Abstract
Cardiovascular diseases remain the leading global cause of mortality, largely due to the limited regenerative capacity of adult cardiac tissue. Thyroid hormones, particularly tri-iodothyronine (T3), have been shown to stimulate cardiomyocyte proliferation through activation of the thyroid hormone receptor alpha (TRα), making this receptor a promising therapeutic target. Here we report a hierarchical and consensus, multi-level virtual screening pipeline integrating Molecular Mechanics (MM), Quantum Mechanics (QM), hybrid QM/MM calculations, and reactivity analysis based on the Fukui function to identify novel TRα agonists. Starting from 412 million compounds in the ZINC15 database, physicochemical filtering, validated pharmacophore matching, and docking guided by ROC curve optimization yielded 568 candidates, from which eight compounds were selected through chemically guided visual inspection. Binding affinity was evaluated with MD/MM-PBSA, PM7, and QM/MM (B3LYP/6-31G*/CHARMM36), and complemented by Fukui reactivity mapping to rationalize protein-ligand recognition. Two ligands, including the approved drug Cetraxate, consistently showed favorable interaction energies and reactivity patterns comparable to T3, suggesting agonistic potential. This work provides a rigorous, multi-scale computational framework and identifies two mechanistically supported TRα agonist candidates for future experimental validation in cardiac regeneration.