Elongin B/C-containing E3 ligases: fragment-based ligand design and examining resistance mechanisms for targeted protein degradation

Small molecule modulation and recruitment of E3 ligases is gaining huge popularity in the scientific community due to the ability to interfere with or leverage the ubiquitin proteasome system (UPS) using inhibitors or PROTACs respectively. In this work Elongin B/C containing E3 ligases are investigated by a variety of fragment-based approaches in the aim to develop chemical probes which can be used as tool molecules to interrogate E3 ligase biology. This thesis describes a multidisciplinary approach which includes computational chemistry, synthesis, biophysical evaluation, X-ray crystallography all supported by core molecular biology techniques and protein expression/purification. Binding pockets on VHL, Elongin C and over the surface of the SBC E3 ligase are explored, building on key work established by current and previous lab members. This has led to new chemotypes which are confirmed to bind to these ligase complexes which will be crucial for further development with the aim to provide tools for the scientific community. In the final chapter a collaborative work investigating functional E3 ligase hotspots and resistance mechanisms is described, combining deep mutational scanning with biophysical techniques and structural analysis to provide a picture of what resistance mechanisms for degrader molecules are likely to look like in the future.