Computational and Molecular Dynamics Insights into the Antithrombotic Mechanism of Triterpenes Derived from Melaleuca bracteata var. Revolution Gold (Myrtaceae)

TL;DR

This study uses computational methods to explore how triterpenes from a plant inhibit thrombin, a key protein in blood clotting, and finds that acetylation improves their effectiveness.

Contribution

The study reveals how acetylation enhances thrombin inhibition by triterpenes through detailed molecular dynamics and binding analysis.

Findings

Baa shows the strongest thrombin binding with a ΔG of −29.58 ± 2.97 kcal/mol.

Baa forms a persistent hydrogen bond with Trp96 and stabilizes thrombin's structure.

Acetylation at C-3 improves thrombin inhibition via cooperative hydrogen bonding and van der Waals interactions.

Abstract

Background/Objectives: Thrombin, a serine protease central to coagulation and platelet activation, remains an important target for the development of safer and more effective antithrombotic agents. Naturally derived pentacyclic triterpenoids, such as betulinic acid and its acetylated derivatives, 3β-acetoxybetulinic acid, exhibit promising antiplatelet aggregation activity in validated in vitro and ex vivo assays; however, the molecular determinants underlying their direct thrombin inhibition remain unexplored. Results: Docking and MM/GBSA analyses revealed that Baa exhibits the strongest binding affinity (ΔG = −29.58 ± 2.97 kcal/mol), exceeding those of Ba (−20.94 ± 5.81 kcal/mol) and Asp (−18.87 ± 4.18 kcal/mol). Baa forms a highly persistent hydrogen bond with Trp96 (95.5% occupancy) and extensive hydrophobic contacts with Trp215, Leu99, Ile174, and Tyr60A residues defining thrombin’s aryl-binding pocket. MD trajectories demonstrated that Baa binding reduced solvent-accessible surface area (SASA) and residue fluctuations, indicating enhanced structural compaction and stability. In contrast, Ba exhibited weaker, transient hydrogen bonding, while Asp bound primarily near the catalytic triad. The triterpenes exhibit limited oral bioavailability, free PAINS alerts, favourable permeability and metabolic stability. Conclusions: Acetylation at C-3 (acetoxy substitution) substantially enhances thrombin binding via cooperative hydrogen bonding and van der Waals stabilisation, explaining the superior experimental inhibitory potency of Baa. These findings provide a mechanistic framework for structure-guided optimisation of triterpenoid-based thrombin inhibitors and support their further experimental development. Methods: In this study, molecular docking, molecular dynamics (MD) simulations (400 ns), and MM/GBSA free energy analyses were employed to elucidate the binding mechanisms of 3β-acetoxybetulinic acid (Baa), betulinic acid (Ba), and aspirin (Asp) within the thrombin receptor active site. The simulations were explicitly grounded in previously reported chromogenic antithrombin assays and platelet aggregation studies and were designed to mechanistically rationalise the experimentally observed inhibitory potency.

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