Thinking Outside the Binding Site: A Self-Encapsulating Kinase Inhibitor Remodels Its Pocket to Achieve Selectivity.

Abstract

Rendering kinase inhibitors selective is a strict requirement in drug development and remains a persistent challenge. To identify new routes to engineer selectivity, we have discovered a first-in-class p38δ-isoform selective inhibitor reflecting 12 000-fold selectivity improvement over currently available compounds and superior kinome targeting. X-ray crystallographic characterization indicates that these molecules bind through noncanonical n-π-π stacking sandwich interactions enabled by structural remodeling of the P-loop. Structural and functional analysis indicates that these selective inhibitors are self-encapsulating agents due to direct steric clashing that occludes the binding site in a conformation reinforced by a hydrogen-bonding network involving p38δ-unique H30. This work reveals how inhibitor selectivity is achieved by deliberate remodeling of the drug binding site leveraging structural features outside the binding site commonly overlooked in structure-guided design.