Utilization of the Nortropinone Scaffold in the Structure-Guided Design of Potent Inhibitors of Human Cathepsin L and the Chymotrypsin-like Proteases of SARS-CoV-2 and MERS-CoV

Abstract Coronaviruses, including SARS-CoV-2 and MERS-CoV, encode two large polyproteins, pp1a and pp1ab, that are primarily processed by highly conserved 3C-like proteases, yielding an array of structural and nonstructural proteins essential for viral replication. SARS-CoV-2 3CLpro is deemed to be a well-established and validated antiviral target. During cell entry, pathogenic coronaviruses, particularly the SARS-CoV-2 Omicron variants, utilize host cell cathepsins, including cathepsin L (CatL), and the endosomal pathway for successful infection. Furthermore, SARS-CoV-2 infection results in overexpression of CatL, which, in turn, intensifies SARS-CoV-2 infection. Consequently, CatL has emerged as a potential target for the development of COVID-19 therapeutics. We report herein a series of inhibitors that incorporate in their structure a nortropinone scaffold as a design element for probing and exploiting poorly explored regions of chemical space. The inhibitors were found to be noncytotoxic and to potently inhibit CatL and the 3CLpro of MERS-CoV and SARS-CoV-2. The IC50 values of compound 12 against human CatL, MERS-CoV 3CLpro, and SARS-CoV-2 3CLpro were determined to be 0.12 nM, 0.11 μM, and 0.38 μM, respectively. Furthermore, compound 12 was found to inhibit SARS-CoV-2 infection in vitro with an EC50 value of 0.09 ± 0.05 μM and a Safety Index >1100. High-resolution cocrystal structures with SARS-CoV-2 3CLpro and MERS-CoV 3CLpro confirmed the mechanism of action of the compounds, illuminated the molecular determinants associated with binding, and informed the optimization of the inhibitors.