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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Main Authors: López-Orozco Wendolyne, Mendoza-Huizar Humberto Luis, Álvarez-Romero Giaan Arturo, Torres-Valencia Jesús Martín, Sanchez-Zavala Maricruz
Format: Article
Language:English
Published: Serbian Chemical Society 2024-01-01
Series:Journal of the Serbian Chemical Society
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Online Access:https://doiserbia.nb.rs/img/doi/0352-5139/2024/0352-51392300078L.pdf
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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.
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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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AT alvarezromerogiaanarturo chemicalreactivityofalliinanditsmolecularinteractionswiththemproteaseproofsarscov2
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