Structure-based drug design, virtual screening and high-throughput screening rapidly identify antiviral leads targeting COVID-19

A coronavirus identified as 2019 novel coronavirus (COVID-19) is the etiological agent responsible for the 2019-2020 viral pneumonia outbreak that commenced in Wuhan. Currently there is no targeted therapeutics and effective treatment options remain very limited. In order to rapidly discover lead compounds for clinical use, we initiated a program of combined structure-assisted drug design, virtual drug screening, and high-throughput screening to identify new drug leads that target the COVID-19 main protease (Mpro). Mpro is a key coronavirus enzyme, which plays a pivotal role in mediating viral replication and transcription, making it an attractive drug target for this virus. Here, we identified a mechanism-based inhibitor, N3, by computer-aided drug design and subsequently determined the crystal structure of COVID-19 Mpro in complex with this compound. Next, through a combination of structure-based virtual and high-throughput screening, we assayed over 10,000 compounds including approved drugs, drug candidates in clinical trials, and other pharmacologically active compounds as inhibitors of Mpro. Seven of these inhibit Mpro with IC50 values ranging from 0.48 to 16.62 μM. Ebselen, thiadiazolidinone-8 (TDZD-8) and N3 also exhibited strong antiviral activity in cell-based assays. Our results demonstrate the efficacy of this screening strategy, and establishes a new paradigm for the rapid discovery of drug leads with clinical potential in response to new infectious diseases where no specific drugs or vaccines are available.