Development of Substituted Phenyl Dihydrouracil as the Novel Achiral Cereblon Ligands for Targeted Protein Degradation

Abstract

Glutarimides such as thalidomide, pomalidomide, and lenalidomide are the most frequently used ligands to recruit E3 ubiquitin ligase cereblon (CRBN) for the development of proteolysistargeting chimeras (PROTACs). Due to the rapid and spontaneous racemization of glutarimides, most CRBN-recruiting PROTACs are synthesized as a mixture of racemates or diastereomers. Since the (S)enantiomer is primarily responsible for binding to CRBN, the existence of the largely inactive (R)-enantiomer complicates the drug development process. Herein, we report that substituted achiral phenyl dihydrouracil (PDHU) can be used as a novel class of CRBN ligands for the development of PROTACs. Although the parent PDHU has a minimal binding affinity to CRBN, we found that some substituted PDHUs had a comparable binding affinity to lenalidomide. Structural modeling provided a further understanding of the molecular interactions between PDHU ligands and CRBN. PDHUs also have greater stability than lenalidomide. Finally, potent BRD4 degraders were developed by employing trisubstituted PDHUs.

Design and Synthesis of Novel Cereblon Binders for Use in Targeted Protein Degradation

“…Separation of the individual enantiomers of racemic 11, indicated the S-isomer (14) had slightly greater affinity than the R-isomer (15), with IC 50 of 1.2 and 2.6 μM, respectively. Maintaining the heteroatom linkage to the glutarimide, two different 5,6-fused heterocycles were explored.…”

“…In this manuscript, we report the identification, synthesis, and characterization of a series of such nontraditional CRBN binders. While there have been several recent disclosures of similar nontraditional CRBN binders in the scientific − and patent literature, these had not been disclosed at the time of the work described here.…”

PROTACs Targeting MLKL Protect Cells from Necroptosis

“…63,64 Phenyl dihydrouracil 27 was viewed as particularly attractive as it eliminates the racemization prone chiral center in the glutarimide motif of IMiD ligands, while maintaining CRBN binding affinity, and also exhibits greater chemical stability. 65,66 CRBN ligands 27 and 30 were synthesized following reported literature procedures (Scheme 3). 64,67 The dihydrouracil 27 was further derivatized with substituted piperidine (31) and spiropiperidine (32,33) motifs to introduce rigidity to the linker.…”

“…In recent years, much effort has been dedicated to developing new CRBN recruiting ligands with the goal of optimizing binding affinity, improving stability, and abrogating the molecular glue off-target activity of Immunomodulatory Drug (IMiD)-based ligands such as lenalidomide. − With the optimal linker lengths now established, we investigated two recently reported alternative CRBN ligands 27 and 30 in this context. , Phenyl dihydrouracil 27 was viewed as particularly attractive as it eliminates the racemization prone chiral center in the glutarimide motif of IMiD ligands, while maintaining CRBN binding affinity, and also exhibits greater chemical stability. , …”

Leveraging Ligand Affinity and Properties: Discovery of Novel Benzamide-Type Cereblon Binders for the Design of PROTACs

“…Recently, three groups reported on phenyl dihydrouracil derivatives (IV) as CRBN-engaging agents. [20][21][22] These ligands combined several desirable features, including improved resistance to hydrolytic degradation. Furthermore, replacing the C-3 carbon of the glutarimide ring with nitrogen addressed commonly challenged racemization issues of IMiD-based degraders.…”