Identification of structural-kinetic and structural-thermodynamic relationships for thrombin inhibitors

To improve our understanding of drug-target interactions, we explored the effect of introducing substituted amine residues with increased chain length in the P3 residue of the thrombin inhibitor melagatran. Inhibition, kinetic, and thermodynamic data obtained via stopped-flow spectroscopy (SF), isothermal microcalorimetry (ITC), and surface plasmon resonance (SPR) biosensor analysis were interpreted with the help of X-ray crystal structures of the enzyme-inhibitor complexes. The association rate became faster when the lipophilicity of the inhibitors was increased. This was coupled to an increased enthalpic component and a corresponding decreased entropic component. The dissociation rates were reduced with an increase in chain length, with only a smaller increase and a decrease in the enthalpic and entropic components, respectively. Overall, the affinity increased with an increase in chain length, with similar changes in the enthalpic and entropic components. ITC analysis confirmed the equilibrium data from SPR analysis, showing that the interaction of melagatran was the most enthalpy-driven interaction. Structural analysis of the thrombin-inhibitor complex showed that the orientation of the P1 and P2 parts of the molecules was very similar, but that there were significant differences in the interaction between the terminal part of the P3 side chain and the binding pocket. A combination of charge repulsion, H-bonds, and hydrophobic interactions could be used to explain the observed kinetic and thermodynamic profiles for the ligands. In conclusion, changes in the structure of a lead compound can have significant effects on its interaction with the target that translate directly into kinetic and thermodynamic effects. In contrast to what may be intuitively expected, hydrogen bond formation and breakage are not necessarily reflected in enthalpy gains and losses, respectively.

Abstract sourced from PubMed (NCBI) for the cited record. See the original publication for the authoritative version.

Peer-reviewed research on leech salivary compounds and their pharmacology. Indexed in PubMed and verified against the NCBI record.

Explore cómo esta investigación se conecta con la práctica clínica

More peer-reviewed studies in Farmacología salival.

• Novel Leech Antimicrobial Peptides — Hirunipins — Kumar et al. (2025)
• 434 Salivary Proteins — Integrated Proteomics of Hirudo medicinalis — Liu et al. (2019)
• Medicinal Leech Genome Assembly — Anticoagulant Gene Catalog — Kvist et al. (2020)
• Effects of hirudotherapy on liver functions, lipid profile, and insulin sensitivity in rats with metabolic syndrome — Bilden A et al. (2026)
• [Research progress in hirudin fusion protein--review] — Zhang C et al. (2007)
• A unique proteolytic fragment of human fibrinogen containing the A alpha COOH-terminal domain of the native molecule — Kirschbaum NE, Budzynski AZ (1990)
• Updates on Use and Monitoring of Direct Thrombin Inhibitors — Navaei A et al. (2026)
• Production and functional characteristics of a novel hirudin variant with better anticoagulant activities than bivalirudin — Ge P et al. (2025)
• Traditional Chinese medicine in the treatment of diabetic kidney disease: the mechanisms of signaling pathways regulations — Li W et al. (2026)
• Prostaglandin E1 is an efficient molecular tool for forest leech blood sucking — Zheng F et al. (2021)

Browse all ASH-analysed research →