Chemical Proteomics Identifies RBBP7 as a New E3 Ligase Supporting Targeted Protein Degradation

Abstract

Abstract Targeted protein degradation (TPD) has been recognized as a powerful therapeutic strategy for the treatment of a wide range of diseases. However, the application of existing degraders is constrained by their dependence on a limited number of E3 ubiquitin ligases, such as CRBN and VHL. To address this limitation, we developed a suite of novel small‐molecule degraders by integrating an ynamide electrophile into protein‐targeting ligands. These compounds demonstrated remarkable target degradation capability. Subsequent proteome profiling and functional validation revealed that Cys97 residue of retinoblastoma binding protein 7 (RBBP7) E3 ligase was covalently engaged and responsible for the degradation mechanism. Furthermore, the ynamide motif has proved to be a versatile and transplantable chemical handle, facilitating the development of degraders targeting a wide range of proteins, including CDK4, PDE5, PI3K, AKT, BCR‐ABL, BRD4, EGFR L858R , and EGFR L858R/T790M/C797S . Notably, incorporation of ynamide into the “pan‐kinase” inhibitor XO44 yielded degraders capable of simultaneously degrading various kinases, such as PI3K, Syk, AKT, and GSK‐3β, further highlighting the general feasibility of this approach. Importantly, the ynamide‐containing degraders demonstrated significantly enhanced anticancer potency compared to their parent inhibitors.