Structural Superimposition

Abstact

Constant changes in SARS-CoV-2 in human populations as well as potential future spillovers from animal coronaviruses have provided the impetus for the development of additional direct-acting antivirals. We describe herein the discovery of a new class of broad-spectrum inhibitors of coronavirus 3C-like protease (3CLpro), a cysteine protease essential for viral replication and a validated drug target, that incorporate in their structure a 1,3,2-oxazaphospholidin-3-one scaffold. Inhibitors 1 and 2 potently inhibited SARS-CoV-2 3CLpro (IC(50) = 0.34 and 0.23 muM) and MERS-CoV 3CLpro (IC(50) = 0.12 and 0.09 muM), and displayed antiviral activity against SARS-CoV-2 (EC(50) = 60 and 50 nM) with low cytotoxicity (CC(50) > 100 muM). Importantly, several of the synthesized compounds inhibited recombinant human cathepsin L with IC(50) values in the low nM to sub-nM range. Thus, the compounds can potentially exhibit high antiviral potency by abrogating viral entry via the inhibition of cathepsin L and viral replication by inhibition of 3CLpro. High resolution cocrystal structures were determined to elucidate the mechanism of action, identify the molecular determinants associated with binding, and to inform the optimization process.