Proteomics core

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CORE 8: PROTEOMICS SUMMARY Readily distributed, orally bioavailable small molecule antiviral agent could play an outsized role not only in the response to COVID-19, but also to future pandemics by reducing the severity of disease for those at highest risk for serious outcomes, and by curtailing the strain that serious illness puts on hospitals and healthcare infrastructure. Determining the molecular mechanism of biologically active viral proteins is a critical component to a successful drug development pipeline. Proteomics approaches represent a critical tool for the study of viral biology and drug development pipelines due to the capacity to assess viral protein activity in living cells using high-throughput multiplexed assays. Furthermore, the agnostic nature of protein detection allows for proteomics assays to be rapidly adapted to different viruses or host organisms. The work proposed by this core will be performed at the Thermo Fisher Scientific Proteomics Facility for Disease Target Discovery located at the J. David Gladstone Institutes at the UCSF campus. This facility and the Proteomics Core, will be led by Dr. Swaney, an expert in mass-spectrometry based proteomics research with a track record in the development and application of novel proteomics approaches to enable biological discovery. Within the QCRG Pandemic Response Program, the goal of the Proteomics Core is to provide high-quality, accurate, and reproducible proteomic analyses that measure viral proteins and their cellular activities. This will enable the QCRG Drug Discovery Platform to design and identify lead compounds and develop effective cell- based assays that measure drug candidate effectiveness in living cells. The proteomics assays described in this core are essential to the success of the QCRG Pandemic Response Program and will support all Projects, as well as the Screening Core, Integrative Modeling Core, and the In Vivo and In Vitro Virology Cores. Efforts of the Proteomics Core will include measuring the direct effect that drugs have on viral protein abundance and post-translational modifications during infection time courses in physiologically relevant cell models, and drug target specificity using cellular thermal shift assays. To aid flexible structure determination and viral protein assembly in cells and recombinant expression systems, we will also provide structural proteomics approaches to measure subunit stoichiometry, domain topology, and protein and drug interaction interfaces. Finally, we will develop assays to measure viral protein activity, including an ADP-ribosylation assay to measure macrodomain activity, and a protease cleavage assay to measure vial protease proteolytic activity.