UC San Diego

The constant emergence of SARS-CoV-2 resistance drives the search for new antivirals. We screened the SARS-CoV-2 cysteine proteases, the main protease (M^pro) and papain-like protease (PL^pro), with 141 peptidyl and peptidomimetic inhibitors designed to target a trypanosome cysteine protease. Five compounds (1a-5a) inhibited M^pro (IC₅₀ of 0.1601-16.42 µM), whereas none inhibited PL^pro. Compounds 1a-4a inhibited human cathepsin L (hCatL; 0.184-10.74 µM), which is important for viral entry into human cells. Compounds 1a and 5a, and its synthesised (R,S) enantiomer, 5b, which share a benzyl carbamate moiety, inhibited the M^pro of SARS-CoV/MERS-CoV (0.0732-0.8295 µM). The three compounds were biochemically characterised as covalent reversible inhibitors. Compounds 5a and 5b, which contain vinyl ketone warheads, were specific for M^pro, and this behaviour was supported by covalent and noncovalent computational simulations. This study highlights the importance of revisiting legacy assets to identify starting points for new antiviral drugs.