Targeting the S1' Pocket of SARS-CoV‑2 Papain-Like Protease Yields Highly Potent Inhibitors

SARS-CoV-2 and -CoV viruses are major human pathogens. Due to their zoonotic nature as well as emerging drug-resistant mutations, new antivirals are needed. The viral papain-like protease (PLpro) is a drug target. Targeting the mostly hydrophobic S1' pocket of PLpro, we designed and synthesized 21 amide compounds, among which several highly potent PLpro inhibitors were identified with IC₅₀ values as low as 16 nM. Structure-activity relationship analysis showed that an electron-deficient pyridine-containing amide group can significantly enhance the activity. The X-ray structure of the PLpro-compound 15 complex revealed that the pyridine ring has favorable π-π and electrostatic interactions with the electron-rich indole group of Trp106. Compound 15 is inactive against human Ubiquitin-Specific Protease 7 and noncytotoxic to mammalian cells, showing excellent selectivity. It can potently inhibit cellular replication of SARS-CoV-2 with an EC₅₀ of 96 nM. These results show that compound 15 represents a novel pharmaceutical lead for further drug development.

Antiviral agents; Enzyme inhibitor; Papain-like protease; SARS-CoV-2; X-ray crystallography.