Molecular Dynamics Study of Glues that Selectively Degrade CK1α

Targeted protein degradation has emerged as a novel therapeutic strategy to eliminate disease-associated proteins, particularly those considered undruggable by conventional inhibitors. Molecular glues are small molecules that induce or stabilize interactions between E3 ubiquitin ligases and their substrates, leading to selective protein degradation. In this study, we focus on the degradation of Casein Kinase 1 alpha (CK1α) via the CRL4–CRBN E3 ligase complex, mediated by two different ligands: the first-generation immunomodulatory drug Lenalidomide and the next-generation compound SJ3149. Using molecular dynamics (MD) simulations and MMGBSA binding free energy calculations, we analyzed the structural stability and binding affinity of CK1α– CRBN–ligand ternary complexes. Both full and DDB1-free systems were simulated to assess the role of DDB1 in complex stability. Additionally, four point mutations (I35G, I37E, N39G, G40N) were introduced in the CK1α β-hairpin loop to evaluate their impact on protein–ligand interactions. The results show that both ligands form stable complexes with CRBN and CK1α, although SJ3149 exhibits stronger binding affinity than Lenalidomide. The removal of DDB1 had minimal effect on the structural integrity of the complex. MMGBSA pairwise decomposition identified key residues within CRBN and CK1α that contribute most to ligand binding. Among the mutations, I35G showed distinct dynamic behavior, suggesting that subtle structural changes in the β-hairpin can influence complex flexibility and stability. Overall, this study provides detailed structural and energetic insights into the molecular mechanisms of CK1α degradation, contributing to the rational design of more selective and potent molecular glue degraders for therapeutic use.