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In silico molecular docking: Evaluation of coumarin based derivatives against SARS-CoV-2
BACKGROUND: The unique anthropological coronavirus which has been titled as SARS-CoV-2 was originally arisen in late 2019 in Wuhan, China affecting respiratory infection named as COVID-19. Coronavirus is disturbing human life in an exceptional method and has converted a public health global crisis....
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Author(s). Published by Elsevier Ltd on behalf of King Saud Bin Abdulaziz University for Health Sciences.
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7505582/ https://www.ncbi.nlm.nih.gov/pubmed/33008777 http://dx.doi.org/10.1016/j.jiph.2020.09.002 |
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author | Chidambaram, Sathish Kumar Ali, Daoud Alarifi, Saud Radhakrishnan, Surendrakumar Akbar, Idhayadhulla |
author_facet | Chidambaram, Sathish Kumar Ali, Daoud Alarifi, Saud Radhakrishnan, Surendrakumar Akbar, Idhayadhulla |
author_sort | Chidambaram, Sathish Kumar |
collection | PubMed |
description | BACKGROUND: The unique anthropological coronavirus which has been titled as SARS-CoV-2 was originally arisen in late 2019 in Wuhan, China affecting respiratory infection named as COVID-19. Coronavirus is disturbing human life in an exceptional method and has converted a public health global crisis. Natural products are ahead consideration due to the huge beneficial window and effective anti-inflammatory, immunomodulatory, antioxidant and antiviral possessions. Consequently, the present study was intended to display inhibition ability of natural products coumarins and their analogues against SARS coronavirus. METHODS: The present study, aims to forecast theoretical assembly for the protease of COVID-19 and to discover advance whether this protein may assist as a target for protease inhibitors such as psoralen, bergapten, imperatorin, heraclenin, heraclenol, saxalin, oxepeucedanin, angelicin, toddacoumaquinone, and aesculetin. The docking score of these natural coumarin analogues compared with standard Hydroxychloroquine. Whereas the 3D assembly of main protease of SARS coronavirus was forecast with SWISS MODEL web server, and molecular interaction studies amongst target protein and ligands were done with AutoDock Vina software. RESULTS: The study more exposed that all the inhibitors acquired with negative dock energy against the target protein. Molecular docking investigation displayed that natural coumarin analogue toddacoumaquinone displayed a remarkable inhibition ability with the binding energy of −7.8 kcal/mol than other compounds against main protease of SARS coronavirus in intricate with α-ketoamide (PDB ID: 5N5O). The synthetic coumarin analogue (1 m) also displayed the comparable inhibition ability with a binding energy of −7.1 kcal/mol against main protease of SARS coronavirus in intricate with α-ketoamide. Keeping the overhead results of ADME and toxicity, all tested compounds were recognized as drug-like nature, passing Lipinski’s “Rule of 5” with 0 violation except α-ketoamide passes Lipinski’s “Rule of 5” with 1 violation MW > 500. The projected constraints are within the assortment of recognized values. CONCLUSIONS: Based upon the results of the manifold sequence alliance, natural and synthetic coumarin binding sites were preserved. The present in silico examination thus, delivers structural awareness about the protease of COVID-19 and molecular relations with some of the recognised protease inhibitors. |
format | Online Article Text |
id | pubmed-7505582 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | The Author(s). Published by Elsevier Ltd on behalf of King Saud Bin Abdulaziz University for Health Sciences. |
record_format | MEDLINE/PubMed |
spelling | pubmed-75055822020-09-23 In silico molecular docking: Evaluation of coumarin based derivatives against SARS-CoV-2 Chidambaram, Sathish Kumar Ali, Daoud Alarifi, Saud Radhakrishnan, Surendrakumar Akbar, Idhayadhulla J Infect Public Health Original Article BACKGROUND: The unique anthropological coronavirus which has been titled as SARS-CoV-2 was originally arisen in late 2019 in Wuhan, China affecting respiratory infection named as COVID-19. Coronavirus is disturbing human life in an exceptional method and has converted a public health global crisis. Natural products are ahead consideration due to the huge beneficial window and effective anti-inflammatory, immunomodulatory, antioxidant and antiviral possessions. Consequently, the present study was intended to display inhibition ability of natural products coumarins and their analogues against SARS coronavirus. METHODS: The present study, aims to forecast theoretical assembly for the protease of COVID-19 and to discover advance whether this protein may assist as a target for protease inhibitors such as psoralen, bergapten, imperatorin, heraclenin, heraclenol, saxalin, oxepeucedanin, angelicin, toddacoumaquinone, and aesculetin. The docking score of these natural coumarin analogues compared with standard Hydroxychloroquine. Whereas the 3D assembly of main protease of SARS coronavirus was forecast with SWISS MODEL web server, and molecular interaction studies amongst target protein and ligands were done with AutoDock Vina software. RESULTS: The study more exposed that all the inhibitors acquired with negative dock energy against the target protein. Molecular docking investigation displayed that natural coumarin analogue toddacoumaquinone displayed a remarkable inhibition ability with the binding energy of −7.8 kcal/mol than other compounds against main protease of SARS coronavirus in intricate with α-ketoamide (PDB ID: 5N5O). The synthetic coumarin analogue (1 m) also displayed the comparable inhibition ability with a binding energy of −7.1 kcal/mol against main protease of SARS coronavirus in intricate with α-ketoamide. Keeping the overhead results of ADME and toxicity, all tested compounds were recognized as drug-like nature, passing Lipinski’s “Rule of 5” with 0 violation except α-ketoamide passes Lipinski’s “Rule of 5” with 1 violation MW > 500. The projected constraints are within the assortment of recognized values. CONCLUSIONS: Based upon the results of the manifold sequence alliance, natural and synthetic coumarin binding sites were preserved. The present in silico examination thus, delivers structural awareness about the protease of COVID-19 and molecular relations with some of the recognised protease inhibitors. The Author(s). Published by Elsevier Ltd on behalf of King Saud Bin Abdulaziz University for Health Sciences. 2020-11 2020-09-21 /pmc/articles/PMC7505582/ /pubmed/33008777 http://dx.doi.org/10.1016/j.jiph.2020.09.002 Text en © 2020 The Author(s) Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. |
spellingShingle | Original Article Chidambaram, Sathish Kumar Ali, Daoud Alarifi, Saud Radhakrishnan, Surendrakumar Akbar, Idhayadhulla In silico molecular docking: Evaluation of coumarin based derivatives against SARS-CoV-2 |
title | In silico molecular docking: Evaluation of coumarin based derivatives against SARS-CoV-2 |
title_full | In silico molecular docking: Evaluation of coumarin based derivatives against SARS-CoV-2 |
title_fullStr | In silico molecular docking: Evaluation of coumarin based derivatives against SARS-CoV-2 |
title_full_unstemmed | In silico molecular docking: Evaluation of coumarin based derivatives against SARS-CoV-2 |
title_short | In silico molecular docking: Evaluation of coumarin based derivatives against SARS-CoV-2 |
title_sort | in silico molecular docking: evaluation of coumarin based derivatives against sars-cov-2 |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7505582/ https://www.ncbi.nlm.nih.gov/pubmed/33008777 http://dx.doi.org/10.1016/j.jiph.2020.09.002 |
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