Leveraging Cryptic Ligand Envelopes through Enhanced\nMolecular Simulations

Protein-bound\nligands can adopt a range of different conformations,\ncollectively defining a ligand envelope that has proven to be crucial\nfor the design of potent and selective drugs. Yet, the cryptic nature\nof this ligand envelope makes it difficult to visualize, characterize,\nand ultimately exploit for drug design. Using enhanced molecular dynamics\nsimulations, here, we provide a general framework to reconstruct the\ncryptic ligand envelope that is dynamically accessible by protein-bound\nsmall molecules in solution. We apply this approach to quantify hidden\nconformational heterogeneity in structurally complex ligands including\nthe marine natural product plitidepsin. The computed conformational\nheterogeneity expands the small-molecule footprint beyond that typically\nobserved in experiments, also revealing key thermodynamic and kinetic\nproperties of single ligand–target interactions. The model\nagrees quantitatively with solution NMR, X-ray crystallography, and\nbiochemical measurements, showcasing a versatile strategy to integrate\nreceptor-bound ligand conformational ensembles in molecular design.