Indole Chloropyridinyl Ester-Derived SARS-CoV-2 3CLpro Inhibitors: Enzyme Inhibition, Antiviral Efficacy, Structure–Activity Relationship, and X-ray Structural Studies

Abstract

Here, we report the synthesis, structure-activity relationship studies, enzyme inhibition, antiviral activity, and X-ray crystallographic studies of 5-chloropyridinyl indole carboxylate derivatives as a potent class of SARS-CoV-2 chymotrypsin-like protease inhibitors. Compound <b>1</b> exhibited a SARS-CoV-2 3CLpro inhibitory IC₅₀ value of 250 nM and an antiviral EC₅₀ value of 2.8 μM in VeroE6 cells. Remdesivir, an RNA-dependent RNA polymerase inhibitor, showed an antiviral EC₅₀ value of 1.2 μM in the same assay. Compound <b>1</b> showed comparable antiviral activity with remdesivir in immunocytochemistry assays. Compound <b>7d</b> with an <i>N</i>-allyl derivative showed the most potent enzyme inhibitory IC₅₀ value of 73 nM. To obtain molecular insight into the binding properties of these molecules, X-ray crystal structures of compounds <b>2</b>, <b>7b</b>, and <b>9d</b>-bound to SARS-CoV 3CLpro were determined, and their binding properties were compared.