Targeted protein degradation with molecular glue degraders has arisen as a powerful therapeutic modality for eliminating classically undruggable disease-causing proteins through proteasomemediated degradation. However, we currently lack rational chemical design principles for converting protein-targeting ligands into molecular glue degraders. To overcome this challenge, we sought to identify a transposable chemical handle that would convert protein-targeting ligands into molecular degraders of their corresponding targets. Using the CDK4/6 inhibitor ribociclib as a prototype, we identified a covalent handle that, when appended to the exit vector of ribociclib, induced the proteasome-mediated degradation of CDK4 in cancer cells. Further modification of our initial covalent scaffold led to an improved CDK4 degrader with the development of a but-2-ene-1,4-dione ("fumarate") handle that showed improved interactions with RNF126. Subsequent chemoproteomic profiling revealed interactions of the CDK4 degrader and the optimized fumarate handle with RNF126 as well as additional RING-family E3 ligases. We then transplanted this covalent handle onto a diverse set of protein-targeting ligands to induce the degradation of BRD4, BCR-ABL and c-ABL, PDE5, AR and AR-V7, BTK, LRRK2, HDAC1/3, and SMARCA2/4. Our study undercovers a design strategy for converting protein-targeting ligands into covalent molecular glue degraders.

Targeted protein degradation with molecular glue degraders has arisen as powerful therapeutic modality for eliminating classically undruggable disease-causing proteins through proteasome-mediated degradation. However, we currently lack rational chemical design principles for converting protein-targeting ligands into molecular glue degraders. To overcome this challenge, we sought to identify chemical handles that would convert protein-targeting ligands into molecular glue degraders of their targets. Using the CDK4/6 inhibitor Ribociclib as a testbed, we identified a covalent handle that, when appended to the exit vector of Ribociclib, induced the proteasome-mediated degradation of CDK4 in cancer cells. Covalent chemoproteomic profiling of this CDK4 degrader revealed covalent interactions with cysteine 32 of the RING family E3 ubiquitin ligase RNF126. Optimization of this covalent scaffold led to an improved CDK4 degrader with a methoxyphenyl fumarate handle that showed improved interactions with RNF126. We then identified the minimum covalent chemical handle required for interaction with RNF126. With this knowledge in hand, we transplanted this covalent fumarate handle onto chemically related and un-related protein-targeting ligands to induce the degradation of several proteins across diverse protein classes, including BRD4, BCR-ABL and c-ABL, PDE5, AR and AR-V7, BTK, LRRK2, and SMARCA2. Our study undercovers a potential chemical rational design strategy for converting protein-targeting ligands into covalent molecular glue degraders.

Metrics & MoreArticle Recommendations W e realized after publication that there was an error in Figure 3e in the structure of JP-2-200 where the hydrogen atom from the amine in JP-2-200 was far above the structure in the figure. We have corrected Figure 3 here.