Chemical reactivity of alliin and its molecular interactions with the M proteasepro of SARS-CoV-2
In the present work, a computational study of the chemical reactivity of alliin at the X/DGDZVP level of theory (where X is B3LYP, M06, M06L or wB97XD) was performed. The distribution of active sites on alliin was determined by evaluating the Fukui function. For electrophilic attacks, the more react...
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Serbian Chemical Society
2024-01-01
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author | López-Orozco Wendolyne Mendoza-Huizar Humberto Luis Álvarez-Romero Giaan Arturo Torres-Valencia Jesús Martín Sanchez-Zavala Maricruz |
author_facet | López-Orozco Wendolyne Mendoza-Huizar Humberto Luis Álvarez-Romero Giaan Arturo Torres-Valencia Jesús Martín Sanchez-Zavala Maricruz |
author_sort | López-Orozco Wendolyne |
collection | DOAJ |
description | In the present work, a computational study of the chemical reactivity of alliin at the X/DGDZVP level of theory (where X is B3LYP, M06, M06L or wB97XD) was performed. The distribution of active sites on alliin was determined by evaluating the Fukui function. For electrophilic attacks, the more reactive sites are on the carbon atoms of the prop-2-ene moiety. The more active sites for nucleophilic attacks are located on the thioether group. In the case of free radical attacks, the more reactive sites are on the carbonyl, thioether and prop-2-ene moieties. Additionally, the molecular docking study revealed that, alliin is able to dock to the protease Mpro of SARS-CoV-2 through interactions with the catalytic CYS145-HSD164 dyad via van der Waals interactions, with MET49 with interactions alkyl-type ions and with PHE140 by hydrogen bonds. Also, the molecular dynamic study indicates that alliin remains in the pocket site. Last result suggests that this molecule is a potential candidate for further in vitro evaluation as a drug for the treatment of the major protease-based SARS-CoV-2 virus. |
format | Article |
id | doaj-art-3053d753f0914c94a3fa3a92dfd5b923 |
institution | Kabale University |
issn | 0352-5139 1820-7421 |
language | English |
publishDate | 2024-01-01 |
publisher | Serbian Chemical Society |
record_format | Article |
series | Journal of the Serbian Chemical Society |
spelling | doaj-art-3053d753f0914c94a3fa3a92dfd5b9232025-01-30T06:45:49ZengSerbian Chemical SocietyJournal of the Serbian Chemical Society0352-51391820-74212024-01-0189111433144510.2298/JSC230817078L0352-51392300078LChemical reactivity of alliin and its molecular interactions with the M proteasepro of SARS-CoV-2López-Orozco Wendolyne0https://orcid.org/0000-0003-4614-2234Mendoza-Huizar Humberto Luis1https://orcid.org/0000-0003-2373-4624Álvarez-Romero Giaan Arturo2https://orcid.org/0000-0002-9525-3937Torres-Valencia Jesús Martín3https://orcid.org/0000-0001-6426-7562Sanchez-Zavala Maricruz4Academic Area of Chemistry, Universidad Autónoma del Estado de Hidalgo, Carretera Pachuca-Tulancingo, Mineral de la Reforma, Hidalgo, MexicoAcademic Area of Chemistry, Universidad Autónoma del Estado de Hidalgo, Carretera Pachuca-Tulancingo, Mineral de la Reforma, Hidalgo, MexicoAcademic Area of Chemistry, Universidad Autónoma del Estado de Hidalgo, Carretera Pachuca-Tulancingo, Mineral de la Reforma, Hidalgo, MexicoAcademic Area of Chemistry, Universidad Autónoma del Estado de Hidalgo, Carretera Pachuca-Tulancingo, Mineral de la Reforma, Hidalgo, MexicoAcademic Area of Chemistry, Universidad Autónoma del Estado de Hidalgo, Carretera Pachuca-Tulancingo, Mineral de la Reforma, Hidalgo, MexicoIn the present work, a computational study of the chemical reactivity of alliin at the X/DGDZVP level of theory (where X is B3LYP, M06, M06L or wB97XD) was performed. The distribution of active sites on alliin was determined by evaluating the Fukui function. For electrophilic attacks, the more reactive sites are on the carbon atoms of the prop-2-ene moiety. The more active sites for nucleophilic attacks are located on the thioether group. In the case of free radical attacks, the more reactive sites are on the carbonyl, thioether and prop-2-ene moieties. Additionally, the molecular docking study revealed that, alliin is able to dock to the protease Mpro of SARS-CoV-2 through interactions with the catalytic CYS145-HSD164 dyad via van der Waals interactions, with MET49 with interactions alkyl-type ions and with PHE140 by hydrogen bonds. Also, the molecular dynamic study indicates that alliin remains in the pocket site. Last result suggests that this molecule is a potential candidate for further in vitro evaluation as a drug for the treatment of the major protease-based SARS-CoV-2 virus.https://doiserbia.nb.rs/img/doi/0352-5139/2024/0352-51392300078L.pdffukui functionmolecular dockingnon-covalent |
spellingShingle | López-Orozco Wendolyne Mendoza-Huizar Humberto Luis Álvarez-Romero Giaan Arturo Torres-Valencia Jesús Martín Sanchez-Zavala Maricruz Chemical reactivity of alliin and its molecular interactions with the M proteasepro of SARS-CoV-2 Journal of the Serbian Chemical Society fukui function molecular docking non-covalent |
title | Chemical reactivity of alliin and its molecular interactions with the M proteasepro of SARS-CoV-2 |
title_full | Chemical reactivity of alliin and its molecular interactions with the M proteasepro of SARS-CoV-2 |
title_fullStr | Chemical reactivity of alliin and its molecular interactions with the M proteasepro of SARS-CoV-2 |
title_full_unstemmed | Chemical reactivity of alliin and its molecular interactions with the M proteasepro of SARS-CoV-2 |
title_short | Chemical reactivity of alliin and its molecular interactions with the M proteasepro of SARS-CoV-2 |
title_sort | chemical reactivity of alliin and its molecular interactions with the m proteasepro of sars cov 2 |
topic | fukui function molecular docking non-covalent |
url | https://doiserbia.nb.rs/img/doi/0352-5139/2024/0352-51392300078L.pdf |
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