In silico study of phytochemicals in the Receptor-Binding Domain (RBD) region of the SARS-CoV-2 spike protein (Omicron variant, B.1.1.529)
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | por |
Título da fonte: | Research, Society and Development |
Texto Completo: | https://rsdjournal.org/index.php/rsd/article/view/33126 |
Resumo: | COVID-19 is a highly contagious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) becoming a major threat worldwide due to its fast-spreading nature and more aggressive variants, such as the case of Omicron. The main interaction structure of the virus with the host cell is the spike region of the Spike protein called RBD, a structure that has had several mutations, making the search for drugs difficult. Based on this scenario, the present work aimed to evaluate the profile of interactions between molecules of natural origin against the RBD region of the Spike (S) protein of SARS-CoV-2, Ômicron variant. In the first methodological step, there was a molecular modeling of the RBD structure of a sequence obtained in Brazil and tests for its characterization and structural validation. Then, molecular docking was performed between 6 phytochemical ligands: Curcumin, Carvacrol (±)-Limonene, Glycyrrhizin, Allicin and Quercetin-3-Arabinoside in the specific region modeled RBD, after obtaining the best results, the complexes formed were evaluated by RMSD and RMSF. In the homology of the RBD region, a structure with low structural errors was obtained. In the interactions of each phytochemical, the molecules glycyrrhizin and quercetin showed higher molecular affinity, binding to the active site found in RBD. Molecular dynamics confirmed the interaction of ligands and the stability of the complexes during the simulations. Quercetin and glycyrrhizin showed a potential molecule binding to the RBD region of protein S, from the genome of the unprecedented omicron variant of SARS-CoV-2 sequenced in Brazil. |
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In silico study of phytochemicals in the Receptor-Binding Domain (RBD) region of the SARS-CoV-2 spike protein (Omicron variant, B.1.1.529)Estudio in silico de fitoquímicos en la región del Receptor-Binding Domain (RBD) de la proteína spike del SARS-CoV-2 (variante Omicron, B.1.1.529)Estudo in silico de fitoquímicos na região Receptor-Binding Domain (RBD) da proteína spike do SARS-CoV-2 (variante Ômicron, B.1.1.529)Covid-19Docking molecularMoléculas naturais.Covid-19Molecular dockingNatural molecules.Covid-19Acoplamiento molecularMoléculas naturales.COVID-19 is a highly contagious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) becoming a major threat worldwide due to its fast-spreading nature and more aggressive variants, such as the case of Omicron. The main interaction structure of the virus with the host cell is the spike region of the Spike protein called RBD, a structure that has had several mutations, making the search for drugs difficult. Based on this scenario, the present work aimed to evaluate the profile of interactions between molecules of natural origin against the RBD region of the Spike (S) protein of SARS-CoV-2, Ômicron variant. In the first methodological step, there was a molecular modeling of the RBD structure of a sequence obtained in Brazil and tests for its characterization and structural validation. Then, molecular docking was performed between 6 phytochemical ligands: Curcumin, Carvacrol (±)-Limonene, Glycyrrhizin, Allicin and Quercetin-3-Arabinoside in the specific region modeled RBD, after obtaining the best results, the complexes formed were evaluated by RMSD and RMSF. In the homology of the RBD region, a structure with low structural errors was obtained. In the interactions of each phytochemical, the molecules glycyrrhizin and quercetin showed higher molecular affinity, binding to the active site found in RBD. Molecular dynamics confirmed the interaction of ligands and the stability of the complexes during the simulations. Quercetin and glycyrrhizin showed a potential molecule binding to the RBD region of protein S, from the genome of the unprecedented omicron variant of SARS-CoV-2 sequenced in Brazil.El COVID-19 es una enfermedad altamente contagiosa causada por el síndrome respiratorio agudo severo coronavirus 2 (SARS-CoV-2) convirtiéndose en una gran amenaza a nivel mundial debido a su rápida propagación y variantes más agresivas, como es el caso de Omicron. La principal estructura de interacción del virus con la célula huésped es la región de la espiga de la proteína Spike llamada RBD, una estructura que ha tenido varias mutaciones, lo que dificulta la búsqueda de fármacos. Con base en este escenario, el presente trabajo tuvo como objetivo evaluar el perfil de interacciones entre moléculas de origen natural contra la región RBD de la proteína Spike (S) del SARS-CoV-2, variante Ômicron. En el primer paso metodológico, hubo un modelado molecular de la estructura RBD de una secuencia obtenida en Brasil y pruebas para su caracterización y validación estructural. Luego, se realizó acoplamiento molecular entre 6 ligandos fitoquímicos: Curcumina, Carvacrol (±)-Limoneno, Glicirricina, Alicina y Quercetina-3-Arabinósido en la región específica modelada RBD, luego de obtener los mejores resultados, los complejos formados fueron evaluados por RMSD y RMSF. En la homología de la región RBD se obtuvo una estructura con bajos errores estructurales. En las interacciones de cada fitoquímico, las moléculas glicirricina y quercetina mostraron mayor afinidad molecular, uniéndose al sitio activo que se encuentra en RBD. La dinámica molecular confirmó la interacción de los ligandos y la estabilidad de los complejos durante las simulaciones. La quercetina y la glicirricina mostraron una molécula potencial que se une a la región RBD de la proteína S, del genoma de la variante omicron sin precedentes del SARS-CoV-2 secuenciada en Brasil.COVID-19 é uma doença altamente contagiosa causada pelo coronavírus da síndrome respiratória aguda grave 2 (SARS-CoV-2) tornando-se uma grande ameaça em todo o mundo devido à sua rápida natureza de disseminação e variantes mais agressivas, como o caso da Ômicron. A principal estrutura de interação do vírus com a célula hospedeira é a região de pico da proteína Spike chamada de RBD, uma estrutura que teve diversas mutações, dificultando a busca de fármacos. Com base nesse cenário, o presente trabalho teve como objetivo avaliar o perfil de interações entre moléculas de origem naturais frente a região RBD da proteína Spike (S) do SARS-CoV-2, variante Ômicron. Na primeira etapa metodológica ocorreu uma modelagem molecular da estrutura RBD de sequência obtida no Brasil e testes para sua caracterização e validação estrutural. Em seguida, foi realizado o docking molecular entre 6 ligantes fitoquímicos: Curcumina, Carvacrol (±)-Limoneno, Glicirrizina, Alicina e Quercetina-3-Arabinoside na região específica RBD modelada, após obter os melhores resultados, os complexos formados foram avaliados por RMSD e RMSF. Na homologia da região RBD obteve-se uma estrutura com baixos erros estruturais. Nas interações de cada fitoquímico, as moléculas glicirrizina e quercetina apresentaram maior afinidade molecular, ligando-se ao sítio ativo encontrado na RBD. A dinâmica molecular confirmou a interação dos ligantes e a estabilidade dos complexos durante as simulações. A quercetina e glicirrizina apresentaram um potencial molécula ligando-se à região RBD da proteína S, a partir do genoma da variante ômicron inédita do SARS-CoV-2 sequenciada no Brasil.Research, Society and Development2022-08-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfhttps://rsdjournal.org/index.php/rsd/article/view/3312610.33448/rsd-v11i10.33126Research, Society and Development; Vol. 11 No. 10; e404111033126Research, Society and Development; Vol. 11 Núm. 10; e404111033126Research, Society and Development; v. 11 n. 10; e4041110331262525-3409reponame:Research, Society and Developmentinstname:Universidade Federal de Itajubá (UNIFEI)instacron:UNIFEIporhttps://rsdjournal.org/index.php/rsd/article/view/33126/27912Copyright (c) 2022 Helyson Lucas Bezerra Braz; Fernanda Martins de Souza; João Junior Faustino Soares; Renata de Sousa Alves; Roberta Jeane Bezerra Jorge; Gilberto Santos Cerqueirahttps://creativecommons.org/licenses/by/4.0info:eu-repo/semantics/openAccessBraz, Helyson Lucas Bezerra Souza, Fernanda Martins de Soares, João Junior Faustino Alves, Renata de SousaJorge, Roberta Jeane BezerraCerqueira, Gilberto Santos2022-08-12T22:23:03Zoai:ojs.pkp.sfu.ca:article/33126Revistahttps://rsdjournal.org/index.php/rsd/indexPUBhttps://rsdjournal.org/index.php/rsd/oairsd.articles@gmail.com2525-34092525-3409opendoar:2024-01-17T09:48:52.620021Research, Society and Development - Universidade Federal de Itajubá (UNIFEI)false |
dc.title.none.fl_str_mv |
In silico study of phytochemicals in the Receptor-Binding Domain (RBD) region of the SARS-CoV-2 spike protein (Omicron variant, B.1.1.529) Estudio in silico de fitoquímicos en la región del Receptor-Binding Domain (RBD) de la proteína spike del SARS-CoV-2 (variante Omicron, B.1.1.529) Estudo in silico de fitoquímicos na região Receptor-Binding Domain (RBD) da proteína spike do SARS-CoV-2 (variante Ômicron, B.1.1.529) |
title |
In silico study of phytochemicals in the Receptor-Binding Domain (RBD) region of the SARS-CoV-2 spike protein (Omicron variant, B.1.1.529) |
spellingShingle |
In silico study of phytochemicals in the Receptor-Binding Domain (RBD) region of the SARS-CoV-2 spike protein (Omicron variant, B.1.1.529) Braz, Helyson Lucas Bezerra Covid-19 Docking molecular Moléculas naturais. Covid-19 Molecular docking Natural molecules. Covid-19 Acoplamiento molecular Moléculas naturales. |
title_short |
In silico study of phytochemicals in the Receptor-Binding Domain (RBD) region of the SARS-CoV-2 spike protein (Omicron variant, B.1.1.529) |
title_full |
In silico study of phytochemicals in the Receptor-Binding Domain (RBD) region of the SARS-CoV-2 spike protein (Omicron variant, B.1.1.529) |
title_fullStr |
In silico study of phytochemicals in the Receptor-Binding Domain (RBD) region of the SARS-CoV-2 spike protein (Omicron variant, B.1.1.529) |
title_full_unstemmed |
In silico study of phytochemicals in the Receptor-Binding Domain (RBD) region of the SARS-CoV-2 spike protein (Omicron variant, B.1.1.529) |
title_sort |
In silico study of phytochemicals in the Receptor-Binding Domain (RBD) region of the SARS-CoV-2 spike protein (Omicron variant, B.1.1.529) |
author |
Braz, Helyson Lucas Bezerra |
author_facet |
Braz, Helyson Lucas Bezerra Souza, Fernanda Martins de Soares, João Junior Faustino Alves, Renata de Sousa Jorge, Roberta Jeane Bezerra Cerqueira, Gilberto Santos |
author_role |
author |
author2 |
Souza, Fernanda Martins de Soares, João Junior Faustino Alves, Renata de Sousa Jorge, Roberta Jeane Bezerra Cerqueira, Gilberto Santos |
author2_role |
author author author author author |
dc.contributor.author.fl_str_mv |
Braz, Helyson Lucas Bezerra Souza, Fernanda Martins de Soares, João Junior Faustino Alves, Renata de Sousa Jorge, Roberta Jeane Bezerra Cerqueira, Gilberto Santos |
dc.subject.por.fl_str_mv |
Covid-19 Docking molecular Moléculas naturais. Covid-19 Molecular docking Natural molecules. Covid-19 Acoplamiento molecular Moléculas naturales. |
topic |
Covid-19 Docking molecular Moléculas naturais. Covid-19 Molecular docking Natural molecules. Covid-19 Acoplamiento molecular Moléculas naturales. |
description |
COVID-19 is a highly contagious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) becoming a major threat worldwide due to its fast-spreading nature and more aggressive variants, such as the case of Omicron. The main interaction structure of the virus with the host cell is the spike region of the Spike protein called RBD, a structure that has had several mutations, making the search for drugs difficult. Based on this scenario, the present work aimed to evaluate the profile of interactions between molecules of natural origin against the RBD region of the Spike (S) protein of SARS-CoV-2, Ômicron variant. In the first methodological step, there was a molecular modeling of the RBD structure of a sequence obtained in Brazil and tests for its characterization and structural validation. Then, molecular docking was performed between 6 phytochemical ligands: Curcumin, Carvacrol (±)-Limonene, Glycyrrhizin, Allicin and Quercetin-3-Arabinoside in the specific region modeled RBD, after obtaining the best results, the complexes formed were evaluated by RMSD and RMSF. In the homology of the RBD region, a structure with low structural errors was obtained. In the interactions of each phytochemical, the molecules glycyrrhizin and quercetin showed higher molecular affinity, binding to the active site found in RBD. Molecular dynamics confirmed the interaction of ligands and the stability of the complexes during the simulations. Quercetin and glycyrrhizin showed a potential molecule binding to the RBD region of protein S, from the genome of the unprecedented omicron variant of SARS-CoV-2 sequenced in Brazil. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-08-05 |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://rsdjournal.org/index.php/rsd/article/view/33126 10.33448/rsd-v11i10.33126 |
url |
https://rsdjournal.org/index.php/rsd/article/view/33126 |
identifier_str_mv |
10.33448/rsd-v11i10.33126 |
dc.language.iso.fl_str_mv |
por |
language |
por |
dc.relation.none.fl_str_mv |
https://rsdjournal.org/index.php/rsd/article/view/33126/27912 |
dc.rights.driver.fl_str_mv |
https://creativecommons.org/licenses/by/4.0 info:eu-repo/semantics/openAccess |
rights_invalid_str_mv |
https://creativecommons.org/licenses/by/4.0 |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Research, Society and Development |
publisher.none.fl_str_mv |
Research, Society and Development |
dc.source.none.fl_str_mv |
Research, Society and Development; Vol. 11 No. 10; e404111033126 Research, Society and Development; Vol. 11 Núm. 10; e404111033126 Research, Society and Development; v. 11 n. 10; e404111033126 2525-3409 reponame:Research, Society and Development instname:Universidade Federal de Itajubá (UNIFEI) instacron:UNIFEI |
instname_str |
Universidade Federal de Itajubá (UNIFEI) |
instacron_str |
UNIFEI |
institution |
UNIFEI |
reponame_str |
Research, Society and Development |
collection |
Research, Society and Development |
repository.name.fl_str_mv |
Research, Society and Development - Universidade Federal de Itajubá (UNIFEI) |
repository.mail.fl_str_mv |
rsd.articles@gmail.com |
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1797052813198491648 |