Selection of DNA-encoded Chemical Libraries for Compounds that can Induce Protein Ubiquitination

We report a selection method of DNA-encoded libraries (DELs) that can identify the compounds able to induce ubiquitination of the protein of intertest (POI). Since the selection readout of the method is based on POI ubiquitination, rather than POI binding or ternary complex formation, the identified compounds are more functionally relevant and more predicative of active protein degraders. In this study, by selecting a DEL of 950 different combinations of POI ligands, linkers, and E3 ligase ligands against the BD1 domain of bromodomain-containing protein 4 (BRD4-BD1) in the presence and absence of ATP, we have identified a potent BRD4-BD1 degrader (DC50: ~9.7 nM) and also a short-isoform-selective BRD4 degrader (DC50: 0.26 μM). Furthermore, we show that the selection based on POI binding or ternary complex formation identified compounds that may have induced stable complexes but are inactive degraders. This approach may be an efficient and broadly applicable method for discovering functional protein degraders, as well as E3 ligase ligands, by harnessing the vast chemical diversity of DELs.