Studies on SARS-CoV-2 Mpro and nucleocapsid protein: implications for therapeutics, diagnostics, and research.

Abstract

SARS-CoV-2 has left an indelible mark on society over the last four years claiming the lives of1.2 million people in the US alone and leaving millions more severely disabled. Despite many successes such as the rapid development of vaccines and antivirals such as nirmatrelvir, approximately 1000 people die every week from COVID-19 and COVID-19 continues to exert a societal burden on par with cancer or heart disease. We sought to study one of the most potent resistance mutations towards the active ingredient ofthe drug Paxlovid (nirmatrelvir), to understand the mechanistic basis of resistance and also determine the extent to which ensitrelvir and bofutrelvir are impacted and the structural basis by which their resistance profiles differ. The second project seeks to develop a nucleic acid probe to study the nucleic acid bindinginteractions of SARS-CoV-2 nucleocapsid protein, an essential viral protein, one of the most abundant proteins encoded by SARS-CoV-2, and the basis of rapid antigen tests. We performed studies and determined the structure of the RNA binding domain bound to a DNA aptamer via x-ray crystallography and were able to utilize the aptamer for pulldowns, detection, and as a probe to study the nucleic acid binding interface of the RNA binding domain.