Exposing Hidden Binding Pockets in Cereblon: His378 Conformational Dynamics Inform Novel Ligand Design

Cereblon (CRBN), a core component of the CRL4 ubiquitin ligase complex, regulates substrate ubiquitination and degradation, thereby exerting broad control over essential cellular processes. Its pivotal role has been exploited in the development of therapeutic modalities such as proteolysis-targeting chimeras and molecular glues. However, most existing ligands are derived from immunomodulatory drug scaffolds, which present limitations including suboptimal selectivity and intellectual property restrictions. This underscores the need for novel chemotypes capable of engaging CRBN. To address this challenge, we performed extensive molecular dynamics (MD) simulations to explore the conformational dynamics of the CRBN ligand-binding pocket. Based on the MD trajectories, we constructed free energy landscapes and Markov state models to characterize the dynamics of key binding site residues. Our analysis identified multiple (meta)stable states defined primarily by the conformational and tautomeric variability of His378. Importantly, the dominant C1 conformation of His378 is associated with a previously unrecognized cavity adjacent to the canonical ligand-binding site, presenting new opportunities for the design of novel CRBN ligands. These insights provide a structural and dynamic framework for the discovery of next-generation CRBN binders with improved selectivity and therapeutic potential.