pearlstein R. A. CHEMLAB-II Users Guide, Version 11.1; Molecular Simulations Inc.: 16 New England Executive Park, Burlington, MA 01803, 1991.
11. Tokarski, J. T.; Hopfinger, A. J. Constructing Protein Models for Ligand-Receptor Binding Thermodynamics Simulations: An Application to a Set of Renin Inhibitors. J. Chem. Inf. Comput. Sci. 1997 37, 779-791.
12. QUANTA Version 3.3; Molecular Simulations Inc.: 16 New England Executive Park, Burlington, MA 01803, 1993.
13. Doherty, D. C. MOLSIM User Guide; The Chem21 Group, 1780 Wilson Dr., Lake Forest, IL 60045, 1994.
14. Weiner, S. J.; Kollman, P. A.; Nguyen, D. T. An All Atom Force Field for Simulations of Proteins and Nucleic Acids. J. Comput. Chem. 1986, 7, 230-252.
15. Epps, D. E.; Schostarez, H.; Argoudelis, C. V.; Poorman, R. A.; Hinzmann, J.; Sawyer, T. K.; Mandel, F. An Experimental Method for the Determination of Enzyme-Competitive Inhibitor Dissociation Constants form Displacement Curves: Application to Human Renin Using Flourescence Energy Transfer to a Synthetic Dansylated Inhibitor Peptide. Anal. Biochem. 1989, 181, 172-181.
16. Epps, personal communication, 1994.
17. Stewart J. J. P.; Seiler, F. K. QCPE #455 (Ver 4.0), 1987.
18. Blundell, T. L.; Cooper, J.; Foundling, S. I.; Jones, D. M.; Atrash, B.; Szelke, M. On the Rational Design of Renin Inhibitors: X-ray Studies of Aspartic Proteinases Complexed with Transition-State Analogues. Biochemistry 1987, 26, 5585-5590.
19. Swain. A. L.; Gustchina, A.; Wlodawer, A. A Comparison of Three Inhibitors of Human Immunodeficiency Virus Protease. Adv. Exp. Med. Biol. 1992, 306, 433-441.
20. 180 Isotope Exchange. Biochemistry 1991, 30, 8441-8453.
21. Hyland, L. J.; Tomaszek, T. A, 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 1991, 30, 8454-8463.
22. Goldblum, A.; Rayan, A.; Fliess, A.; Glick, M. Extending Crystallographic Information with Semiempirical Quantum Mechanics and Molecular Mechanics: A Case of Aspartic Proteinases. J. Chem. Inf. Comput. Sci. 1993, 33, 270-274.
23. Harte, W. E.; Beveridge, D. L. Molecular Dynamics of HTV-1 Protease. J. Am. Chem. Soc. 1993, 115, 3883-3886.
24. 2 Torsional Terms. J. Am. Chem. Soc. 1977, 99, 8127-8134.
25. Hopfinger, A. J. In Conformational Properties of Macromolecules; Academic Press: New York, 1973; p 38.
26. (a) Hopfinger, A. J. In Conformational Properties of Macromolecules; Academic Press: New York, 1973; p 71.
27. (b) Forsythe, K. H.; Hopfinger, A. J. The Influence of Solvent on the Secondary Structures of Poly(L-Alanine) and Poly (L-Proline). Macromolecules 1973, 6, 423-437.
28. Koehler, M. G.; Hopfinger, A. J. Molecular Modelling of Polymers: 5. Inclusion of Intermolecular Energetics in Estimating Glass and Crystal-melt Transition Temperatures. Polymer 1989, 30, 116-126.
29. Rogers, D.; Hopfinger, A. J. Application of Genetic Function Approximation to Quantitative Structure-Activity Relationships and Quantitative Structure-Property Relationships. J. Chem. Inf. Comput. Sci. 1994, 34, 854-866.
30. Rogers, D. G/SPLINES: An Hybrid of Friedman's Multivariate Adaptive Regression Splines (MARS) Algorithm with Holland's Genetic Algorithm. In The Proceedings of the Fourth International Conference on Genetic Algorithms; San Diego, 1991; p 38.
31. Rogers, D. WOLF Reference Manual Version 5.5; Molecular Simulation Inc.: 1994.
32. Cramer III, R. D.; Bunce, J. D.; Patterson, D. E.; Frank, I. E. Crossvalidation, Bootstrapping, and Partial Least Squares Compared with Multiple Regression in Conventional QSAR Studies. Quant. Struct. Act. Relat. 1988, 7, 18-25.
33. Vajda, S.; Weng, Z.; Rosenfeld, R.; DeLisi, C. Effect of Conformational Flexibility and Solvation on Receptor-Ligand Binding Free Energies. Biochemistry 1994, 33, 13977-13988.
34. 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..; 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.; Drake, P. L.; Zuagy, J. A. A priori Prediction of Activity for HIV-1 Protease Inhibitors Employing Energy Minimization in the Active Site. J. Med. Chem. 1995, 38, 305-317.
35. Baroni, M.; Constantino, G.; Cruciani, G.; Riganelli, D.; Valigi, R.; and Clementi S. GOLPE: An Advanced Chemometric Tool for 3D-QSAR Problems. Quant. Struct. Act. Relat. 1993, 12, 9-20.
36. Schechter, I.; Berger, A. On the Size of the Active Site in Proteases. I. Papain. Biochem. Biophys. Res. Commun. 1967, 27, 157-162.