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 (Mpro, 3CLpro) 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 Mpro inhibitors. Compounds 3w and 3x exhibited excellent SARS-CoV-2 Mpro inhibition with kinac/Ki of 58,700 M–1 s–1 (Ki = 0.0141 μM) and 27,200 M–1 s–1 (Ki = 0.0332 μM), respectively. In Calu-3 and Vero76 cells, compounds 3h, 3i, 3l, 3r, 3v, 3w, and 3x displayed antiviral activity in the
nanomolar range without host cell toxicity. Co-crystallization of 3w and 3af with SARS-CoV-2 Mpro 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 Mpro 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.