Multi-step computational identification of small molecules targeting the TLT-1 stalk peptide: structural insights into platelet function and thrombosis.

Abstract

The need for safer and more targeted antithrombotic medications is highlighted by the fact that platelet activation and thrombosis are significant causes of cardiovascular morbidity and mortality. Potential small molecules targeting Triggering Receptor Expressed on Myeloid Cells-Like Transcript-1 (TLT-1), expressed by the TREML1 gene that regulates platelet aggregation and thrombus stabilization, were identified in this study using a thorough in silico approach. Protein-protein interaction analysis, Gene Ontology, KEGG pathway enrichment, and GTEx-based tissue expression were used in network pharmacology of TREML1 to demonstrate its connection to thrombotic processes and platelet activation. Pharmacophore models were created utilizing TLT-1 stalk peptide residues based on the 8CHE crystal structure, and Pharmit was used to screen virtual libraries of synthetic and natural chemicals. AutoDock Vina was used for molecular docking, and compounds with docking scores ≤ - 7.0 kcal/mol were shortlisted, producing 81 synthetic and 27 natural hits. Two natural (ZINC000225509830 and ZINC000015671940) and three synthetic (ZINC000063467474, ZINC000215029558, and ZINC000257255111) candidates were selected after further ADME and toxicity profiling. Interaction profiling revealed that the synthetic compound ZINC000063467474 showed strong hydrogen bonding and π-π stacking interactions with low projected toxicity, whereas the natural compound ZINC000225509830 also showed extensive engagement with TLT-1 stalk-peptide residues. According to molecular dynamics simulations, ZINC000063467474 maintained steady and persistent binding within the TLT-1 pocket for 100 ns, whereas the natural compound exhibited positional drift and decreased stability. These results indicate that ZINC000063467474 may serve as a promising scaffold for targeting the TLT-1 stalk peptide and represents a potential lead for modulating platelet function and thrombosis; however, this requires further experimental validation.