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Molecular design and characterization of an alpha-thrombin inhibitor containing a novel P1 moiety.
Biochemistry. 1997 Feb 04; 36(5):1034-40.B

Abstract

An inhibitor of alpha-thrombin was designed on the basis of the X-ray crystal structures of thrombin and trypsin. The design strategy employed the geometric and electrostatic differences between the specificity pockets of the two enzymes. These differences arise due to the replacement of Ser 190 in trypsin by Ala 190 in thrombin. The new inhibitor contained a tryptophan side chain instead of the arginine side chain that is present in the prototypical thrombin inhibitors. This inhibitor had a Ki value of 0.25 microM, displayed more than 400-fold specificity for thrombin over trypsin, and doubled the rat plasma APTT at a concentration of 44.9 microM. The X-ray crystal structure of the inhibitor/alpha-thrombin complex was determined. This represents the first reported three-dimensional structure of a thrombin/ inhibitor complex where the specificity pocket of the enzyme is occupied by a chemical moiety other than a guanidino or an amidino group. As was predicted by the molecular model, the tryptophan side chain docks into the specificity pocket of the enzyme. This finding is in contrast with the indole binding region of thrombin reported earlier [Berliner, L. J., & Shen, Y. Y. L. (1977) Biochemistry 16, 4622-4626]. The lower binding affinity of the new inhibitor for trypsin, compared to that for thrombin, appears to be due to (i) the extra energy required to deform the smaller specificity pocket of trypsin to accommodate the bulky indole group and (ii) the favorable electrostatic interactions of the indole group with the more hydrophobic specificity pocket of thrombin. The neutral indole group may be of pharmacological significance because the severe hypotension and respiratory distress observed following the administration of some thrombin inhibitors have been linked to the positively charged guanidino or amidino functionalities.

Authors+Show Affiliations

Hoechst Marion Roussel, Inc., Cincinnati, Ohio 45215, USA.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article

Language

eng

PubMed ID

9033393

Citation

Malikayil, J A., et al. "Molecular Design and Characterization of an Alpha-thrombin Inhibitor Containing a Novel P1 Moiety." Biochemistry, vol. 36, no. 5, 1997, pp. 1034-40.
Malikayil JA, Burkhart JP, Schreuder HA, et al. Molecular design and characterization of an alpha-thrombin inhibitor containing a novel P1 moiety. Biochemistry. 1997;36(5):1034-40.
Malikayil, J. A., Burkhart, J. P., Schreuder, H. A., Broersma, R. J., Tardif, C., Kutcher, L. W., Mehdi, S., Schatzman, G. L., Neises, B., & Peet, N. P. (1997). Molecular design and characterization of an alpha-thrombin inhibitor containing a novel P1 moiety. Biochemistry, 36(5), 1034-40.
Malikayil JA, et al. Molecular Design and Characterization of an Alpha-thrombin Inhibitor Containing a Novel P1 Moiety. Biochemistry. 1997 Feb 4;36(5):1034-40. PubMed PMID: 9033393.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Molecular design and characterization of an alpha-thrombin inhibitor containing a novel P1 moiety. AU - Malikayil,J A, AU - Burkhart,J P, AU - Schreuder,H A, AU - Broersma,R J,Jr AU - Tardif,C, AU - Kutcher,L W,3rd AU - Mehdi,S, AU - Schatzman,G L, AU - Neises,B, AU - Peet,N P, PY - 1997/2/4/pubmed PY - 2001/3/28/medline PY - 1997/2/4/entrez SP - 1034 EP - 40 JF - Biochemistry JO - Biochemistry VL - 36 IS - 5 N2 - An inhibitor of alpha-thrombin was designed on the basis of the X-ray crystal structures of thrombin and trypsin. The design strategy employed the geometric and electrostatic differences between the specificity pockets of the two enzymes. These differences arise due to the replacement of Ser 190 in trypsin by Ala 190 in thrombin. The new inhibitor contained a tryptophan side chain instead of the arginine side chain that is present in the prototypical thrombin inhibitors. This inhibitor had a Ki value of 0.25 microM, displayed more than 400-fold specificity for thrombin over trypsin, and doubled the rat plasma APTT at a concentration of 44.9 microM. The X-ray crystal structure of the inhibitor/alpha-thrombin complex was determined. This represents the first reported three-dimensional structure of a thrombin/ inhibitor complex where the specificity pocket of the enzyme is occupied by a chemical moiety other than a guanidino or an amidino group. As was predicted by the molecular model, the tryptophan side chain docks into the specificity pocket of the enzyme. This finding is in contrast with the indole binding region of thrombin reported earlier [Berliner, L. J., & Shen, Y. Y. L. (1977) Biochemistry 16, 4622-4626]. The lower binding affinity of the new inhibitor for trypsin, compared to that for thrombin, appears to be due to (i) the extra energy required to deform the smaller specificity pocket of trypsin to accommodate the bulky indole group and (ii) the favorable electrostatic interactions of the indole group with the more hydrophobic specificity pocket of thrombin. The neutral indole group may be of pharmacological significance because the severe hypotension and respiratory distress observed following the administration of some thrombin inhibitors have been linked to the positively charged guanidino or amidino functionalities. SN - 0006-2960 UR - https://www.unboundmedicine.com/medline/citation/9033393/Molecular_design_and_characterization_of_an_alpha_thrombin_inhibitor_containing_a_novel_P1_moiety_ L2 - https://doi.org/10.1021/bi9622231 DB - PRIME DP - Unbound Medicine ER -