A novel conformational state for SARS-CoV-2 main protease

Fornasier, Emanuele; Macchia, Maria Ludovica; Giachin, Gabriele; Sosic, Alice; Pavan, Matteo; Sturlese, Mattia; Salata, Cristiano; Moro, Stefano; Gatto, Barbara; Bellanda, Massimo; Battistutta, Roberto

The SARS-CoV-2 main protease (Mpro) has a pivotal role in mediating viral genome replication and transcription of coronavirus, making it a promising target for drugs against Covid-19 pandemic. Here we present a crystal structure of Mpro disclosing new structural features of key regions of the enzyme. We show that the oxyanion loop, involved in substrate recognition and enzymatic activity, can adopt a new conformation, which is stable and significantly different from the known ones. In this new state the S1 subsite of the substrate binding region is completely reshaped and a new cavity near the S2’ subsite is created. This new structural information expands the knowledge of the conformational space available to Mpro, paving the way for the design of novel classes of inhibitors specifically designed to target this unprecedented binding site conformation, thus enlarging the chemical space for urgent antiviral drugs against Covid-19 pandemic.