A theoretical investigation of tight-binding thermolysin inhibitors

Journal of Medicinal Chemistry

Volumn 40, Issue 18, 1997, Pages 2953-2958

  Shen, Jian ^a  

^a SANOFI   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DRUG RECEPTOR; PROTEINASE INHIBITOR; THERMOLYSIN; THERMOLYSIN INHIBITOR; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; DRUG RECEPTOR BINDING; ENERGY TRANSFER; KINETICS; LIGAND BINDING; PROTON TRANSPORT; RECEPTOR AFFINITY; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS;

BINDING SITES; CALORIMETRY; ELECTROSTATICS; ENTROPY; MOLECULAR STRUCTURE; OLIGOPEPTIDES; POISSON DISTRIBUTION; PROTEASE INHIBITORS; STRUCTURE-ACTIVITY RELATIONSHIP; THERMOLYSIN; WATER;

EID: 0030803237     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm9606958     Document Type: Article

References (31)

1. (a) Bartlett, P. A.; Marlowe, C. K. Evaluation of intrinsic binding energy from a hydrogen bonding group in an enzyme inhibitor. Science 1987, 235, 569-571.
2. (b) Bartlett, P. A.; Marlowe, C. K. Possible role for water dissociation in the slow binding of phosphorus-containing transition-state-analogue inhibitors of thermolysin. Biochemistry 1987, 26, 8553-8561.
3. Holden, H. M.; Tronrud, D. E.; Monzingo, A. F.; Weaver, L. H.; Matthews, B. W. Slow- and fast-binding inhibitors of thermolysin display different modes of binding: Crystallographic analysis of extended phosphonamidate transition-state analogues. Biochemistry 1987, 26, 8542-8552.
4. Tronrud, D. E.; Holden, H. M.; Matthews, B. W. Structures of two thermolysin-inhibitor complexes that differ by a single hydrogen bond. Science 1987, 235, 571-574.
5. Matthews, B. W. Structural Basis of the action of thermolysin and related zinc peptidases. Acc. Chem. Res. 1988, 21, 333-340.
6. Grohelny, D.; Goli, U. B.; Galardy, R. E. Binding of phosphorus-containing inhibitors of thermolysin. Biochemistry 1989, 28 4948-4951.
7. Morgan, B. P,; Scholtz, J. M.; Ballinger, M. D.; Zipkin, I. D.; Bartlett, P. A. Differential Binding Energy, A detailed evaluation of the influence of hydrogen-bonding and hydrophobic groups on the inhibition of thermolysin phosphorus-containing inhibitors. J. Am. Chem. Soc. 1991, 113, 297-307.
8. Rich, D. H.; Northrop, D. B. Enzyme kinetics in drug design: Implications of multiple forms of enzyme on substrate and inhibitor structure-activity correlations. In Computer-aided Drug Design; Perun, T. J., Propst, C. L., Eds.; Marcel Dekker: New York, 1989; pp 185-250.
9. Hangauer, D. G. Computer-aided design and evaluation of angiotensin converting enzyme inhibitor. In Computer-aided Drug Design; Perun, T. J., Propst, C. L., Eds.; Marcel Dekker, New York, 1989; pp 253-326.
10. Henderson, B.; Docherty, A. J. P.; Beeley, N. R. A. Design of inhibitors of articular cartilage destruction. Drug Future 1990, 15, 495-507.
11. Bash, P. A; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A. 1987. Calculation of the relative change in binding free energy of a protein-inhibitor complex. Science 1987, 235, 574-576.
12. Merz, K. M.; Kollman, P. A. Free energy perturbation simulations of the inhibition of thermolysin: Prediction of the free energy of binding of a new inhibitors. J. Am. Chem. Soc. 1989, 111, 5649-5658.
13. Wendoloski, J. J.; Shen, J.; Oliva, M. R.; Weber, P. C. Biophysical Tools for Structure-Based Drug Design. Pharmacol. Ther. 1993, 60, 169-183.
14. Shen, J.; Wendoloski, J. J. 1995. Binding of phosphorus-containing inhibitors to thermolysin studied by the Poisson-Boltzmann Method. Protein Sci. 1995, 4, 373-381.
15. Head, R. D.; Smythe, M. L.; Oprea, T. I.; Waller, C. L.; Green, S. M.; Marshall, G. R. Validate: A new method for the receptor-based prediction of binding affinities of novel ligands. J. Am. Chem. Soc. 1996, 118, 3959-3969.
16. Wasserman, Z. R.; Hodge, C. N. Fitting an inhibitor into the active site of thermolysin: A molecular dynamics case study. Protein 1996, 24, 227-237.
17. 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.
18. Harvey, S. C. Treatment of electrostatic effects in macromolecular modeling. Proteins 1989, 5, 78-92.
19. Davis, M. E.; McCammon, J. A. Electrostatics in biomolecular structure and dynamics. Chem. Rev. 1990, 90, 509-521.
20. Sharp, K. A.; Honig, B. Electrostatic interaction in macromolecules: Theory and applications. Annu. Rev. Biophys. Chem. 1990, 19, 301-332.
21. Shen, J.; Wendoloski, J. J. Electrostatic binding energy Calculation Using the finite difference solution to the linearized Poisson-Boltzmann equation: Assessment of its accuracy. J. Compt. Chem. 1995, 17, 350-357.
22. Ben-Naim, A.; Marcus, Y. Solvation thermodynamics of nonionic solutes. J. Chem. Phys. 1984, 81, 2016-2027
23. Davis, M. E.; Madura, J. D.; Luty, B. A.; McCammon, J. A. Electrostatic diffusion of molecules in solution: simulation with the University of Houston Brownian Dynamics program. Comp. Phys. Commun. 1991, 62, 187-190.
24. Briggs, J. M.; Madura, J. D.; Davis, M. E.; Gilson, M. K.; Antosiewicz, J.; Luty, B. A.; Wade, R. C.; Bagheri, B.; Ilin, A.; Tan, R. C.; McCammon, J. A. University of Houston Brownian Dynamics Program User's Guide and Programmer's Manual Release 5.1.exp, available at Molecular Simulations, Inc., San Diego, 1995.
25. van Gunsteren, W. F.; Berendsen, H. J. C. Groningen Molecular Simulation (GROMOS) Library Manual; Biomos: Nijenborgh 16, The Netherlands, 1987.
26. Brunger, A. T. X-PLOR Manual v 2.0; Yale University: New Haven, CT, 1991.
27. Tanford, C. The hydrophobic Effect: Formation of Micelles and Biological Membranes; John Wiley & Sons: New York, 1973.
28. Hansch, C.; Leo, A. Exploring QSAR; American Chemical Society: Washington, DC, 1995.
29. Gao, J.; Qiao, S.; Whitesides, G. M. Increasing binding constants of ligands to carbonic anhydrase by using "greasy tails". J. Med. Chem. 1995, 38, 2292-2301.
30. Testa, B.; Carrupt, P-A.; Gatrick, C.; Billois, F.; Weber, P. Lipophilicity in molecular modeling. Pharm. Res. 1996, 13, 335-343.
31. Ajay; Murcko, M. A. Computational methods to predict binding free energy in ligand-receptor complex. J. Med. Chem. 1995, 38, 4953-4967.