Inhibition Potencies of Phytochemicals Derived from Sesame Against SARS-CoV-2 Main Protease: A Molecular Docking and Simulation Study
The ongoing COVID-19 pandemic, caused by SARS-CoV-2, has now spread across the nations with high mortality rates and multifaceted impact on human life. The proper treatment methods to overcome this contagious disease are still limited. The main protease enzyme (Mpro, also called 3CLpro) is essential...
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| Format: | Article |
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Frontiers Media S.A.
2021-10-01
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| Series: | Frontiers in Chemistry |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fchem.2021.744376/full |
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| author | Anuj Kumar Dwijesh Chandra Mishra Ulavappa Basavanneppa Angadi Rashmi Yadav Anil Rai Dinesh Kumar |
| author_facet | Anuj Kumar Dwijesh Chandra Mishra Ulavappa Basavanneppa Angadi Rashmi Yadav Anil Rai Dinesh Kumar |
| author_sort | Anuj Kumar |
| collection | DOAJ |
| description | The ongoing COVID-19 pandemic, caused by SARS-CoV-2, has now spread across the nations with high mortality rates and multifaceted impact on human life. The proper treatment methods to overcome this contagious disease are still limited. The main protease enzyme (Mpro, also called 3CLpro) is essential for viral replication and has been considered as one of the potent drug targets for treating COVID-19. In this study, virtual screening was performed to find out the molecular interactions between 36 natural compounds derived from sesame and the Mpro of COVID-19. Four natural metabolites, namely, sesamin, sesaminol, sesamolin, and sesamolinol have been ranked as the top interacting molecules to Mpro based on the affinity of molecular docking. Moreover, stability of these four sesame-specific natural compounds has also been evaluated using molecular dynamics (MD) simulations for 200 nanoseconds. The molecular dynamics simulations and free energy calculations revealed that these compounds have stable and favorable energies, causing strong binding with Mpro. These screened natural metabolites also meet the essential conditions for drug likeness such as absorption, distribution, metabolism, and excretion (ADME) properties as well as Lipinski’s rule of five. Our finding suggests that these screened natural compounds may be evolved as promising therapeutics against COVID-19. |
| first_indexed | 2024-12-17T18:51:54Z |
| format | Article |
| id | doaj.art-10e23e84083744bc8de6533de3833670 |
| institution | Directory Open Access Journal |
| issn | 2296-2646 |
| language | English |
| last_indexed | 2024-12-17T18:51:54Z |
| publishDate | 2021-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Chemistry |
| spelling | doaj.art-10e23e84083744bc8de6533de38336702022-12-21T21:36:31ZengFrontiers Media S.A.Frontiers in Chemistry2296-26462021-10-01910.3389/fchem.2021.744376744376Inhibition Potencies of Phytochemicals Derived from Sesame Against SARS-CoV-2 Main Protease: A Molecular Docking and Simulation StudyAnuj Kumar0Dwijesh Chandra Mishra1Ulavappa Basavanneppa Angadi2Rashmi Yadav3Anil Rai4Dinesh Kumar5Centre for Agricultural Bioinformatics (CABin), ICAR- Indian Agricultural Statistics Research Institute, New Delhi, IndiaCentre for Agricultural Bioinformatics (CABin), ICAR- Indian Agricultural Statistics Research Institute, New Delhi, IndiaCentre for Agricultural Bioinformatics (CABin), ICAR- Indian Agricultural Statistics Research Institute, New Delhi, IndiaDivision of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, IndiaCentre for Agricultural Bioinformatics (CABin), ICAR- Indian Agricultural Statistics Research Institute, New Delhi, IndiaCentre for Agricultural Bioinformatics (CABin), ICAR- Indian Agricultural Statistics Research Institute, New Delhi, IndiaThe ongoing COVID-19 pandemic, caused by SARS-CoV-2, has now spread across the nations with high mortality rates and multifaceted impact on human life. The proper treatment methods to overcome this contagious disease are still limited. The main protease enzyme (Mpro, also called 3CLpro) is essential for viral replication and has been considered as one of the potent drug targets for treating COVID-19. In this study, virtual screening was performed to find out the molecular interactions between 36 natural compounds derived from sesame and the Mpro of COVID-19. Four natural metabolites, namely, sesamin, sesaminol, sesamolin, and sesamolinol have been ranked as the top interacting molecules to Mpro based on the affinity of molecular docking. Moreover, stability of these four sesame-specific natural compounds has also been evaluated using molecular dynamics (MD) simulations for 200 nanoseconds. The molecular dynamics simulations and free energy calculations revealed that these compounds have stable and favorable energies, causing strong binding with Mpro. These screened natural metabolites also meet the essential conditions for drug likeness such as absorption, distribution, metabolism, and excretion (ADME) properties as well as Lipinski’s rule of five. Our finding suggests that these screened natural compounds may be evolved as promising therapeutics against COVID-19.https://www.frontiersin.org/articles/10.3389/fchem.2021.744376/fullCOVID-19main proteasesesamenatural compoundsmolecular dockingmolecular dynamics simulations |
| spellingShingle | Anuj Kumar Dwijesh Chandra Mishra Ulavappa Basavanneppa Angadi Rashmi Yadav Anil Rai Dinesh Kumar Inhibition Potencies of Phytochemicals Derived from Sesame Against SARS-CoV-2 Main Protease: A Molecular Docking and Simulation Study Frontiers in Chemistry COVID-19 main protease sesame natural compounds molecular docking molecular dynamics simulations |
| title | Inhibition Potencies of Phytochemicals Derived from Sesame Against SARS-CoV-2 Main Protease: A Molecular Docking and Simulation Study |
| title_full | Inhibition Potencies of Phytochemicals Derived from Sesame Against SARS-CoV-2 Main Protease: A Molecular Docking and Simulation Study |
| title_fullStr | Inhibition Potencies of Phytochemicals Derived from Sesame Against SARS-CoV-2 Main Protease: A Molecular Docking and Simulation Study |
| title_full_unstemmed | Inhibition Potencies of Phytochemicals Derived from Sesame Against SARS-CoV-2 Main Protease: A Molecular Docking and Simulation Study |
| title_short | Inhibition Potencies of Phytochemicals Derived from Sesame Against SARS-CoV-2 Main Protease: A Molecular Docking and Simulation Study |
| title_sort | inhibition potencies of phytochemicals derived from sesame against sars cov 2 main protease a molecular docking and simulation study |
| topic | COVID-19 main protease sesame natural compounds molecular docking molecular dynamics simulations |
| url | https://www.frontiersin.org/articles/10.3389/fchem.2021.744376/full |
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