Lenalidomide stabilizes protein-protein complexes by turning labile intermolecular H-bonds into robust interactions

Targeted protein degradation (TPD) is emerging as a very promising strategy to modulate protein activities in several diseases, spearheaded by anti–myeloma drugs lenalidomide and pomalidomide. It has been recently demonstrated that the mechanism of action of these drugs involves the increased degradation of several proteins, including the transcription factors Ikaros and Aiolos as well as the enzyme Caseine Kinase 1 alpha (CK1a). It has been shown that lenalidomide and pomalidomide are able to stabilize the complex between the E3 ligase Cereblon (CRL4CRBN) and the aforementioned proteins, while, remarkably, the stability of the protein-protein interaction is very low. Even though the structures for these complexes have been determined, there are no evident interactions that can account for the high formation efficiency of the ternary complex. In this work, we have leveraged Molecular Dynamics to shed light into the molecular determinants underlying the stabilization effect exerted by lenalidomide in the complex between CRL4CRBN and CK1a. Furthermore, we evaluated the effect that different mutations of CK1a in the stability of the ternary complex CRL4CRBN–lenalidomide–CK1a and provide a thermodynamic and kinetic rational for the stabilization effect. These results pave the way to further understand cooperativity effects in drug–induced protein–protein complexes and could help in the future design of improved targeted molecular degraders.