FuzzAletheia: Mapping dynamic interaction landscapes of intrinsically disordered protein-ligand complexes to accelerate ligand optimization

Intrinsically disordered proteins (IDPs), representing more than 30% of human proteome, present great challenges in rational drug design due to their highly flexible conformations and dynamic interactions. Though their malfunction is linked to major diseases, IDPs are difficult to target. A critical roadblock lies in hit-to-lead optimization due to their dynamic interactions with hit compounds. Here we developed FuzzAletheia, an IDP-ligand dynamic binding pattern analyzer, to accelerate hit optimization. It analyzes the molecular dynamics simulation trajectories of IDP-ligand to cluster interactions into distinct spatiotemporal stable binding features, which are then visualized and quantified to provide insights into the dynamic binding orientation, strength, and stability. This analysis pinpoints modification sites on hit compounds for optimization. We applied FuzzAletheia to the disordered p53 transactivation domain 1 and its hit compound 1050. Guided by FuzzAletheia analysis, we designed and synthesized six derivatives of 1050 and the most potent compound achieved a 10-fold enhancement in activity, demonstrating its power to accelerate IDP hit optimization.