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.