Fitting an inhibitor into the active site of thermolysin: A molecular dynamics case study

Proteins: Structure, Function and Genetics

Volumn 24, Issue 2, 1996, Pages 227-237

  Wasserman, Zelda R ^a   Hodge, C Nicholas ^a  

^a DUPONT COMPANY   (United States)

Author keywords

computer simulation; metalloenzymes; protein ligand interactions; rational drug design; substrate docking

Indexed keywords

BACTERIAL ENZYME; CARBONATE DEHYDRATASE; CARBOXYPEPTIDASE A; ENZYME INHIBITOR; HYDROXAMIC ACID; LEUCINE; LIGAND; SULFONAMIDE; THERMOLYSIN;

ARTICLE; COMPUTER SIMULATION; DRUG DESIGN; ENZYME ACTIVE SITE; ENZYME INHIBITION; ENZYME SUBSTRATE; LIGAND BINDING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL;

BINDING SITES; COMPUTER SIMULATION; DRUG DESIGN; LEUCINE; MODELS, MOLECULAR; MOTION; PROTEASE INHIBITORS; REPRODUCIBILITY OF RESULTS; THERMODYNAMICS; THERMOLYSIN;

EID: 0029979312     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199602)24:2<227::AID-PROT9>3.0.CO;2-F     Document Type: Article

References (34)

1. Matthews, B.W., Weaver, L.H., Kester, W.R. Conformation of thermolysin. J. Biol. Chem. 249:8030-8044, 1974.
2. Matthews, B.W. Structural basis of the action of thermolysin and related zinc peptidases. Acc. Chem. Res. 21:333-340, 1988.
3. Merz, K.M. Jr., Kollman, P.A. Free energy perturbation simulations of the inhibition of thermolysin: Prediction of the free energy of binding of a new inhibitor. J. Am. Chem. Soc. 111:5649-5658, 1989.
4. 2 to the active site of human carbonic anhydrase. II: A molecular dynamics study. Proc. Natl. Acad. Sci. USA 87:3675-3679, 1990.
5. Zheng, Y J., Merz, K.M. Jr. Mechanism of the human carbonic anhydrase II catalyzed hydration of carbon dioxide. J. Am. Chem. Soc. 114:10498-10507, 1992.
6. Peng, Z., Merz, K.M. Jr., Banci, L. Binding of cyanide, cyanate and thiocyanate to human carbonic anhydrase II. Proteins 17:203-216, 1993.
7. Merz, K.M. Jr., Murcko, M.A., Kollman, P.A. Inhibition of carbonic anhydrase. J. Am. Chem. Soc. 113:4484-4490, 1991.
8. Rossi, K.A., Merz, K.M. Jr., Smith, G.M., Baldwin, J.J. Application of the free energy perturbation method to human carbonic anhydrase. II. Inhibitors. J. Med. Chem. 38: 2061-2069, 1995.
9. Ryde, U. Molecular dynamics simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion. Proteins 21:40-56, 1995.
10. Hoops, S.C., Anderson, K.W., Merz, K.M. Jr. Force field design for metalloproteins. J. Am. Chem. Soc. 113:8262-8270, 1991.
11. DiNola, A., Roccatano, D., Berendsen, H.J.C. Molecular dynamics simulation of the docking of substrates to proteins. Proteins 19:174-182, 1994.
12. Abagyan, R., Totrov, M., Kuznetsov, D. ICM - a new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation, J. Comp. Chem. 15:488-506, 1994.
13. Goodford, P.J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 28:849-857, 1985.
14. Goodsell, D.S., Olson, A.J. Automated docking of substrates to proteins by simulated annealing. Proteins 8:195-202, 1990.
15. Guida, W.C., Bohacek, R.S., Erion, M.D. Probing the conformational space available to inhibitors in the thermolysin active site using Monte Carlo/energy minimization techniques. J. Comp. Chem. 13:214-228, 1992.
16. Meng, E.C., Shoichet, B.K., Kuntz, I.D. Automated docking with grid-based energy evaluation. J. Comp. Chem. 13:505-524, 1992.
17. Leach, A.R. Ligand docking to proteins with discrete side-chain flexibility. J. Mol. Biol. 235:345-356, 1994.
18. Judson, R.S., Jaeger, E.P., Treasurywala, A.M. A genetic algorithm based method for docking flexible molecules. J. Mol. Struct. 308:191-206, 1994.
19. 1/2.
20. Weiner, P.K., Kollman, P.A. AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions. J. Comp. Chem. 2:287-303, 1981.
21. Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., Profeta, S. Jr., Weiner, P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106:765-784, 1984.
22. Stouten, P.F.W., Frömmel, C., Nakamura, H., Sander, C. An effective solvation term based on atomic occupancies for use in protein simulations. Mol. Sim. 10:97-120, 1993.
23. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F. Jr., Brice, M.D., Rodgers, J.R., Kennard, O., Simanouchi, T., Tasumi, M. The Protein Data Bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542, 1977.
24. Lovejoy, B., Cleasby, B., Hassell, A.M., Longley, K., Luther, M.A., Weigl, D., McGeehan, G., McElroy, A.B., Drewry, D., Lambert, M.H., Jordan, S.R. Structure of the catalytic domain of fibroblast collagenase complexed with an inhibitor. Science 263:375-377, 1994.
25. Borkakoti, N., Winkler, F.K., Williams, D.H., D'Arcy, A., Broadhurst, M.J., Brown, P.A., Johnson, W.H., Murray, E.J. Structure of the catalytic domain of human fibroblast collagenase complexed with an inhibitor. Struct. Biol. 1:106-110, 1994.
26. Gooley, P.R., O'Connell, J.F., Marcy, A.I., Cuca, G.C., Salowe, S.P., Bush, B.L., Hermes, J.D., Esser, C.K., Hagmann, W.K., Springer, J.P., Johnson, B.A. The NMR structure of the uninhibited catalytic domain of human stromelysin-1. Struct. Biol. 1:111-118, 1994.
27. Stams, T., Spurlino, J.C., Smith, D.L., Wahl, R.C., Ho, T.F., Qoronfleh, M.W., Banks, T.M., Rubin, B. Structure of human neutrophil collagenase revelas large S1′ specificity pocket. Struct. Biol. 1:119-123, 1994.
28. Spurlino, J.C., Smallwood, A.M., Carlton, D.D., Banks, T.M., Vavra, K.J., Johnson, J.S., Cook, E.R., Falvo, J., Wahl, R.C., Pulvino, T.A., Wendoloski, J.J., Smith, D.L. 1.56Å structure of mature truncated human fibroblast collagenase. Proteins 19:98-109, 1994.
29. Holmes, M.A., Matthews, B.W. Binding of hydroxamic acid inhibitors to crystalline thermolysin suggests a pentacoordinate zinc intermediate in catalysis. Biochemistry 20:6912-6920, 1981.
30. Izquierdo-Martin, M., Stein, R.L., Mechanistic studies on the inhibition of thermolysin by a peptide hydroxamic acid. J. Am. Chem. Soc. 114:325-331, 1992.
31. Blaney, J.M., Crippen, G.M., Dearing, A., Dixon, J.S. DGEOM: Distance geometry program. Quantum Chemistry Program Exchange, Indiana University, Bloomington, IN, program #590.
32. Kester, W.R., Matthews, B.W. Crystallographic study of the binding of dipeptide inhibitors to thermolysin: Implications for the mechanism of catalysis. Biochemistry 16: 2506-2516, 1977.
33. 2+ in complexes in solution. Quantification of equilibria involving a change of the coordination number of the metal ion. Chem. Soc. Rev. 23: 83-91, 1994.
34. Stote, R.H., Karplus, M. Zinc binding in proteins and solution: A simple but accurate nonbonded representation. Proteins 23:12-31, 1995.