Design, synthesis, and biological evaluation of novel PROTACs based on unnatural dipeptide CRBN ligands

Cereblon (CRBN), the target of immunomodulatory drugs (IMiDs) such as thalidomide and lenalidomide, serves as the substrate recognition subunit of the CRL4^CRBN E3 ubiquitin Ligase complex. This E3 Ligase is widely expressed across multiple human tissues and organs, and is commonly utilized in PROTAC design. However, PROTACs derived from classical IMiD-based CRBN ligands face several limitations, including the risk of teratogenicity due to the degradation of CRBN neosubstrates, such as SALL4, and suboptimal drug metabolism and pharmacokinetic (DMPK) properties resulting from the hydrolytic susceptibility of the IMiD scaffold. Therefore, the development of novel chemotypes of CRBN ligands is important for advancing PROTAC development. In this study, we developed novel unnatural dipeptide CRBN ligands for designing PROTAC targeting BRD4 and ALK, the resulting PROTACs demonstrated potent protein degradation and antiproliferative activities, exhibiting comparable or superior efficacy to IMiD-based PROTACs. Our study demonstrated that: (i) dipeptide CRBN ligands-based PROTACs were well tolerated to unnatural hydrophobic Amino acids at the N-1 position; (ii) unnatural cyclic imide dipeptides could serve as versatile CRBN ligands for PROTACs design cross distinct targets; and (iii) unnatural dipeptide PROTACs attenuated degradation of IMiD-associated neosubstrates but induced degradation of novel CRBN neosubstrates. Collectively, these unnatural dipeptide CRBN ligands would expand the chemical space and target scope of CRBN-recruiting PROTACs, and they also showed potential for developing Molecular Glues targeting more proteins.

ALK; BRD4; C-terminal cyclic imide dipeptide; CRBN; PROTAC.