UC Berkeley

Traditionally the pharmaceutical industry has relied on small molecule inhibitors to function through occupancy driven pharmacology. However, proteins that are disease related and contain well-defined binding pockets make up less than 10% of the proteome leaving a large percentage undruggable by traditional drug discovery. To combat this the field of induced proximity was discovered to use drugs to harness the cell’s natural protein-protein interactions and processes instead of relying solely on binding to cause a therapeutic function. These processes include degradation where either small molecule drugs called molecular glues or larger compounds made up of two protein binging ligands linked together call Proteolysis Targeting Chimeras (PROTACs) bring a protein of interest into proximity with a member of the E3 ubiquitin machinery to cause the ubiquitination and subsequent proteasomal degradation of the protein of interest. While there are over 600 E3 ligases and even more members of the E3 ubiquitin ligase machinery only a few have been exploited for PROTAC purposes. It has also been found that not every E3 can be used to degrade every target and some E3 ligases degrade certain targets better than others. Additionally, some E3 ligases such as cereblon are not necessary for cell survival and have been mutated in cancer cells causing the inactivation of the PROTAC. The discovery of new E3 machinery ligands can help broaden the targeted protein degradation toolbox to continue to build a platform that might one day be able to degrade every undruggable protein target.

This dissertation focuses on the discovery of a covalent cysteine-reactive ligand that targets a cysteine on an E3 substrate receptor adaptor protein DNA damage binding protein 1 (DDB1), a member of the Cullen Ring Ligase 4A system. When linked to an inhibitor of a protein of interest, the ligand was shown to bind to DDB1 and induce the degradation of the protein targets: BRD4 and AR. This degradation was found to be NEDDylation, proteosome and DDB1 dependent. This study demonstrated that covalent chemoproteomic approaches can be used to discover recruiters against Cullin RING adapter proteins and that these recruiters can be used for PROTAC applications to degrade neo-substrates.