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Molecular dynamics simulations of thrombin inhibitors at the S' subsites of thrombin.
Drug Des Discov 1994; 12(1):1-17DD

Abstract

Molecular dynamics were carried out to simulate binding interactions between S' subsites of thrombin and hirudin-based thrombin inhibitors. These inhibitors include three segments: an active-site segment, N alpha-acetyl-(D-Phe)-Pro-Arg-Pro-; a fibrinogen-recognition exo-site segment, hirudin 55-65; and a 13-atom-long linker. These linkers have been reported (Szewczuk et al. (1993) Biochemistry 32, 3396) to influence the binding potency while keeping the same active and exo-site segments. The study found that, by combining different omega-amino acids, the potency could be increased 8-fold or decreased 4-fold compared to the native hirudin linker, -Gln-Ser-His-Asn-Asp-Gly-. Five typical linkers were simulated and compared. Analyzing the trajectory files led to the classification of three different dynamic behaviours for the linkers. The flexible linkers had no influence on the antithrombin activity. Other linkers formed hydrogen bonds with the thrombin S' subsite residues Glu39, leu40, and Gln 151. Formations of some hydrogen bonds enhanced the potency of the inhibitor. In other cases, the hydrogen bonds caused the distortion of the inhibitor conformation while affected the binding potency. Based on these observations, a general binding mode in the S' subsites of thrombin is proposed and potential applications are discussed.

Authors+Show Affiliations

Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec.No affiliation info available

Pub Type(s)

Comparative Study
Journal Article

Language

eng

PubMed ID

7578804

Citation

Yue, S Y., and Y Konishi. "Molecular Dynamics Simulations of Thrombin Inhibitors at the S' Subsites of Thrombin." Drug Design and Discovery, vol. 12, no. 1, 1994, pp. 1-17.
Yue SY, Konishi Y. Molecular dynamics simulations of thrombin inhibitors at the S' subsites of thrombin. Drug Des Discov. 1994;12(1):1-17.
Yue, S. Y., & Konishi, Y. (1994). Molecular dynamics simulations of thrombin inhibitors at the S' subsites of thrombin. Drug Design and Discovery, 12(1), pp. 1-17.
Yue SY, Konishi Y. Molecular Dynamics Simulations of Thrombin Inhibitors at the S' Subsites of Thrombin. Drug Des Discov. 1994;12(1):1-17. PubMed PMID: 7578804.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Molecular dynamics simulations of thrombin inhibitors at the S' subsites of thrombin. AU - Yue,S Y, AU - Konishi,Y, PY - 1994/7/1/pubmed PY - 1994/7/1/medline PY - 1994/7/1/entrez SP - 1 EP - 17 JF - Drug design and discovery JO - Drug Des Discov VL - 12 IS - 1 N2 - Molecular dynamics were carried out to simulate binding interactions between S' subsites of thrombin and hirudin-based thrombin inhibitors. These inhibitors include three segments: an active-site segment, N alpha-acetyl-(D-Phe)-Pro-Arg-Pro-; a fibrinogen-recognition exo-site segment, hirudin 55-65; and a 13-atom-long linker. These linkers have been reported (Szewczuk et al. (1993) Biochemistry 32, 3396) to influence the binding potency while keeping the same active and exo-site segments. The study found that, by combining different omega-amino acids, the potency could be increased 8-fold or decreased 4-fold compared to the native hirudin linker, -Gln-Ser-His-Asn-Asp-Gly-. Five typical linkers were simulated and compared. Analyzing the trajectory files led to the classification of three different dynamic behaviours for the linkers. The flexible linkers had no influence on the antithrombin activity. Other linkers formed hydrogen bonds with the thrombin S' subsite residues Glu39, leu40, and Gln 151. Formations of some hydrogen bonds enhanced the potency of the inhibitor. In other cases, the hydrogen bonds caused the distortion of the inhibitor conformation while affected the binding potency. Based on these observations, a general binding mode in the S' subsites of thrombin is proposed and potential applications are discussed. SN - 1055-9612 UR - https://www.unboundmedicine.com/medline/citation/7578804/full_citation/Molecular_dynamics_simulations_of_thrombin_inhibitors_at_the_S&apos DB - PRIME DP - Unbound Medicine ER -