2-Pyridone natural products as inhibitors of SARS-CoV-2 main protease

Abstract

The disease, COVID-19, is caused by the severe acute respiratory coronavirus 2 (SARS-CoV-2) for which there is currently no treatment. The SARS-CoV-2 main protease (M ^pro) is an important enzyme for viral replication. Small molecules that inhibit this protease could lead to an effective COVID-19 treatment. The 2-pyridone scaffold was previously identified as a possible key pharmacophore to inhibit SARS-CoV-2 M ^pro. A search for natural, antimicrobial products with the 2-pyridone moiety was undertaken herein, and their calculated potency as inhibitors of SARS-CoV-2 M ^pro was investigated. Thirty-three natural products containing the 2-pyridone scaffold were identified from the literature. An in silico methodology using AutoDock was employed to predict the binding energies and inhibition constants ( K _i values) for each 2-pyridone-containing compound with SARS-CoV-2 M ^pro. This consisted of molecular optimization of the 2-pyridone compound, docking of the compound with a crystal structure of SARS-CoV-2 M ^pro, and evaluation of the predicted interactions and ligand-enzyme conformations. All compounds investigated bound to the active site of SARS-CoV-2 M ^pro, close to the catalytic dyad (His-41 and Cys-145). Thirteen molecules had predicted K _i values < 1 μM. Glu-166 formed a key hydrogen bond in the majority of the predicted complexes, while Met-165 had some involvement in the complex binding as a close contact to the ligand. Prominent 2-pyridone compounds were further evaluated for their ADMET properties. This work has identified 2-pyridone natural products with calculated potent inhibitory activity against SARS-CoV-2 M ^pro and with desirable drug-like properties, which may lead to the rapid discovery of a treatment for COVID-19.

Highlights

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  2-pyridone-scaffold is an inhibitory pharmacophore for SARS-CoV-2 M ^pro.

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  Thirty-three natural, antimicrobial products identified with 2-pyridone moiety.

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  All 2-pyridone natural products bind to active site of SARS-CoV-2 M ^pro in silico.

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  Thirteen molecules found to have potent inhibitory activity against SARS-CoV-2 M ^pro.

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  Inhibition of SARS-CoV-2 by natural 2-pyridones may lead to treatment of COVID-19.