Discovery and characterization of potent spiro-isoxazole-based cereblon ligands with a novel binding mode

• Published in: European journal of medicinal chemistry 2024-04, Vol.270, p.116328-116328, Article 116328
• Main Authors: Shevalev, Robert, Bischof, Luca, Sapegin, Alexander, Bunev, Alexander, Olga, Grigor'eva, Kantin, Grigory, Kalinin, Stanislav, Hartmann, Marcus D.
• Format: Article
• Language: English
• Subjects: Cereblon ligands; Crystallographic analysis; Microscale thermophoresis; Non-cytotoxic profile; Novel binding mode; Spirocyclic glutarimide derivatives
• ISSN: 0223-5234; 1768-3254
• DOI: 10.1016/j.ejmech.2024.116328

The vast majority of current cereblon (CRBN) ligands is based on the thalidomide scaffold, relying on glutarimide as the core binding moiety. With this architecture, most of these ligands inherit the overall binding mode, interactions with neo-substrates, and thereby potentially also the cytotoxic and teratogenic properties of the parent thalidomide. In this work, by incorporating a spiro-linker to the glutarimide moiety, we have generated a new chemotype that exhibits an unprecedented binding mode for glutarimide-based CRBN ligands. In total, 16 spirocyclic glutarimide derivatives incorporating an isoxazole moiety were synthesized and tested for different criteria. In particular, all ligands showed a favorable lipophilicity, and several were able to outperform the binding affinity of thalidomide as a reference. In addition, all compounds showed favorable cytotoxicity profiles in myeloma cell lines and human peripheral blood mononuclear cells. The novel binding mode, which we determined in co-crystal structures, provides explanations for these improved properties: The incorporation of the spiro-isoxazole changes both the conformation of the glutarimide moiety within the canonical tri-trp pocket and the orientation of the protruding moiety. In this new orientation it forms additional hydrophobic interactions and is not available for direct interactions with the canonical neo-substrates. We therefore propose this chemotype as an attractive building block for the design of PROTACs. [Display omitted] •Sixteen spirocyclic glutarimide derivatives featuring an isoxazole ring were synthesized.•These ligands demonstrated favorable lipophilicity and high CRBN binding affinity with some outperforming thalidomide.•Mild to non-cytotoxic profiles were observed in myeloma cell lines and human peripheral blood mononuclear cells.•The spiro-isoxazole moiety modifies the glutarimide's conformation and orientation in CRBN's tri-Trp pocket, enhancing hydrophobic interactions without interfering with canonical neo-substrates.