Dual Inhibitors of Main Protease (M) and Cathepsin L as Potent Antivirals against SARS-CoV2.

Given the current impact of SARS-CoV2 and COVID-19 on human health and the global economy, the development of direct acting antivirals is of paramount importance. Main protease (M), a cysteine protease that cleaves the viral polyprotein, is essential for viral replication. Therefore, M is a novel therapeutic target. We identified two novel M inhibitors, D-FFRCMKyne and D-FFCitCMKyne, that covalently modify the active site cysteine (C145) and determined cocrystal structures. Medicinal chemistry efforts led to and , which adopt a unique binding mode within the M active site. Notably, these inhibitors do not inhibit the other cysteine protease, papain-like protease (PL), involved in the life cycle of SARS-CoV2. and block SARS-CoV2 replication in hACE2 expressing A549 cells with IC values of 8.2 and 14.7 nM. Detailed studies indicate that these compounds also inhibit cathepsin L (CatL), which cleaves the viral S protein to promote viral entry into host cells. Detailed biochemical, proteomic, and knockdown studies indicate that the antiviral activity of and results from the dual inhibition of M and CatL. Notably, intranasal and intraperitoneal administration of and lead to reduced viral replication, viral loads in the lung, and enhanced survival in SARS-CoV2 infected K18-ACE2 transgenic mice. In total, these data indicate that and represent promising scaffolds on which to develop antiviral drugs against SARS-CoV2.