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TitleApplication of Weighted Interaction-Fingerprints for Rationalizing Neosubstrate Potency and Selectivity of Cereblon-Based Molecular Glues.
Journal, issue, pagesJ Med Chem, Vol. 68, Issue 19, Page 20657-20674, Year 2025
Publish dateOct 9, 2025
AuthorsGuilian Luchini / Shuang Liu / Hannah L Powers / Emily Cherney / Jinyi Zhu / Kristina Danga / Joel W Thompson / Lihong Shi / Barbra Pagarigan / Dong Donna Wei / Peter Park / Andrew P Degnan / Christoph W Zapf / Jennifer R Riggs / Scott Johnson / Thomas Cummins /
PubMed AbstractCullin-RING Ligase 4 Cereblon (CRL4) (CRBN) E3 ligase modulatory drugs (CELMoDs) make up a successful class of compounds targeting neosubstrates for proteasome-dependent degradation. Early ...Cullin-RING Ligase 4 Cereblon (CRL4) (CRBN) E3 ligase modulatory drugs (CELMoDs) make up a successful class of compounds targeting neosubstrates for proteasome-dependent degradation. Early immunomodulatory drugs (IMiDs) target Ikaros and Aiolos degradation. In addition, there are ongoing clinical trials targeting the degradation of biologically relevant proteins such as GSPT1, CK1α, and Helios with CRBN-based molecular glues. To date, most advanced preclinical and clinical CRBN-based molecular glues recruit their neosubstrates through canonical G-motifs, secondary protein features that are structurally similar but have significantly different amino acid sequence identities. Analogous to the development of kinase inhibitors, optimizing both neosubstrate recruitment and degradation selectivity is important to minimize potential off-target activity. Here, we describe a computational structure-based approach to analyze and predict putative ligand interactions important in the neosubstrate ternary complex. This approach provides valuable insights for enhanced designs toward the development of more selective and efficacious CRBN-based molecular glues.
External linksJ Med Chem / PubMed:40994183
MethodsEM (single particle) / X-ray diffraction
Resolution2.94 - 3.406 Å
Structure data

72160

9q2d

EMDB-72160, PDB-9q2d:
Cryo-EM structure of ternary complex Ikaros-ZF2:CC-885:CRBN:DDB1 (molecular glue degrader)
Method: EM (single particle) / Resolution: 2.94 Å

PDB-9q22:
Crystal structure of ternary complex Helios-ZF2:I-19:CRBN:DDB1
Method: X-RAY DIFFRACTION / Resolution: 3.406 Å

Chemicals

PDB-1cnp:
THE STRUCTURE OF CALCYCLIN REVEALS A NOVEL HOMODIMERIC FOLD FOR S100 CA2+-BINDING PROTEINS, NMR, 22 STRUCTURES

ChemComp-ZN:
Unknown entry

ChemComp-85C:
1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea

Source
  • homo sapiens (human)
KeywordsLIGASE / CEREBLON / DEGRADER / HELIOS / IKZF2 / DDB1 / MOCLECULAR GLUE / Ikaros / IKZF1 / molecular glue

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