Decoding Viral Control of Host Kinase Signaling to Design Combination Therapy

PROJECT SUMMARY Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a single-stranded RNA beta-coronavirus of the family Coronaviridae that emerged in late 2019 and causes the infectious disease COVID-19 (Coronavirus Disease-2019). The emergence of the global pandemic has resulted in a public health emergency with detrimental societal and global economic effects. At present, there are no vaccines or curative treatments available. The search for antiviral therapies constitutes a global research priority. Combinatorial host-directed antiviral treatments present a low propensity for resistance and a high potential for potent efficacy. Pathogens often provoke dramatic changes to host cellular signaling to enhance their fitness. Proteomic approaches that globally quantify changes in protein abundance and phosphorylation represent an unbiased way to elucidate how host pathways are rewired during infection. We previously observed that SARS-CoV-2 provokes dramatic changes to host phosphorylation, suggesting the regulation of host kinases to be an important mediator of coronavirus infection and disease. We additionally found many SARS-CoV-2 proteins to physically interact with several human kinases. Furthermore, we and others have shown that targeting host kinases hijacked by SARS-CoV-2 is an effective means of discovering antiviral therapies. We identified 49 kinases to be dysregulated during infection-including p38, casein kinase II, cyclin dependent kinases, AXL, and PIKFYVE- finding 38/68 (>50%) drugs targeting these kinases to be antiviral in cell culture assays (CC50/IC50>10). Here, I propose to expand upon my prior work by (Aim 1) mapping the global regulation of host phosphorylation signaling by SARS-CoV-2 and OC43, a non-lethal coronavirus and cause of common cold, infection in human cells using mass spectrometry-based proteomics to identify novel kinases and pathways dysregulated during coronavirus infection. Next, I will (Aim 2) validate coronavirus dependency on host responses and use this information to design and test novel combination therapy to treat infection in human cell culture models. Lastly, I will (Aim 3) decode how kinases impinge upon the coronavirus life cycle as well as how kinases control phosphorylation of viral/host proteins during infection. This systematic approach will shed light on coronavirus biology and therapeutic strategies, with general applicability to other infectious agents and diseases. My request for additional mentored training is based on a need to master skills in (1) mass spectrometry-based proteomics, (2) virology theory and methods, and (3) functional genetics. My background is in mathematical modeling, bioinformatics, and cancer, which I plan to integrate with skills in proteomics, genetics, and virology to gain independence from my advisor and start a dual wet/dry independent research lab studying post-translational modifications and signaling rewiring in infectious disease and cancer. My mentor, co-mentor, and advisory committee will train and mentor me as I progress towards becoming an independent investigator.