Computer Aided Drug Design Approach to Screen Phytoconstituents of <i>Adhatoda vasica</i> as Potential Inhibitors of SARS-CoV-2 Main Protease Enzyme
A novel coronavirus (COVID-19) was identified as one of the severe acute respiratory syndrome coronaviruses (SARS-CoV-2) and emerged as a pandemic in 2020. Thus, there is an urgent need to screen and develop an agent to suppress the proliferation of viral particles of SARS-CoV-2, and several drugs h...
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MDPI AG
2022-02-01
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| author | Bathula Siva Kumar Singh Anuragh Ananth Kumar Kammala Kaliappan Ilango |
| author_facet | Bathula Siva Kumar Singh Anuragh Ananth Kumar Kammala Kaliappan Ilango |
| author_sort | Bathula Siva Kumar |
| collection | DOAJ |
| description | A novel coronavirus (COVID-19) was identified as one of the severe acute respiratory syndrome coronaviruses (SARS-CoV-2) and emerged as a pandemic in 2020. Thus, there is an urgent need to screen and develop an agent to suppress the proliferation of viral particles of SARS-CoV-2, and several drugs have entered clinical trial phases to assess their therapeutic potential. The objective of the present study is to screen phytochemicals against the main viral protease using molecular docking studies. The phytochemicals vasicine, vasicinone, vasicinolone, vasicol, vasicolinone, adhatodine, adhavasicinone, aniflorine, anisotine, vasnetine, and orientin from <i>Adhatoda vasica</i> were selected, and the compounds were docked with various viral protein targets, including specific SARS-CoV-2 main protease (PDBID:6Y84), using AutoDock, Schrodinger, Biovia discovery studio, and virtual screening tools. Adhatodine and vasnetine showed a better binding affinity of −9.60 KJ/mol and −8.78 KJ/mol, respectively. In molecular docking simulations for 10 ns, these compounds illustrated strong hydrogen-bonding interactions with the protein active site and induced a potential conformational change in the ligand-binding site. The results were compared with the antiviral drugs nirmatrelvir and ritonavir. These results suggest that these phytochemicals can be studied as potential inhibitors against SARS-CoV-2 protease and may have an antiviral effect on coronavirus. However, further in vitro and in vivo efficacy activity needs to be investigated for these phytochemicals. |
| first_indexed | 2024-03-09T21:34:42Z |
| format | Article |
| id | doaj.art-d1f181057d7c4874812242523a6c6234 |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-09T21:34:42Z |
| publishDate | 2022-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-d1f181057d7c4874812242523a6c62342023-11-23T20:47:24ZengMDPI AGLife2075-17292022-02-0112231510.3390/life12020315Computer Aided Drug Design Approach to Screen Phytoconstituents of <i>Adhatoda vasica</i> as Potential Inhibitors of SARS-CoV-2 Main Protease EnzymeBathula Siva Kumar0Singh Anuragh1Ananth Kumar Kammala2Kaliappan Ilango3Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu 603203, Tamil Nadu, IndiaDepartment of Pharmacology, SRM College of Pharmacy, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu 603203, Tamil Nadu, IndiaDepartment of Obstetrics and Gynecology, The University of Texas Medical Branch, Galveston, TX 77555, USADepartment of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu 603203, Tamil Nadu, IndiaA novel coronavirus (COVID-19) was identified as one of the severe acute respiratory syndrome coronaviruses (SARS-CoV-2) and emerged as a pandemic in 2020. Thus, there is an urgent need to screen and develop an agent to suppress the proliferation of viral particles of SARS-CoV-2, and several drugs have entered clinical trial phases to assess their therapeutic potential. The objective of the present study is to screen phytochemicals against the main viral protease using molecular docking studies. The phytochemicals vasicine, vasicinone, vasicinolone, vasicol, vasicolinone, adhatodine, adhavasicinone, aniflorine, anisotine, vasnetine, and orientin from <i>Adhatoda vasica</i> were selected, and the compounds were docked with various viral protein targets, including specific SARS-CoV-2 main protease (PDBID:6Y84), using AutoDock, Schrodinger, Biovia discovery studio, and virtual screening tools. Adhatodine and vasnetine showed a better binding affinity of −9.60 KJ/mol and −8.78 KJ/mol, respectively. In molecular docking simulations for 10 ns, these compounds illustrated strong hydrogen-bonding interactions with the protein active site and induced a potential conformational change in the ligand-binding site. The results were compared with the antiviral drugs nirmatrelvir and ritonavir. These results suggest that these phytochemicals can be studied as potential inhibitors against SARS-CoV-2 protease and may have an antiviral effect on coronavirus. However, further in vitro and in vivo efficacy activity needs to be investigated for these phytochemicals.https://www.mdpi.com/2075-1729/12/2/315SARS-CoV-2COVID-19<i>Adhatoda vasica</i>molecular dockingmolecular dynamic simulations |
| spellingShingle | Bathula Siva Kumar Singh Anuragh Ananth Kumar Kammala Kaliappan Ilango Computer Aided Drug Design Approach to Screen Phytoconstituents of <i>Adhatoda vasica</i> as Potential Inhibitors of SARS-CoV-2 Main Protease Enzyme Life SARS-CoV-2 COVID-19 <i>Adhatoda vasica</i> molecular docking molecular dynamic simulations |
| title | Computer Aided Drug Design Approach to Screen Phytoconstituents of <i>Adhatoda vasica</i> as Potential Inhibitors of SARS-CoV-2 Main Protease Enzyme |
| title_full | Computer Aided Drug Design Approach to Screen Phytoconstituents of <i>Adhatoda vasica</i> as Potential Inhibitors of SARS-CoV-2 Main Protease Enzyme |
| title_fullStr | Computer Aided Drug Design Approach to Screen Phytoconstituents of <i>Adhatoda vasica</i> as Potential Inhibitors of SARS-CoV-2 Main Protease Enzyme |
| title_full_unstemmed | Computer Aided Drug Design Approach to Screen Phytoconstituents of <i>Adhatoda vasica</i> as Potential Inhibitors of SARS-CoV-2 Main Protease Enzyme |
| title_short | Computer Aided Drug Design Approach to Screen Phytoconstituents of <i>Adhatoda vasica</i> as Potential Inhibitors of SARS-CoV-2 Main Protease Enzyme |
| title_sort | computer aided drug design approach to screen phytoconstituents of i adhatoda vasica i as potential inhibitors of sars cov 2 main protease enzyme |
| topic | SARS-CoV-2 COVID-19 <i>Adhatoda vasica</i> molecular docking molecular dynamic simulations |
| url | https://www.mdpi.com/2075-1729/12/2/315 |
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