A proximity biotinylation-based approach to identify protein-E3 ligase interactions induced by PROTACs and molecular glues

Nat Commun. 2022 Jan 10;13(1):183. doi: 10.1038/s41467-021-27818-z.

Abstract

Proteolysis-targeting chimaeras (PROTACs) as well as molecular glues such as immunomodulatory drugs (IMiDs) and indisulam are drugs that induce interactions between substrate proteins and an E3 ubiquitin ligases for targeted protein degradation. Here, we develop a workflow based on proximity-dependent biotinylation by AirID to identify drug-induced neo-substrates of the E3 ligase cereblon (CRBN). Using AirID-CRBN, we detect IMiD-dependent biotinylation of CRBN neo-substrates in vitro and identify biotinylated peptides of well-known neo-substrates by mass spectrometry with high specificity and selectivity. Additional analyses reveal ZMYM2 and ZMYM2-FGFR1 fusion protein-responsible for the 8p11 syndrome involved in acute myeloid leukaemia-as CRBN neo-substrates. Furthermore, AirID-DCAF15 and AirID-CRBN biotinylate neo-substrates targeted by indisulam and PROTACs, respectively, suggesting that this approach has the potential to serve as a general strategy for characterizing drug-inducible protein-protein interactions in cells.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptor Proteins, Signal Transducing / genetics*
  • Adaptor Proteins, Signal Transducing / metabolism
  • Biological Assay*
  • Biotinylation
  • Cell Line, Tumor
  • DNA-Binding Proteins / genetics*
  • DNA-Binding Proteins / metabolism
  • Gene Expression Regulation
  • HEK293 Cells
  • Hepatocytes / cytology
  • Hepatocytes / drug effects
  • Hepatocytes / metabolism*
  • Humans
  • Immunologic Factors / pharmacology
  • Intracellular Signaling Peptides and Proteins / genetics
  • Intracellular Signaling Peptides and Proteins / metabolism
  • Lymphocytes / cytology
  • Lymphocytes / drug effects
  • Lymphocytes / metabolism*
  • Neurons / cytology
  • Neurons / drug effects
  • Neurons / metabolism
  • Protein Binding
  • Protein Interaction Mapping
  • Proteolysis / drug effects
  • Receptor, Fibroblast Growth Factor, Type 1 / genetics
  • Receptor, Fibroblast Growth Factor, Type 1 / metabolism
  • Substrate Specificity
  • Sulfonamides / pharmacology
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism
  • Ubiquitin-Protein Ligases / genetics*
  • Ubiquitin-Protein Ligases / metabolism

Substances

  • Adaptor Proteins, Signal Transducing
  • CRBN protein, human
  • DCAF15 protein, human
  • DNA-Binding Proteins
  • Immunologic Factors
  • Intracellular Signaling Peptides and Proteins
  • N-(3-chloro-7-indolyl)-1,4-benzenedisulphonamide
  • Sulfonamides
  • Transcription Factors
  • ZMYM2 protein, human
  • Ubiquitin-Protein Ligases
  • FGFR1 protein, human
  • Receptor, Fibroblast Growth Factor, Type 1