Discovery of Small Molecule-Mediated Protein Degradation Pathways in Human Cancer

Ligand-dependent protein degradation has emerged as a compelling strategy to pharmacologically control the protein content of cells. This strategy has advantages that include converting silent ‘protein-binding’ small molecules to ‘protein degraders’, which has the potential to substantially increase the number of druggable proteins in human disease such as cancer, and to operate in a catalytic manner that may lower the drug concentrations required to produce a pharmacological effect. Nonetheless, until recently, only a handful of the 600+ human E3 ligases have been found to support this process. Importantly, these E3 ligases have been found to show distinct and restricted substrate specificities, underscoring the need to discover additional ligandable E3 ligases with differentiated properties to realize the full scope of targeted protein degradation as a pharmacological strategy. We recently leveraged chemoproteomic platforms and molecular biology approaches to identify DCAF16, a poorly characterized E3 ligase, as a target of electrophilic probes that promotes the nuclear-restricted degradation of proteins. During the K99 award period, we have screened a focused library of bifunctional electrophilic compounds across a panel of human cancer cell lines and identified DCAF11 as an additional E3 ligase that supports electrophilic PROTACs (proteolysis targeting chimeras)-mediated targeted protein degradation. Moreover, to understand DCAF16-mediated endogenous protein degradation pathway, we used proteomics and molecular biology approaches and identified SPIN4 as a principle protein substrate of DCAF16. For the R00 award period, we plan to 1) understand the physiological functions of DCAF16-SPIN4 degradation pathway in human cancer, 2) identify additional E3 ligases that support ligand-induced protein degradation in human cancer, and 3) develop advanced ligands for DCAF16. Our long-term goals are to develop advanced chemical probes and pharmacological tools to intervene hard-to-drug or even ‘undruggable’ targets in human cancer. The proposed studies will be carried out at Northwestern University, a top-ranking research university which combines cutting edge biological and chemical research to offer a unique cross-disciplinary scientific environment. The proposed studies will not only push the boundaries of our knowledge of targeted protein degradation, but may also be the starting point for the development of novel therapeutics targeting important yet undruggable proteins in human cancer.