A method to identify small molecule/protein pairs susceptible to protein ubiquitination

Although using DNA encoded libraries (DELs) to find small molecule binders of target proteins is well-established, identifying DEL hits for functions other than binding remains challenging. We demonstrate here a technique where pools of DNA-linked small molecules are mixed with pools of DNA-linked protein targets and optimal small/protein pairs are identified based on their ability to catalyze the transfer of ubiquitin (Ub) onto the target proteins. Since the transfer of Ub is the first step in the tagging of proteins for proteasomal destruction, finding small molecules that can selectively reprogram Ub-transfer is one of the great challenges in contemporary drug development. Our work provides the framework for a new type of functional DEL screen that matches small molecule Ub-transfer catalysts with their optimal protein substrates. We believe the technology could be especially useful in discovering and optimizing molecular glue degraders.