Leveraging E2 ligases for induced proximity and modulation of novel cancer-relevant targets and neosubstrates

Ubiquitin-conjugating enzymes (E2s) govern ubiquitin chain topology and flux through the ubiquitin-proteasome system, thereby shaping proteostasis, DNA-damage responses, and oncogenic signaling. Although targeted protein degradation (TPD) has largely focused on E3 ligases, convergent evidence from recent chemical biology and oncology studies indicates that E2s are druggable nodes with dual therapeutic potential for reprogramming using bifunctional and molecular glue degraders. Here, we demonstrate that E2s can act as a recruitment engine for proximity-induced degradation when E3 access or cooperativity is limiting for a distinct set of targets. We introduce a first-in-class, selective, small-molecule-based bifunctional degrader platform that exploits E2 recruitment to degrade oncology-relevant targets, including nuclear receptors and kinases. In biochemical and cellular systems, the ligand engages its E2 target with high selectivity, induces proximity through ternary complex formation and degrades the protein of interest in a proteasome- and Cullen-dependent manner. We validated our approach by designing bifunctional degraders of ERalpha, coupling ERalpha and E2 ligands with short linkers, and demonstrating target degradation in MCF7, T47D, SH-SY5Y, and K562 cell lines. We demonstrate early degradation by 6 hours and maximal degradation at 24 hours with a D max of 85% and DC 50 of 83nM. Further, by conjugating 4 kinase inhibitor scaffolds with 2-6 linker designs, we screened the proteome to cover almost 500 potential kinase targets in K562 and MCF7. We demonstrated dose-dependent degradation of dozens of kinases, including kinases of potential therapeutic interest such as SYK, FYN, and MAPK2. We observed dramatically different sensitivity to degradation across the cell lines tested, and degradation activity was more robust at the 24h timepoint compared to 5h. Collectively, these findings validate E2 ligases as functional recruiters for TPD, expanding the degrader toolbox beyond canonical E3 ligases and establishing a complementary, generalizable framework for therapeutic development.