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.
| Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| 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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| 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 |
| author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
| 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 |
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SCOPUS_ID:85111991934 |
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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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info:eu-repo/semantics/embargoedAccess |
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embargoedAccess |
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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 |
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reponame:UPC-Institucional instname:Universidad Peruana de Ciencias Aplicadas instacron:UPC |
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Universidad Peruana de Ciencias Aplicadas |
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UPC |
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UPC-Institucional |
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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 |
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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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 |
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Nota importante:
La información contenida en este registro es de entera responsabilidad de la institución que gestiona el repositorio institucional donde esta contenido este documento o set de datos. El CONCYTEC no se hace responsable por los contenidos (publicaciones y/o datos) accesibles a través del Repositorio Nacional Digital de Ciencia, Tecnología e Innovación de Acceso Abierto (ALICIA).
La información contenida en este registro es de entera responsabilidad de la institución que gestiona el repositorio institucional donde esta contenido este documento o set de datos. El CONCYTEC no se hace responsable por los contenidos (publicaciones y/o datos) accesibles a través del Repositorio Nacional Digital de Ciencia, Tecnología e Innovación de Acceso Abierto (ALICIA).