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TitleUnveiling the hidden interactome of CRBN molecular glues.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 6831, Year 2025
Publish dateJul 24, 2025
AuthorsKheewoong Baek / Rebecca J Metivier / Shourya S Roy Burman / Jonathan W Bushman / Hojong Yoon / Ryan J Lumpkin / Julia K Ryan / Dinah M Abeja / Megha Lakshminarayan / Hong Yue / Samuel Ojeda / Yuan Xiong / Jianwei Che / Alyssa L Verano / Anna M Schmoker / Nathanael S Gray / Katherine A Donovan / Eric S Fischer /
PubMed AbstractInduced proximity by molecular glues refers to strategies that leverage the recruitment of proteins to facilitate their modification, regulation or degradation. As prospective design of molecular ...Induced proximity by molecular glues refers to strategies that leverage the recruitment of proteins to facilitate their modification, regulation or degradation. As prospective design of molecular glues remains challenging, unbiased discovery methods are necessary to discover new chemical targets. Here we establish a high throughput affinity proteomics workflow leveraging E3 ligase activity-impaired CRBN-DDB1ΔB in cell lysates for the unbiased identification of molecular glue targets. By mapping the interaction landscape of CRBN-binding molecular glues, we unveil 298 protein targets and demonstrate the utility of enrichment methods for identifying targets overlooked by established methods. We use a computational workflow to estimate target confidence and perform biochemical and structural validation of uncharacterized neo-substrates. We further identify a lead compound for the previously untargeted non-zinc finger PPIL4 through a biochemical screen. Our study provides a comprehensive inventory of targets chemically recruited to CRBN and delivers a robust and scalable workflow for identifying drug-induced protein interactions in cell lysates.
External linksNat Commun / PubMed:40707481 / PubMed Central
MethodsEM (single particle)
Resolution3.3 - 3.5 Å
Structure data

47268

9dwv

EMDB-47268, PDB-9dwv:
Ternary complex of CRBN-DDB1-PPIL4 RRM domain with FPFT-2216
Method: EM (single particle) / Resolution: 3.5 Å

47269

9dww

EMDB-47269, PDB-9dww:
Ternary complex of CRBN-DDB1-PDE6D with FPFT-2216
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-47270: Ternary complex of CRBN-DDB1-PDE6D with FPFT-2216 local refinement
Method: EM (single particle) / Resolution: 3.4 Å

Chemicals

ChemComp-ZN:
Unknown entry

PDB-1bc8:
STRUCTURES OF SAP-1 BOUND TO DNA SEQUENCES FROM THE E74 AND C-FOS PROMOTERS PROVIDE INSIGHTS INTO HOW ETS PROTEINS DISCRIMINATE BETWEEN RELATED DNA TARGETS

Source
  • homo sapiens (human)
KeywordsLIGASE / CRBN / molecular glue / E3 ligase / PPIL4 / PDE6D

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