Chemoproteomics-Enabled Ligand Screening Yields Covalent RNF114-Based Degraders that Mimic Natural Product Function

Abstract

The translation of natural product function to fully synthetic small molecules has remained an important process in medicinal chemistry for decades resulting in numerous FDA-approved medicines. We recently discovered that the terpene natural product nimbolide can be utilized as a covalent recruiter of the E3 ubiquitin ligase RNF114 for use in targeted protein degradation (TPD) -- a powerful therapeutic modality within modern day drug discovery. Using activity-based protein profiling-enabled covalent ligand screening approaches, we herein report the discovery of fully synthetic RNF114-based recruiter molecules that can also be exploited for PROTAC applications, and demonstrate their utility in degrading therapeutically relevant targets such as BRD4 and BCR-ABL in cells. The identification of simple and easily manipulated drug-like scaffolds that can mimic the function of a complex natural product is beneficial in further expanding the toolbox of E3 ligase recruiters, an area of great importance in drug discovery and chemical biology.

Fragment-based covalent ligand discovery

“…Additionally, a recent ABPP-based covalent screen against purified RNF4, a RING-domain E3 ligase identified new covalent fragments that target this protein. 114,115 The most promising hit TRH 1-23 was shown to label either Cys132 or Cys135, two cysteine residues that form one of zinc-coordinating sites within the RING domain. Although disrupting either one of these sites through mutagenesis was previously shown to inhibit RNF4 function, Ward et al included evidence to suggest that RNF4 retains in vitro self-ubiquitination activity, suggesting that TRH 1-23 did not disrupt RNF4 E3 ligase function.…”

Proteolysis targeting chimeras (PROTACs) come of age: entering the third decade of targeted protein degradation

“… 93 To enhance the utility of RNF114 in TPD applications, a fully-synthetic RNF114 E3RE has been identified and used successfully to induce BRD4 and BCR-ABL degradation. 96 The identification of this compound should increase the use of RNF114 in PROTAC design.…”