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

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

ACS chemical biology (2019-05-07)
Carl C Ward, Jordan I Kleinman, Scott M Brittain, Patrick S Lee, Clive Yik Sham Chung, Kenneth Kim, Yana Petri, Jason R Thomas, John A Tallarico, Jeffrey M McKenna, Markus Schirle, Daniel K Nomura
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.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
CCW16-PEG3-BocNH, ≥95%
Sigma-Aldrich
CCW16-PEG2-butyl-BocNH, ≥95%
Sigma-Aldrich
CCW16-PEG5-BocNH, ≥95%
Sigma-Aldrich
CCW16, ≥95%
Sigma-Aldrich
CCW16-C6-PEG3-butyl-BocNH
Sigma-Aldrich
CCW16-C4-BocNH, 95%
Sigma-Aldrich
CCW16-PEG1-BocNH
Sigma-Aldrich
CCW16-C9-BocNH, ≥95%
Sigma-Aldrich
CCW16-C6-BocNH