UC Berkeley

One of the largest obstacles in modern drug discovery is that a significant portion (>90%) of the proteome is considered “undruggable,” in that these proteins lack a characterized, functional binding pocket or ligandable hotspot which small molecules can bind to and modulate the protein’s function for therapeutic benefit. To overcome such disease-causing proteins, targeted protein degradation (TPD) strategies have arisen, where the cell’s endogenous degradation machinery is hijacked to ubiquitinate and degrade the classically undruggable protein. Molecular glue degraders serve as a promising modality to achieve TPD. These are monovalent compounds that induce the proximity of a target protein with a component of the ubiquitin proteasome system to degrade the protein of interest. While our research group has previously identified a fumarate-based electrophilic handle that covalently modifies the E3 ligase RNF126 to enable degradation of multiple protein targets, the high intrinsic reactivity and cytotoxicity of the fumarate handle limited its translational utility. This work describes the development of an optimized and metabolically stabilized RNF126-targeting covalent handle incorporating a trans-cyclobutane linker that exhibits reduced glutathione reactivity and diminished cytotoxicity while retaining robust degradative activity. Using BRD4 as a benchmark target, we demonstrate that this optimized handle yields a potent and selective BRD4 degrader whose activity is dependent on RNF126. We further extend this strategy to the androgen receptor (AR) and its clinically intractable splice variant AR-V7, demonstrating selective degradation of both AR and AR-V7 in androgen-independent prostate cancer cells and robust inhibition of AR transcriptional activity that surpasses the established AR antagonist enzalutamide. Together, this dissertation establishes a generalizable, chemistry-centric framework for converting small-molecule ligands into covalent molecular glue degraders, offering a roadmap for exploiting event-driven pharmacology against the most intractable targets in the human proteome.