8OU4 image
Entry Detail
PDB ID:
8OU4
Title:
Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11a
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2023-04-21
Release Date:
2023-11-15
Method Details:
Experimental Method:
Resolution:
2.25 Å
R-Value Free:
0.26
R-Value Work:
0.22
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Cereblon isoform 4
Chain IDs:A, B, C
Chain Length:125
Number of Molecules:3
Biological Source:Magnetospirillum gryphiswaldense
Primary Citation
Leveraging Ligand Affinity and Properties: Discovery of Novel Benzamide-Type Cereblon Binders for the Design of PROTACs.
J.Med.Chem. 66 14513 14543 (2023)
PMID: 37902300 DOI: 10.1021/acs.jmedchem.3c00851

Abstact

Immunomodulatory imide drugs (IMiDs) such as thalidomide, pomalidomide, and lenalidomide are the most common cereblon (CRBN) recruiters in proteolysis-targeting chimera (PROTAC) design. However, these CRBN ligands induce the degradation of IMiD neosubstrates and are inherently unstable, degrading hydrolytically under moderate conditions. In this work, we simultaneously optimized physiochemical properties, stability, on-target affinity, and off-target neosubstrate modulation features to develop novel nonphthalimide CRBN binders. These efforts led to the discovery of conformationally locked benzamide-type derivatives that replicate the interactions of the natural CRBN degron, exhibit enhanced chemical stability, and display a favorable selectivity profile in terms of neosubstrate recruitment. The utility of the most potent ligands was demonstrated by their transformation into potent degraders of BRD4 and HDAC6 that outperform previously described reference PROTACs. Together with their significantly decreased neomorphic ligase activity on IKZF1/3 and SALL4, these ligands provide opportunities for the design of highly selective and potent chemically inert proximity-inducing compounds.

Legend

Protein

Chemical

Disease

Primary Citation of related structures