Small-Molecule Thioesters As SARS-CoV-2 Main Protease Inhibitors: Enzyme Inhibition, Structure-Activity Relationships, Antiviral Activity, and X-ray Structure Determination

The main protease (M, 3CL) of SARS-CoV-2 is an attractive target in coronaviruses because of its crucial involvement in viral replication and transcription. Here, we report on the design, synthesis, and structure-activity relationships of novel small-molecule thioesters as SARS-CoV-2 M inhibitors. Compounds and exhibited excellent SARS-CoV-2 M inhibition with / of 58,700 M s ( = 0.0141 μM) and 27,200 M s ( = 0.0332 μM), respectively. In Calu-3 and Vero76 cells, compounds , , , , , and displayed antiviral activity in the nanomolar range without host cell toxicity. Co-crystallization of and with SARS-CoV-2 M was accomplished, and the X-ray structures showed covalent binding with the catalytic Cys145 residue of the protease. The potent SARS-CoV-2 Mpro inhibitors also inhibited the M of other beta-coronaviruses, including SARS-CoV-1 and MERS-CoV, indicating that they might be useful to treat a broader range of coronaviral infections.