Discovery of New OTUB1 Covalent Ligands via Structure–Activity Relationship Studies for Targeted Protein Stabilization

Deubiquitinase-targeting chimera (DUBTAC) has recently emerged as a promising technology for inducing targeted protein stabilization (TPS). DUBTACs are heterobifunctional molecules that recruit deubiquitinases (DUBs) to induce deubiquitination and stabilization of target proteins. However, DUBTAC development has been hindered by the scarcity of DUB ligands. In this study, we report the discovery of novel covalent ligands of the OTUB1 DUB through structure–activity relationship (SAR) studies of the previously reported OTUB1 ligand EN523. Our lead compound 34 (MS8572), which features a new heterocyclic core, covalently modified OTUB1 faster and more effectively, while also displaying enhanced stability and aqueous solubility compared to EN523. Furthermore, 34 was selective for OTUB1 over several cysteine-containing proteins and did not inhibit the OTUB1 deubiquitinase activity. Lastly, by utilizing 34, we developed an effective CFTR DUBTAC. Overall, we developed new and improved OTUB1 covalent ligands, expanding the limited number of DUB ligands that can be harnessed for TPS.