Off-Pocket Activity Cliffs: A Puzzling Facet of Molecular Recognition

While accurate quantitative prediction of ligand–protein binding affinity remains an elusive goal, high-affinity ligands to therapeutic targets are being designed through heuristic optimization of ligand–protein contacts. However, herein, through large-scale data mining and analyses, we demonstrate that a ligand’s binding can also be strongly affected through modifying its solvent-exposed portion that does not make contacts with the protein, thus resulting in “off-pocket activity cliffs” (OAC). We then exposed the roots of the OAC phenomenon by means of molecular dynamics (MD) simulations and MD data analyses. We expect OAC to extend our knowledge of molecular recognition and enhance the drug designer’s toolkit.