Proposal of novel natural inhibitors of severe acute respiratory syndrome coronavirus 2 main protease: Molecular docking and ab initio fragment molecular orbital calculations.

Abstract

This paper proposes natural drug candidate compounds for the treatment of coronavirus disease 2019 (COVID-19). We investigated the binding properties between the compounds in the Moringa oleifera plant and the main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 using molecular docking and ab initio fragment molecular orbital calculations. Among the 12 compounds, niaziminin was found to bind the strongest to Mpro. We furthermore proposed novel compounds based on niaziminin and investigated their binding properties to Mpro. The results reveal that the introduction of a hydroxyl group into niaziminin enhances its binding affinity to Mpro. These niaziminin derivatives can be promising candidate drugs for the treatment of COVID-19.

• Authors: Divya Shaji, Shohei Yamamoto, Ryosuke Saito, Ryo Suzuki, Shunya Nakamura, Noriyuki Kurita
• Journal: Biophysical chemistry (Biophys Chem) Vol. 275 Pg. 106608 (Aug 2021) ISSN: 1873-4200 [Electronic] Netherlands
• PMID: 33962341 (Publication Type: Journal Article)
• Copyright: Copyright © 2021 Elsevier B.V. All rights reserved.

Chemical References

• Antiviral Agents
• Phytochemicals
• Protease Inhibitors
• Thiocarbamates
• niaziminin
• Coronavirus 3C Proteases

Topics

• Antiviral Agents (chemistry, classification, isolation & purification, pharmacology)
• Catalytic Domain
• Coronavirus 3C Proteases (antagonists & inhibitors, chemistry, genetics, metabolism)
• Drug Design
• Drug Discovery
• Gene Expression
• Humans
• Molecular Docking Simulation
• Molecular Dynamics Simulation
• Moringa oleifera (chemistry)
• Phytochemicals (chemistry, classification, isolation & purification, pharmacology)
• Protease Inhibitors (chemistry, classification, isolation & purification, pharmacology)
• Protein Binding
• Protein Interaction Domains and Motifs
• Protein Structure, Secondary
• Quantum Theory
• SARS-CoV-2 (chemistry, drug effects, enzymology)
• Structure-Activity Relationship
• Thermodynamics
• Thiocarbamates (chemistry, classification, isolation & purification, pharmacology)
• COVID-19 Drug Treatment