Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease

Douangamath, Alice; Fearon, Daren; Gehrtz, Paul; Krojer, Tobias; Lukacik, Petra; Owen, C. David; Resnick, Efrat; Strain-Damerell, Claire; Aimon, Anthony; Ábrányi-Balogh, Péter; Brandão-Neto, José; Carbery, Anna; Davison, Gemma; Dias, Alexandre; Downes, Thomas D.; Dunnett, Louise; Fairhead, Michael; Firth, James D.; Jones, S. Paul; Keeley, Aaron; Keserü, György M.; Klein, Hanna F.; Martin, Mathew P.; Noble, Martin E. M.; O’Brien, Peter; Powell, Ailsa; Reddi, Rambabu N.; Skyner, Rachael; Snee, Matthew; Waring, Michael J.; Wild, Conor; London, Nir; von Delft, Frank; Walsh, Martin A.

COVID-19, caused by SARS-CoV-2, lacks effective therapeutics. Additionally, no antiviral drugs or vaccines were developed against the closely related coronavirus, SARS-CoV-1 or MERS-CoV, despite previous zoonotic outbreaks. To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease, one of two cysteine viral proteases essential for viral replication. Our crystallographic screen identified 71 hits that span the entire active site, as well as 3 hits at the dimer interface. These structures reveal routes to rapidly develop more potent inhibitors through merging of covalent and non-covalent fragment hits; one series of low-reactivity, tractable covalent fragments were progressed to discover improved binders. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease.