Covalent Ligand Screening Uncovers a RNF4 E3 Ligase Recruiter for Targeted Protein Degradation Applications

ACS Chem Biol. 2019 Nov 15;14(11):2430-2440. doi: 10.1021/acschembio.8b01083. Epub 2019 May 13.

Abstract

Targeted protein degradation has arisen as a powerful strategy for drug discovery allowing the targeting of undruggable proteins for proteasomal degradation. This approach most often employs heterobifunctional degraders consisting of a protein-targeting ligand linked to an E3 ligase recruiter to ubiquitinate and mark proteins of interest for proteasomal degradation. One challenge with this approach, however, is that only a few E3 ligase recruiters currently exist for targeted protein degradation applications, despite the hundreds of known E3 ligases in the human genome. Here, we utilized activity-based protein profiling (ABPP)-based covalent ligand screening approaches to identify cysteine-reactive small-molecules that react with the E3 ubiquitin ligase RNF4 and provide chemical starting points for the design of RNF4-based degraders. The hit covalent ligand from this screen reacted with either of two zinc-coordinating cysteines in the RING domain, C132 and C135, with no effect on RNF4 activity. We further optimized the potency of this hit and incorporated this potential RNF4 recruiter into a bifunctional degrader linked to JQ1, an inhibitor of the BET family of bromodomain proteins. We demonstrate that the resulting compound CCW 28-3 is capable of degrading BRD4 in a proteasome- and RNF4-dependent manner. In this study, we have shown the feasibility of using chemoproteomics-enabled covalent ligand screening platforms to expand the scope of E3 ligase recruiters that can be exploited for targeted protein degradation applications.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Cycle Proteins / metabolism
  • Coordination Complexes / chemistry*
  • Coordination Complexes / metabolism
  • Cysteine / chemistry
  • Humans
  • Ligands
  • Molecular Docking Simulation
  • Nuclear Proteins / metabolism*
  • Proteasome Endopeptidase Complex / metabolism
  • Protein Binding
  • Protein Domains
  • Proteolysis / drug effects*
  • Small Molecule Libraries / chemistry*
  • Small Molecule Libraries / metabolism
  • Structure-Activity Relationship
  • Transcription Factors / metabolism*
  • Ubiquitin-Protein Ligases / metabolism*
  • Ubiquitination
  • Zinc / chemistry

Substances

  • BRD4 protein, human
  • Cell Cycle Proteins
  • Coordination Complexes
  • Ligands
  • Nuclear Proteins
  • RNF4 protein, human
  • Small Molecule Libraries
  • Transcription Factors
  • Ubiquitin-Protein Ligases
  • Proteasome Endopeptidase Complex
  • Zinc
  • Cysteine