A small molecule inhibitor of the main coronavirus protease 3CLPro based on a carbocyclically substituted peptidomimetic.

The mechanism of action of peptide inhibitors involves two steps. 3CLpro inhibitors, which mimic natural peptide substrates, initially bind to 3CLpro and form a non-covalent complex, while the attacking group (warhead) undergoes a nucleophilic attack, forming covalent bonds with the Cys145 residue. In this paper, we present a new small-molecule inhibitor of the main coronavirus protease, 3CLPro, based on the carbocyclically substituted peptidomimetic N-(4-methyl-1-oxo-1-((1-oxo-3-(2-oxopyrrolidin-3-yl)propan-2-yl)amino)pentan-2-yl)-(2Z)-3-(thiophen-2-yl)prop-2-enamide (TEA-Leu-Pld-CHO).

This low-toxicity compound (CC50 was 187.5 μg/ml) exhibits antiviral activity against modern coronavirus strains, including SARS-CoV-2. This substance exhibits sufficient solubility in aqueous solutions due to the one-step conversion of the aldehyde group to sodium bisulfite as a prodrug. To study the antiviral properties of the TEA-Leu-Pld-CHO compound, the SARS-CoV-2 human coronavirus strain, passage 4, with an infectious activity of 106 TCID50/mL for Vero-E6 cells, was used.

An experiment to assess cell viability in the antiviral efficacy assay was conducted over a range of drug concentrations from 375.0 to 0.37 μg/mL, by titrating the initial concentration in the wells of a 96-well plate. The antiviral activity of the compounds was assessed visually under a microscope 96 hours after infection by inhibiting the viral CPE in a Vero E6 cell culture. The IC50 for TEA-Leu-Pld-CHO was 5.8 μg/mL. Thus, Si was 32.

The proposed compound, given its high antiviral activity and low cytotoxicity, as well as its economic and synthetic availability, can be recommended as a candidate for preclinical and clinical trials to develop an etiotropic antiviral drug aimed at inhibiting an important enzyme—the main protease of the coronavirus, including modern strains of SARS-CoV-2.