Computational and Molecular Dynamics Insights into the Antithrombotic Mechanism of Triterpenes Derived from Melaleuca bracteata var. Revolution Gold (Myrtaceae)
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,…
Read the paper
Related studies
- In silico toxicology protocols
- QM7-X, a comprehensive dataset of quantum-mechanical properties spanning the chemical space of small organic molecules
- Quantum Informed Machine-Learning Potentials for Molecular Dynamics Simulations of CO2's Chemisorption and Diffusion in Mg-MOF-74
- In-silico strategies in nano-drug design: Bridging nanomaterials and pharmacological applications
- mRNA codon optimization with quantum computers
- The computational power of the human brain
Go deeper in Evidence Hub
Evidence Hub adds a study data sheet (design, sample size, evidence level, key numbers), an AI summary and a chat grounded in the paper's text.