Discovery of small molecule-mediated protein degradation pathways in human cancer

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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. Importantly, DCAF16 is capable of supporting ligand- induced protein degradation at low fractional engagement (10-40%), which may enable the degradation of target proteins while minimally perturbing its endogenous substrates. In this proposal, by integrating chemoproteomic platforms with cell biology and molecular biology approaches, I plan to 1) identify endogenous substrates and biological functions of DCAF16, 2) screen and identify small molecules that disrupt cancer cell growth by engaging DCAF16 and inducing neo-substrate degradation, and 3) discover additional E3 ligases with distinct and restricted expressions in different cancer types that support ligand-induced targeted protein degradation. My long-term goals are to develop potent and selective chemical probes for DCAF16 and other druggable E3 ligases and to develop pharmacological tools to intervene hard-to-drug or even ‘undruggable’ cancer targets. The proposed studies will be carried out at The Scripps Research Institute, a top-ranking research institution which combines cutting edge biological and chemical research to offer a unique cross- disciplinary scientific environment. To build a successful career development and training program, I will attend an array of TSRI- or UCSD-hosted courses, workshops and seminars that will comprehensively advance my skills in mentoring, teaching, scientific communication, critical assessment and laboratory management. I will benefit tremendously from the mentored phase training with Dr. Benjamin Cravatt who has over 20 years of experiences in developing small molecule inhibitors of protein targets as well as chemical proteomic technologies, Dr. Michael Erb who has expertise in transcriptional biology in cancer, and my advisory committee, which includes prominent scientists – Dr. Jeffery Kelly and Dr. Dale Boger. 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 cancer.