Exploration of Anti-HIV Phytocompounds against SARS-CoV-2 Main Protease: Structure-Based Screening, Molecular Simulation, ADME Analysis and Conceptual DFT Studies

Autores
Murali, Mahadevamurthy; Gowtham, Hittanahallikoppal Gajendramurthy; Shilpa, Natarajamurthy; Krishnappa, Hemanth Kumar Naguvanahalli; Ledesma, Ana Estela; Jain, Anisha S.; Shati, Ali A.; Alfaifi, Mohammad Y.; Elbehairi, Serag Eldin I.; Achar, Raghu Ram; Silina, Ekaterina; Stupin, Victor; Ortega Castro, Joaquín; Frau, Juan; Flores Holguín, Norma; Amruthesh, Kestur Nagaraj; Shivamallu, Chandan; Kollur, Shiva Prasad; Glossman Mitnik, Daniel
Año de publicación
2022
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The ever-expanding pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has gained attention as COVID-19 and caused an emergency in public health to an unmatched level to date. However, the treatments used are the only options; currently, no effective and licensed medications are available to combat disease transmission, necessitating further research. In the present study, an in silico-based virtual screening of anti-HIV bioactive compounds from medicinal plants was carried out through molecular docking against the main protease (Mpro) (PDB: 6LU7) of SARS-CoV-2, which is a key enzyme responsible for virus replication. A total of 16 anti-HIV compounds were found to have a binding affinity greater than −8.9 kcal/mol out of 150 compounds screened. Pseudohypericin had a high affinity with the energy of −10.2 kcal/mol, demonstrating amino acid residual interactions with LEU141, GLU166, ARG188, and GLN192, followed by Hypericin (−10.1 kcal/mol). Moreover, the ADME (Absorption, Distribution, Metabolism and Excretion) analysis of Pseudohypericin and Hypericin recorded a low bioavailability (BA) score of 0.17 and violated Lipinski’s rule of drug-likeness. The docking and molecular simulations indicated that the quinone compound, Pseudohypericin, could be tested in vitro and in vivo as potent molecules against COVID-19 disease prior to clinical trials.This was also supported by the theoretical and computational studies conducted. The global and local descriptors, which are the underpinnings of Conceptual Density FunctionalTheory (CDFT) have beenpredicted through successful model chemistry, hoping that they could be of help in the comprehension of the chemical reactivity properties of the molecular systems considered in this study.
Fil: Murali, Mahadevamurthy. University Of Mysore; India
Fil: Gowtham, Hittanahallikoppal Gajendramurthy. Nrupathunga University; India
Fil: Shilpa, Natarajamurthy. University Of Mysore; India
Fil: Krishnappa, Hemanth Kumar Naguvanahalli. University Of Mysore; India
Fil: Ledesma, Ana Estela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet Noa Sur. Centro de Investigación en Biofísica Aplicada y Alimentos. - Universidad Nacional de Santiago del Estero. Centro de Investigación en Biofísica Aplicada y Alimentos; Argentina
Fil: Jain, Anisha S.. University Of Mysore; India
Fil: Shati, Ali A.. King Khalid University; Arabia Saudita
Fil: Alfaifi, Mohammad Y.. Vacsera Holding Company; Egipto
Fil: Elbehairi, Serag Eldin I.. Jss Academy Of Higher Education And Research; India
Fil: Achar, Raghu Ram. Pirogov Russian National Research Medical University; Rusia
Fil: Silina, Ekaterina. Universitat de Les Illesbalears; España
Fil: Stupin, Victor. Centro de Investigaciónen Materiales Avanzados; México
Fil: Ortega Castro, Joaquín. Jss Academy Of Higher Education And Research; India
Fil: Frau, Juan. Universitat de Les Illesbalears; España
Fil: Flores Holguín, Norma. Centro de Investigaciónen Materiales Avanzados; México
Fil: Amruthesh, Kestur Nagaraj. University Of Mysore; India
Fil: Shivamallu, Chandan. Jss Academy Of Higher Education And Research; India
Fil: Kollur, Shiva Prasad. University Of Mysore; India
Fil: Glossman Mitnik, Daniel. Centro de Investigaciónen Materiales Avanzados; México
Materia
ANTI-HIV
BIOACTIVE COMPOUNDS
CONCEPTUAL DFT
MAIN PROTEASE
SARS-COV-2
COVID-19
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/214358
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/214358
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Exploration of Anti-HIV Phytocompounds against SARS-CoV-2 Main Protease: Structure-Based Screening, Molecular Simulation, ADME Analysis and Conceptual DFT StudiesMurali, MahadevamurthyGowtham, Hittanahallikoppal GajendramurthyShilpa, NatarajamurthyKrishnappa, Hemanth Kumar NaguvanahalliLedesma, Ana EstelaJain, Anisha S.Shati, Ali A.Alfaifi, Mohammad Y.Elbehairi, Serag Eldin I.Achar, Raghu RamSilina, EkaterinaStupin, VictorOrtega Castro, JoaquínFrau, JuanFlores Holguín, NormaAmruthesh, Kestur NagarajShivamallu, ChandanKollur, Shiva PrasadGlossman Mitnik, DanielANTI-HIVBIOACTIVE COMPOUNDSCONCEPTUAL DFTMAIN PROTEASESARS-COV-2COVID-19https://purl.org/becyt/ford/1.4https://purl.org/becyt/ford/1The ever-expanding pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has gained attention as COVID-19 and caused an emergency in public health to an unmatched level to date. However, the treatments used are the only options; currently, no effective and licensed medications are available to combat disease transmission, necessitating further research. In the present study, an in silico-based virtual screening of anti-HIV bioactive compounds from medicinal plants was carried out through molecular docking against the main protease (Mpro) (PDB: 6LU7) of SARS-CoV-2, which is a key enzyme responsible for virus replication. A total of 16 anti-HIV compounds were found to have a binding affinity greater than −8.9 kcal/mol out of 150 compounds screened. Pseudohypericin had a high affinity with the energy of −10.2 kcal/mol, demonstrating amino acid residual interactions with LEU141, GLU166, ARG188, and GLN192, followed by Hypericin (−10.1 kcal/mol). Moreover, the ADME (Absorption, Distribution, Metabolism and Excretion) analysis of Pseudohypericin and Hypericin recorded a low bioavailability (BA) score of 0.17 and violated Lipinski’s rule of drug-likeness. The docking and molecular simulations indicated that the quinone compound, Pseudohypericin, could be tested in vitro and in vivo as potent molecules against COVID-19 disease prior to clinical trials.This was also supported by the theoretical and computational studies conducted. The global and local descriptors, which are the underpinnings of Conceptual Density FunctionalTheory (CDFT) have beenpredicted through successful model chemistry, hoping that they could be of help in the comprehension of the chemical reactivity properties of the molecular systems considered in this study.Fil: Murali, Mahadevamurthy. University Of Mysore; IndiaFil: Gowtham, Hittanahallikoppal Gajendramurthy. Nrupathunga University; IndiaFil: Shilpa, Natarajamurthy. University Of Mysore; IndiaFil: Krishnappa, Hemanth Kumar Naguvanahalli. University Of Mysore; IndiaFil: Ledesma, Ana Estela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet Noa Sur. Centro de Investigación en Biofísica Aplicada y Alimentos. - Universidad Nacional de Santiago del Estero. Centro de Investigación en Biofísica Aplicada y Alimentos; ArgentinaFil: Jain, Anisha S.. University Of Mysore; IndiaFil: Shati, Ali A.. King Khalid University; Arabia SauditaFil: Alfaifi, Mohammad Y.. Vacsera Holding Company; EgiptoFil: Elbehairi, Serag Eldin I.. Jss Academy Of Higher Education And Research; IndiaFil: Achar, Raghu Ram. Pirogov Russian National Research Medical University; RusiaFil: Silina, Ekaterina. Universitat de Les Illesbalears; EspañaFil: Stupin, Victor. Centro de Investigaciónen Materiales Avanzados; MéxicoFil: Ortega Castro, Joaquín. Jss Academy Of Higher Education And Research; IndiaFil: Frau, Juan. Universitat de Les Illesbalears; EspañaFil: Flores Holguín, Norma. Centro de Investigaciónen Materiales Avanzados; MéxicoFil: Amruthesh, Kestur Nagaraj. University Of Mysore; IndiaFil: Shivamallu, Chandan. Jss Academy Of Higher Education And Research; IndiaFil: Kollur, Shiva Prasad. University Of Mysore; IndiaFil: Glossman Mitnik, Daniel. Centro de Investigaciónen Materiales Avanzados; MéxicoMolecular Diversity Preservation International2022-11info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/214358Murali, Mahadevamurthy; Gowtham, Hittanahallikoppal Gajendramurthy; Shilpa, Natarajamurthy; Krishnappa, Hemanth Kumar Naguvanahalli; Ledesma, Ana Estela; et al.; Exploration of Anti-HIV Phytocompounds against SARS-CoV-2 Main Protease: Structure-Based Screening, Molecular Simulation, ADME Analysis and Conceptual DFT Studies; Molecular Diversity Preservation International; Molecules; 27; 23; 11-2022; 1-161420-3049CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.mdpi.com/1420-3049/27/23/8288info:eu-repo/semantics/altIdentifier/doi/10.3390/molecules27238288info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2026-08-25T14:34:37Zoai:ri.conicet.gov.ar:11336/214358instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982026-08-25 14:34:37.842CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Exploration of Anti-HIV Phytocompounds against SARS-CoV-2 Main Protease: Structure-Based Screening, Molecular Simulation, ADME Analysis and Conceptual DFT Studies
title Exploration of Anti-HIV Phytocompounds against SARS-CoV-2 Main Protease: Structure-Based Screening, Molecular Simulation, ADME Analysis and Conceptual DFT Studies
spellingShingle Exploration of Anti-HIV Phytocompounds against SARS-CoV-2 Main Protease: Structure-Based Screening, Molecular Simulation, ADME Analysis and Conceptual DFT Studies
Murali, Mahadevamurthy
ANTI-HIV
BIOACTIVE COMPOUNDS
CONCEPTUAL DFT
MAIN PROTEASE
SARS-COV-2
COVID-19
title_short Exploration of Anti-HIV Phytocompounds against SARS-CoV-2 Main Protease: Structure-Based Screening, Molecular Simulation, ADME Analysis and Conceptual DFT Studies
title_full Exploration of Anti-HIV Phytocompounds against SARS-CoV-2 Main Protease: Structure-Based Screening, Molecular Simulation, ADME Analysis and Conceptual DFT Studies
title_fullStr Exploration of Anti-HIV Phytocompounds against SARS-CoV-2 Main Protease: Structure-Based Screening, Molecular Simulation, ADME Analysis and Conceptual DFT Studies
title_full_unstemmed Exploration of Anti-HIV Phytocompounds against SARS-CoV-2 Main Protease: Structure-Based Screening, Molecular Simulation, ADME Analysis and Conceptual DFT Studies
title_sort Exploration of Anti-HIV Phytocompounds against SARS-CoV-2 Main Protease: Structure-Based Screening, Molecular Simulation, ADME Analysis and Conceptual DFT Studies
dc.creator.none.fl_str_mv Murali, Mahadevamurthy
Gowtham, Hittanahallikoppal Gajendramurthy
Shilpa, Natarajamurthy
Krishnappa, Hemanth Kumar Naguvanahalli
Ledesma, Ana Estela
Jain, Anisha S.
Shati, Ali A.
Alfaifi, Mohammad Y.
Elbehairi, Serag Eldin I.
Achar, Raghu Ram
Silina, Ekaterina
Stupin, Victor
Ortega Castro, Joaquín
Frau, Juan
Flores Holguín, Norma
Amruthesh, Kestur Nagaraj
Shivamallu, Chandan
Kollur, Shiva Prasad
Glossman Mitnik, Daniel
author Murali, Mahadevamurthy
author_facet Murali, Mahadevamurthy
Gowtham, Hittanahallikoppal Gajendramurthy
Shilpa, Natarajamurthy
Krishnappa, Hemanth Kumar Naguvanahalli
Ledesma, Ana Estela
Jain, Anisha S.
Shati, Ali A.
Alfaifi, Mohammad Y.
Elbehairi, Serag Eldin I.
Achar, Raghu Ram
Silina, Ekaterina
Stupin, Victor
Ortega Castro, Joaquín
Frau, Juan
Flores Holguín, Norma
Amruthesh, Kestur Nagaraj
Shivamallu, Chandan
Kollur, Shiva Prasad
Glossman Mitnik, Daniel
author_role author
author2 Gowtham, Hittanahallikoppal Gajendramurthy
Shilpa, Natarajamurthy
Krishnappa, Hemanth Kumar Naguvanahalli
Ledesma, Ana Estela
Jain, Anisha S.
Shati, Ali A.
Alfaifi, Mohammad Y.
Elbehairi, Serag Eldin I.
Achar, Raghu Ram
Silina, Ekaterina
Stupin, Victor
Ortega Castro, Joaquín
Frau, Juan
Flores Holguín, Norma
Amruthesh, Kestur Nagaraj
Shivamallu, Chandan
Kollur, Shiva Prasad
Glossman Mitnik, Daniel
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv ANTI-HIV
BIOACTIVE COMPOUNDS
CONCEPTUAL DFT
MAIN PROTEASE
SARS-COV-2
COVID-19
topic ANTI-HIV
BIOACTIVE COMPOUNDS
CONCEPTUAL DFT
MAIN PROTEASE
SARS-COV-2
COVID-19
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.4
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv The ever-expanding pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has gained attention as COVID-19 and caused an emergency in public health to an unmatched level to date. However, the treatments used are the only options; currently, no effective and licensed medications are available to combat disease transmission, necessitating further research. In the present study, an in silico-based virtual screening of anti-HIV bioactive compounds from medicinal plants was carried out through molecular docking against the main protease (Mpro) (PDB: 6LU7) of SARS-CoV-2, which is a key enzyme responsible for virus replication. A total of 16 anti-HIV compounds were found to have a binding affinity greater than −8.9 kcal/mol out of 150 compounds screened. Pseudohypericin had a high affinity with the energy of −10.2 kcal/mol, demonstrating amino acid residual interactions with LEU141, GLU166, ARG188, and GLN192, followed by Hypericin (−10.1 kcal/mol). Moreover, the ADME (Absorption, Distribution, Metabolism and Excretion) analysis of Pseudohypericin and Hypericin recorded a low bioavailability (BA) score of 0.17 and violated Lipinski’s rule of drug-likeness. The docking and molecular simulations indicated that the quinone compound, Pseudohypericin, could be tested in vitro and in vivo as potent molecules against COVID-19 disease prior to clinical trials.This was also supported by the theoretical and computational studies conducted. The global and local descriptors, which are the underpinnings of Conceptual Density FunctionalTheory (CDFT) have beenpredicted through successful model chemistry, hoping that they could be of help in the comprehension of the chemical reactivity properties of the molecular systems considered in this study.
Fil: Murali, Mahadevamurthy. University Of Mysore; India
Fil: Gowtham, Hittanahallikoppal Gajendramurthy. Nrupathunga University; India
Fil: Shilpa, Natarajamurthy. University Of Mysore; India
Fil: Krishnappa, Hemanth Kumar Naguvanahalli. University Of Mysore; India
Fil: Ledesma, Ana Estela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet Noa Sur. Centro de Investigación en Biofísica Aplicada y Alimentos. - Universidad Nacional de Santiago del Estero. Centro de Investigación en Biofísica Aplicada y Alimentos; Argentina
Fil: Jain, Anisha S.. University Of Mysore; India
Fil: Shati, Ali A.. King Khalid University; Arabia Saudita
Fil: Alfaifi, Mohammad Y.. Vacsera Holding Company; Egipto
Fil: Elbehairi, Serag Eldin I.. Jss Academy Of Higher Education And Research; India
Fil: Achar, Raghu Ram. Pirogov Russian National Research Medical University; Rusia
Fil: Silina, Ekaterina. Universitat de Les Illesbalears; España
Fil: Stupin, Victor. Centro de Investigaciónen Materiales Avanzados; México
Fil: Ortega Castro, Joaquín. Jss Academy Of Higher Education And Research; India
Fil: Frau, Juan. Universitat de Les Illesbalears; España
Fil: Flores Holguín, Norma. Centro de Investigaciónen Materiales Avanzados; México
Fil: Amruthesh, Kestur Nagaraj. University Of Mysore; India
Fil: Shivamallu, Chandan. Jss Academy Of Higher Education And Research; India
Fil: Kollur, Shiva Prasad. University Of Mysore; India
Fil: Glossman Mitnik, Daniel. Centro de Investigaciónen Materiales Avanzados; México
description The ever-expanding pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has gained attention as COVID-19 and caused an emergency in public health to an unmatched level to date. However, the treatments used are the only options; currently, no effective and licensed medications are available to combat disease transmission, necessitating further research. In the present study, an in silico-based virtual screening of anti-HIV bioactive compounds from medicinal plants was carried out through molecular docking against the main protease (Mpro) (PDB: 6LU7) of SARS-CoV-2, which is a key enzyme responsible for virus replication. A total of 16 anti-HIV compounds were found to have a binding affinity greater than −8.9 kcal/mol out of 150 compounds screened. Pseudohypericin had a high affinity with the energy of −10.2 kcal/mol, demonstrating amino acid residual interactions with LEU141, GLU166, ARG188, and GLN192, followed by Hypericin (−10.1 kcal/mol). Moreover, the ADME (Absorption, Distribution, Metabolism and Excretion) analysis of Pseudohypericin and Hypericin recorded a low bioavailability (BA) score of 0.17 and violated Lipinski’s rule of drug-likeness. The docking and molecular simulations indicated that the quinone compound, Pseudohypericin, could be tested in vitro and in vivo as potent molecules against COVID-19 disease prior to clinical trials.This was also supported by the theoretical and computational studies conducted. The global and local descriptors, which are the underpinnings of Conceptual Density FunctionalTheory (CDFT) have beenpredicted through successful model chemistry, hoping that they could be of help in the comprehension of the chemical reactivity properties of the molecular systems considered in this study.
publishDate 2022
dc.date.none.fl_str_mv 2022-11
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/214358
Murali, Mahadevamurthy; Gowtham, Hittanahallikoppal Gajendramurthy; Shilpa, Natarajamurthy; Krishnappa, Hemanth Kumar Naguvanahalli; Ledesma, Ana Estela; et al.; Exploration of Anti-HIV Phytocompounds against SARS-CoV-2 Main Protease: Structure-Based Screening, Molecular Simulation, ADME Analysis and Conceptual DFT Studies; Molecular Diversity Preservation International; Molecules; 27; 23; 11-2022; 1-16
1420-3049
CONICET Digital
CONICET
url http://hdl.handle.net/11336/214358
identifier_str_mv Murali, Mahadevamurthy; Gowtham, Hittanahallikoppal Gajendramurthy; Shilpa, Natarajamurthy; Krishnappa, Hemanth Kumar Naguvanahalli; Ledesma, Ana Estela; et al.; Exploration of Anti-HIV Phytocompounds against SARS-CoV-2 Main Protease: Structure-Based Screening, Molecular Simulation, ADME Analysis and Conceptual DFT Studies; Molecular Diversity Preservation International; Molecules; 27; 23; 11-2022; 1-16
1420-3049
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.mdpi.com/1420-3049/27/23/8288
info:eu-repo/semantics/altIdentifier/doi/10.3390/molecules27238288
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Molecular Diversity Preservation International
publisher.none.fl_str_mv Molecular Diversity Preservation International
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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