Elucidation of SARS-CoV-2 Mpro protein-inhibitor interactions

Abstract In late 2019 a new virus, later called SARS-CoV-2, started to spread from China all over the globe, causing the disease Covid-19. It was soon declared as a pandemic by the World Health Organization and caused millions of deaths. Researchers around the world began immediately to focus on this virus and to develop strategies to overcome this pandemic. In addition to mRNA vaccines, which successfully entered the market about one year after the breakout of the pandemic, also anti-viral drugs came in the focus of research institutions and companies. The most promising strategy for anti-viral drugs are protease inhibitors, in this case compounds that inhibit the Main protease Mpro of SARS-CoV-2, which is needed for viral replication. Drug repurposing showed to be an efficient tool, as Paxlovid® by Pfizer entered the market in 2021. This thesis focusses on the evaluation of the inhibitory potential of three previously identified hit compounds M-A23, M-B28 and M-C23. Through a FRET-based inhibition assay, all of the three compounds were confirmed to inhibit Mpro with a low mikromolar IC50 value in-vitro. This makes them to potential drugs against Covid-19. Therefore their binding mechanism to the Main protease was further investigated and considered as reversible covalent for M-A23 and M-B28 and non-covalent for M-C23.