Comprehensive virtual screening of 4.8 k flavonoids reveals novel insights into allosteric inhibition of SARS-CoV-2 M<sup>PRO</sup>

Descripción del Articulo

El texto completo de este trabajo no está disponible en el Repositorio Académico UPC por restricciones de la casa editorial donde ha sido publicado.
Detalles Bibliográficos
Autores: Jiménez-Avalos, Gabriel, Vargas-Ruiz, A. Paula, Delgado-Pease, Nicolás E., Olivos-Ramirez, Gustavo E., Sheen, Patricia, Fernández-Díaz, Manolo, Quiliano, Miguel, Zimic, Mirko, Agurto-Arteaga, Andres, Antiparra, Ricardo, Ardiles-Reyes, Manuel, Calderon, Katherine, Cauna-Orocollo, Yudith, de Grecia Cauti-Mendoza, Maria, Chipana-Flores, Naer, Choque-Guevara, Ricardo, Chunga-Girón, Xiomara, Criollo-Orozco, Manuel, De La Cruz, Lewis, Delgado-Ccancce, Elmer, Elugo-Guevara, Christian, Fernández-Sanchez, Manolo, Guevara-Sarmiento, Luis, Gutiérrez, Kristel, Heredia-Almeyda, Oscar, Huaccachi-Gonzalez, Edison, Huerta-Roque, Pedro, Icochea, Eliana, Isasi-Rivas, Gisela, Juscamaita-Bartra, Romina A., Licla-Inca, Abraham, Montalvan, Angela, Montesinos-Millan, Ricardo, Núñez-Fernández, Dennis, Ochoa-Ortiz, Adiana, Páucar-Montoro, Erika, Pauyac, Kathy, Perez-Martinez, Jose L., Perez-M, Norma, Poma-Acevedo, Astrid, Quiñones-Garcia, Stefany, Ramirez-Ortiz, Ingrid, Ramos-Sono, Daniel, Rios-Angulo, Angela A., Rios-Matos, Dora, Rojas-Neyra, Aldo, Romero, Yomara K., Salguedo-Bohorquez, Mario I., Sernaque-Aguilar, Yacory, Soto, Luis F., Tataje-Lavanda, Luis, Ticona, Julio, Vallejos-Sánchez, Katherine, Villanueva-Pérez, Doris, Ygnacio-Aguirre, Freddy
Formato: artículo
Fecha de Publicación:2021
Institución:Universidad Peruana de Ciencias Aplicadas
Repositorio:UPC-Institucional
Lenguaje:inglés
OAI Identifier:oai:repositorioacademico.upc.edu.pe:10757/657336
Enlace del recurso:http://hdl.handle.net/10757/657336
Nivel de acceso:acceso embargado
Materia:SARS-CoV-2
Antiviral Agents
Binding Sites
Coronavirus 3C Proteases
COVID-19
Databases
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network_name_str UPC-Institucional
repository_id_str 2670
dc.title.es_PE.fl_str_mv Comprehensive virtual screening of 4.8 k flavonoids reveals novel insights into allosteric inhibition of SARS-CoV-2 M<sup>PRO</sup>
title Comprehensive virtual screening of 4.8 k flavonoids reveals novel insights into allosteric inhibition of SARS-CoV-2 M<sup>PRO</sup>
spellingShingle Comprehensive virtual screening of 4.8 k flavonoids reveals novel insights into allosteric inhibition of SARS-CoV-2 M<sup>PRO</sup>
Jiménez-Avalos, Gabriel
SARS-CoV-2
Antiviral Agents
Binding Sites
Coronavirus 3C Proteases
COVID-19
Databases
title_short Comprehensive virtual screening of 4.8 k flavonoids reveals novel insights into allosteric inhibition of SARS-CoV-2 M<sup>PRO</sup>
title_full Comprehensive virtual screening of 4.8 k flavonoids reveals novel insights into allosteric inhibition of SARS-CoV-2 M<sup>PRO</sup>
title_fullStr Comprehensive virtual screening of 4.8 k flavonoids reveals novel insights into allosteric inhibition of SARS-CoV-2 M<sup>PRO</sup>
title_full_unstemmed Comprehensive virtual screening of 4.8 k flavonoids reveals novel insights into allosteric inhibition of SARS-CoV-2 M<sup>PRO</sup>
title_sort Comprehensive virtual screening of 4.8 k flavonoids reveals novel insights into allosteric inhibition of SARS-CoV-2 M<sup>PRO</sup>
author Jiménez-Avalos, Gabriel
author_facet Jiménez-Avalos, Gabriel
Vargas-Ruiz, A. Paula
Delgado-Pease, Nicolás E.
Olivos-Ramirez, Gustavo E.
Sheen, Patricia
Fernández-Díaz, Manolo
Quiliano, Miguel
Zimic, Mirko
Agurto-Arteaga, Andres
Antiparra, Ricardo
Ardiles-Reyes, Manuel
Calderon, Katherine
Cauna-Orocollo, Yudith
de Grecia Cauti-Mendoza, Maria
Chipana-Flores, Naer
Choque-Guevara, Ricardo
Chunga-Girón, Xiomara
Criollo-Orozco, Manuel
De La Cruz, Lewis
Delgado-Ccancce, Elmer
Elugo-Guevara, Christian
Fernández-Sanchez, Manolo
Guevara-Sarmiento, Luis
Gutiérrez, Kristel
Heredia-Almeyda, Oscar
Huaccachi-Gonzalez, Edison
Huerta-Roque, Pedro
Icochea, Eliana
Isasi-Rivas, Gisela
Juscamaita-Bartra, Romina A.
Licla-Inca, Abraham
Montalvan, Angela
Montesinos-Millan, Ricardo
Núñez-Fernández, Dennis
Ochoa-Ortiz, Adiana
Páucar-Montoro, Erika
Pauyac, Kathy
Perez-Martinez, Jose L.
Perez-M, Norma
Poma-Acevedo, Astrid
Quiñones-Garcia, Stefany
Ramirez-Ortiz, Ingrid
Ramos-Sono, Daniel
Rios-Angulo, Angela A.
Rios-Matos, Dora
Rojas-Neyra, Aldo
Romero, Yomara K.
Salguedo-Bohorquez, Mario I.
Sernaque-Aguilar, Yacory
Soto, Luis F.
Tataje-Lavanda, Luis
Ticona, Julio
Vallejos-Sánchez, Katherine
Villanueva-Pérez, Doris
Ygnacio-Aguirre, Freddy
author_role author
author2 Vargas-Ruiz, A. Paula
Delgado-Pease, Nicolás E.
Olivos-Ramirez, Gustavo E.
Sheen, Patricia
Fernández-Díaz, Manolo
Quiliano, Miguel
Zimic, Mirko
Agurto-Arteaga, Andres
Antiparra, Ricardo
Ardiles-Reyes, Manuel
Calderon, Katherine
Cauna-Orocollo, Yudith
de Grecia Cauti-Mendoza, Maria
Chipana-Flores, Naer
Choque-Guevara, Ricardo
Chunga-Girón, Xiomara
Criollo-Orozco, Manuel
De La Cruz, Lewis
Delgado-Ccancce, Elmer
Elugo-Guevara, Christian
Fernández-Sanchez, Manolo
Guevara-Sarmiento, Luis
Gutiérrez, Kristel
Heredia-Almeyda, Oscar
Huaccachi-Gonzalez, Edison
Huerta-Roque, Pedro
Icochea, Eliana
Isasi-Rivas, Gisela
Juscamaita-Bartra, Romina A.
Licla-Inca, Abraham
Montalvan, Angela
Montesinos-Millan, Ricardo
Núñez-Fernández, Dennis
Ochoa-Ortiz, Adiana
Páucar-Montoro, Erika
Pauyac, Kathy
Perez-Martinez, Jose L.
Perez-M, Norma
Poma-Acevedo, Astrid
Quiñones-Garcia, Stefany
Ramirez-Ortiz, Ingrid
Ramos-Sono, Daniel
Rios-Angulo, Angela A.
Rios-Matos, Dora
Rojas-Neyra, Aldo
Romero, Yomara K.
Salguedo-Bohorquez, Mario I.
Sernaque-Aguilar, Yacory
Soto, Luis F.
Tataje-Lavanda, Luis
Ticona, Julio
Vallejos-Sánchez, Katherine
Villanueva-Pérez, Doris
Ygnacio-Aguirre, Freddy
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dc.contributor.author.fl_str_mv Jiménez-Avalos, Gabriel
Vargas-Ruiz, A. Paula
Delgado-Pease, Nicolás E.
Olivos-Ramirez, Gustavo E.
Sheen, Patricia
Fernández-Díaz, Manolo
Quiliano, Miguel
Zimic, Mirko
Agurto-Arteaga, Andres
Antiparra, Ricardo
Ardiles-Reyes, Manuel
Calderon, Katherine
Cauna-Orocollo, Yudith
de Grecia Cauti-Mendoza, Maria
Chipana-Flores, Naer
Choque-Guevara, Ricardo
Chunga-Girón, Xiomara
Criollo-Orozco, Manuel
De La Cruz, Lewis
Delgado-Ccancce, Elmer
Elugo-Guevara, Christian
Fernández-Sanchez, Manolo
Guevara-Sarmiento, Luis
Gutiérrez, Kristel
Heredia-Almeyda, Oscar
Huaccachi-Gonzalez, Edison
Huerta-Roque, Pedro
Icochea, Eliana
Isasi-Rivas, Gisela
Juscamaita-Bartra, Romina A.
Licla-Inca, Abraham
Montalvan, Angela
Montesinos-Millan, Ricardo
Núñez-Fernández, Dennis
Ochoa-Ortiz, Adiana
Páucar-Montoro, Erika
Pauyac, Kathy
Perez-Martinez, Jose L.
Perez-M, Norma
Poma-Acevedo, Astrid
Quiñones-Garcia, Stefany
Ramirez-Ortiz, Ingrid
Ramos-Sono, Daniel
Rios-Angulo, Angela A.
Rios-Matos, Dora
Rojas-Neyra, Aldo
Romero, Yomara K.
Salguedo-Bohorquez, Mario I.
Sernaque-Aguilar, Yacory
Soto, Luis F.
Tataje-Lavanda, Luis
Ticona, Julio
Vallejos-Sánchez, Katherine
Villanueva-Pérez, Doris
Ygnacio-Aguirre, Freddy
dc.subject.es_PE.fl_str_mv SARS-CoV-2
Antiviral Agents
Binding Sites
Coronavirus 3C Proteases
COVID-19
Databases
topic SARS-CoV-2
Antiviral Agents
Binding Sites
Coronavirus 3C Proteases
COVID-19
Databases
description El texto completo de este trabajo no está disponible en el Repositorio Académico UPC por restricciones de la casa editorial donde ha sido publicado.
publishDate 2021
dc.date.accessioned.none.fl_str_mv 2021-09-14T15:12:18Z
dc.date.available.none.fl_str_mv 2021-09-14T15:12:18Z
dc.date.issued.fl_str_mv 2021-12-01
dc.type.es_PE.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.doi.none.fl_str_mv 10.1038/s41598-021-94951-6
dc.identifier.uri.none.fl_str_mv http://hdl.handle.net/10757/657336
dc.identifier.eissn.none.fl_str_mv 20452322
dc.identifier.journal.es_PE.fl_str_mv Scientific Reports
dc.identifier.eid.none.fl_str_mv 2-s2.0-85111991934
dc.identifier.scopusid.none.fl_str_mv SCOPUS_ID:85111991934
dc.identifier.isni.none.fl_str_mv 0000 0001 2196 144X
identifier_str_mv 10.1038/s41598-021-94951-6
20452322
Scientific Reports
2-s2.0-85111991934
SCOPUS_ID:85111991934
0000 0001 2196 144X
url http://hdl.handle.net/10757/657336
dc.language.iso.es_PE.fl_str_mv eng
language eng
dc.relation.url.es_PE.fl_str_mv https://www.nature.com/articles/s41598-021-94951-6
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eu_rights_str_mv embargoedAccess
dc.format.es_PE.fl_str_mv application/html
dc.publisher.es_PE.fl_str_mv Nature Research
dc.source.es_PE.fl_str_mv Universidad Peruana de Ciencias Aplicadas (UPC)
Repositorio Academico - UPC
dc.source.none.fl_str_mv reponame:UPC-Institucional
instname:Universidad Peruana de Ciencias Aplicadas
instacron:UPC
instname_str Universidad Peruana de Ciencias Aplicadas
instacron_str UPC
institution UPC
reponame_str UPC-Institucional
collection UPC-Institucional
dc.source.journaltitle.none.fl_str_mv Scientific Reports
dc.source.volume.none.fl_str_mv 11
dc.source.issue.none.fl_str_mv 1
bitstream.url.fl_str_mv https://repositorioacademico.upc.edu.pe/bitstream/10757/657336/1/license.txt
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PaulaDelgado-Pease, Nicolás E.Olivos-Ramirez, Gustavo E.Sheen, PatriciaFernández-Díaz, ManoloQuiliano, MiguelZimic, MirkoAgurto-Arteaga, AndresAntiparra, RicardoArdiles-Reyes, ManuelCalderon, KatherineCauna-Orocollo, Yudithde Grecia Cauti-Mendoza, MariaChipana-Flores, NaerChoque-Guevara, RicardoChunga-Girón, XiomaraCriollo-Orozco, ManuelDe La Cruz, LewisDelgado-Ccancce, ElmerElugo-Guevara, ChristianFernández-Sanchez, ManoloGuevara-Sarmiento, LuisGutiérrez, KristelHeredia-Almeyda, OscarHuaccachi-Gonzalez, EdisonHuerta-Roque, PedroIcochea, ElianaIsasi-Rivas, GiselaJuscamaita-Bartra, Romina A.Licla-Inca, AbrahamMontalvan, AngelaMontesinos-Millan, RicardoNúñez-Fernández, DennisOchoa-Ortiz, AdianaPáucar-Montoro, ErikaPauyac, KathyPerez-Martinez, Jose L.Perez-M, NormaPoma-Acevedo, AstridQuiñones-Garcia, StefanyRamirez-Ortiz, IngridRamos-Sono, DanielRios-Angulo, Angela A.Rios-Matos, DoraRojas-Neyra, AldoRomero, Yomara K.Salguedo-Bohorquez, Mario I.Sernaque-Aguilar, YacorySoto, Luis F.Tataje-Lavanda, LuisTicona, JulioVallejos-Sánchez, KatherineVillanueva-Pérez, DorisYgnacio-Aguirre, Freddy2021-09-14T15:12:18Z2021-09-14T15:12:18Z2021-12-0110.1038/s41598-021-94951-6http://hdl.handle.net/10757/65733620452322Scientific Reports2-s2.0-85111991934SCOPUS_ID:851119919340000 0001 2196 144XEl texto completo de este trabajo no está disponible en el Repositorio Académico UPC por restricciones de la casa editorial donde ha sido publicado.SARS-CoV-2 main protease is a common target for inhibition assays due to its high conservation among coronaviruses. Since flavonoids show antiviral activity, several in silico works have proposed them as potential SARS-CoV-2 main protease inhibitors. Nonetheless, there is reason to doubt certain results given the lack of consideration for flavonoid promiscuity or main protease plasticity, usage of short library sizes, absence of control molecules and/or the limitation of the methodology to a single target site. Here, we report a virtual screening study where dorsilurin E, euchrenone a11, sanggenol O and CHEMBL2171598 are proposed to inhibit main protease through different pathways. Remarkably, novel structural mechanisms were observed after sanggenol O and CHEMBL2171598 bound to experimentally proven allosteric sites. The former drastically affected the active site, while the latter triggered a hinge movement which has been previously reported for an inactive SARS-CoV main protease mutant. The use of a curated database of 4.8 k flavonoids, combining two well-known docking software (AutoDock Vina and AutoDock4.2), molecular dynamics and MMPBSA, guaranteed an adequate analysis and robust interpretation. These criteria can be considered for future screening campaigns against SARS-CoV-2 main protease.Consejo Nacional de Ciencia, Tecnología e Innovación TecnológicaRevisión por paresapplication/htmlengNature Researchhttps://www.nature.com/articles/s41598-021-94951-6info:eu-repo/semantics/embargoedAccessUniversidad Peruana de Ciencias Aplicadas (UPC)Repositorio Academico - UPCScientific Reports111reponame:UPC-Institucionalinstname:Universidad Peruana de Ciencias Aplicadasinstacron:UPCSARS-CoV-2Antiviral AgentsBinding SitesCoronavirus 3C ProteasesCOVID-19DatabasesComprehensive virtual screening of 4.8 k flavonoids reveals novel insights into allosteric inhibition of SARS-CoV-2 M<sup>PRO</sup>info:eu-repo/semantics/articleLICENSElicense.txtlicense.txttext/plain; charset=utf-81748https://repositorioacademico.upc.edu.pe/bitstream/10757/657336/1/license.txt8a4605be74aa9ea9d79846c1fba20a33MD51false10757/657336oai:repositorioacademico.upc.edu.pe:10757/6573362021-09-14 15:12:19.492Repositorio académico upcupc@openrepository.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
score 13.905282
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