Abstract
This paper describes the construction, validation and application of an active site model of the serine protease thrombin. Initial use was made of medium resolution X-ray crystallographic structures of thrombin complexed with low molecular weight, non-specific inhibitors to create a computationally useable active site shell of the enzyme. Molecular mechanics methods were then applied to dock known ligands into the active site region in order to derive a model that would accurately predict binding conformations. Validation of the modelling process was achieved by comparison of the predicted enzyme-bound conformations with their known, crystallographic binding conformations. The resultant model was used extensively for predictive purposes prior to obtaining confirmatory crystal data relating to a ligand possessing a novel and unexpected binding component complexed to thrombin. The data served both to confirm the accuracy of the binding site model and to provide information for the further refinement of the model.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
a. Fenton II, J.W., Ann. N.Y. Acad. Sci., 485 (1986) 5. b. Fenton II, J.W., Ofosu, F.A., Moon, D.G. and Maraganore, J.M., Blood Coag. Fibrinol., 2 (1991) 69. c. Berliner, L.T. (Ed.) Thrombin Structure and Function, Plenum Press, New York, NY, 1992. d. Tapparelli, C., Metternich, R., Ehrhardt, C. and Cook, N.S., Trends Pharmacol. Sci., 14 (1993) 366.
a. Semple, J., Minami, N.K., Tamura, S.Y., Brunck, T.K., Nutt, R.F. and Ripka, W.C., Bioorg. Med. Chem. Lett., 7 (1997) 2421. b. Tucker, T.J., Lumma, W.C., Mulichak, A.M., Chen, Z., Naylor-Olsen, A.M., Lewis, S.D., Lucas, R., Freidinger, R.M. and Kuo, L.C., J. Med. Chem., 40 (1997) 830. c. Dominguez, C., Carini, D.J., Weber, P.C., Knabb, R.M., Alexander, R.S., Kettner, C.A. and Wexler, R.R., Bioorg. Med. Chem. Lett., 7 (1997) 79. d. Wiley, M.R., Chirgadze, N.Y., Clawson, D.K., Craft, T.J., Gifford-Moore, D.S., Jones, N.D., Olkowski, J.L., Weir, L.C. and Smith, G.F., Bioorg. Med. Chem. Lett., 6 (1996) 2387. e. Costanzo, M.J., Maryanoff, B.E., Hecker, L.R., Schott, M.R., Yabut, S.C., Zhang, H.-C., Andreade-Gordan, P., Kauffman, J.A., Lewis, J.M., Krishnan, R. and Tulinsky, A., J.Med. Chem., 39 (1996) 3039.
Topol, E.J., Fuster, V., Harrington, R.A., Califf, R.M., Kleiman, N.S., Kereiakes, D.J., Cohen, M., Chapekis, A., Gold, H.K., Tannenbaum, M.A., Rao, A.K., Debowey, D., Schwarz, D., Henis, M. and Cheseboro, J., Circulation, 89 (1994) 1557.
Lidon, R.M., Theroux, P., Juneau, M., Adelman, B. and Maraganore, J., Circulation, 88 (1993) 1495.
Kikumoto, R., Tamao, Y., Tezuka, T., Tonomura, S., Hara, H., Ninomiya, K., Hijikata, A. and Okamoto, S., Biochemistry, 23 (1984) 85.
a. Sanderson, P.E.J., Dyer, D.L., Naylor-Olsen, A.M., Vacca, J.P., Gardell, S.J., Dale Lewis, S., Lucas Jr., B.J., Lyle, E.A., Lynch Jr., J.J. and Mulichak, A.M., Bioorg. Med. Chem. Lett., 7 (1997) 1497. b. Tamura, S.Y., Goldman, E.A., Brunck, T.K., Ripka, W.C. and Semple, J.E., Bioorg. Med. Chem. Lett., 7 (1997) 331. c. Jiang, H., Chen, K., Tang, Y., Chen, J., Wang, Q. and Ji, R., J. Med. Chem., 40 (1997) 3085. d. Jiang, H., Chen, K., Tang, Y., Chen, J., Li, Q., Wang, Q. and Ji, R., Acta Pharm. Sinica, 18 (1997) 36. e. Bertrand, J.A., Oleksyszyn, J., Kam, C., Boduszek, B., Presnell, S., Plaskon, R.R., Suddath, F.L., Powers, J.C. and Williams, L.D., Biochemistry, 35 (1996) 3147.
Bode, W., Mayr, I., Baumann, U., Uber, R., Stone, S.R. and Hofsteenge, J., EMBO J., 8 (1989) 3467.
Banner, D.W. and Hadvary, P., J. Biol. Chem., 266 (1991) 20085.
Mohamadi, F., Richards, N.G.J., Guida, W.C., Liskamp, R., Lipton, M., Caulfield, C., Chang, T., Hendrickson, T. and Still, W.C., J. Comput. Chem., 11 (1990) 440.
Weiner, S.J., Kollman, P.A., Nguyen, D.T. and Case, D.A., J. Comput. Chem., 7 (1986) 230.
Guida, W.C., Bohacek, R.S. and Erion, M.D., J. Comput. Chem., 13 (1992) 214.
The numbering of the thrombin residues is based on Bode et al.' protocol for chymotrypsin [7].
Chang, G., Guida, W.C. and Still, W.C., J. Am. Chem. Soc., 111 (1989) 4379.
P1, P2, P3 etc., define substrate residues amino-terminal to the scissile peptide bond according to Schecter, I. and Berger, A., Biochem. Biophys. Res. Commun., 27 (1967) 157.
a. Tucker, T.J., Brady, S.F., Lumma, W.C., Dale Lewis, S., Gardell, S.J., Naylor-Olsen, A.M., Yan, Y., Sisko, J.T., Stauffer, K.J., Lucas, B.J., Lynch, J.J., Cook, J.J., Stranieri, M.T., Holahan, M.A., Lyle, E.A., Baskin, E.P., Chen, I., Dancheck, K.B., Krueger, J.A., Cooper, C.M. and Vacca, J.P., J. Med. Chem., 41 (1998) 3210. b. Sall, D.J., Bastian, J.A., Briggs, S.L., Buben, J.A., Chirgadze, N.I., Clawson, D.K., Denney, M.L., Giera, D.D., Gifford-Moore, D.S., Harper, R.W., Hauser, K.L., Klimkowski, V.J., Kohn, T.J., Lin, H., Mc-Cowan, J.R., Palkowitz, A.D., Smith, G.F., Takeuchi, K., Thrasher, K.J., Tinsley, J.M., Utterback, B.G., Yan, S.B. and Zhang, M., J. Med. Chem., 40 (1997) 3489.
Priestle, J., Rahuel, J. and Gruetter, M., Internal CIBA-Geigy Report (11-06-93).
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Allen, M.C., Cockcroft, X.L.F., Gruetter, M.G. et al. A model for the binding of low molecular weight inhibitors to the active site of thrombin. J Comput Aided Mol Des 13, 579–588 (1999). https://doi.org/10.1023/A:1008098615891
Issue Date:
DOI: https://doi.org/10.1023/A:1008098615891