Virtual screening of plant-derived compounds against SARS-CoV-2 viral proteins using computational tools.
Identifieur interne : 000155 ( Main/Corpus ); précédent : 000154; suivant : 000156Virtual screening of plant-derived compounds against SARS-CoV-2 viral proteins using computational tools.
Auteurs : María Antonela Zígolo ; Matías Rivero Goytia ; Hugo Ramiro Poma ; Ver Nica Beatriz Rajal ; Ver Nica Patricia IrazustaSource :
- The Science of the total environment [ 1879-1026 ] ; 2021.
Abstract
The new SARS-CoV-2, responsible for the COVID-19 pandemic, has been threatening public health worldwide for more than a year. The aim of this work was to evaluate compounds of natural origin, mainly from medicinal plants, as potential SARS-CoV-2 inhibitors through docking studies. The viral spike (S) glycoprotein and the main protease Mpro, involved in the recognition of virus by host cells and in viral replication, respectively, were the main molecular targets in this study. Molecular docking was performed using AutoDock, which allowed us to select the plant actives with the highest affinity towards the viral targets and to identify the interaction molecular sites with the SARS-CoV2 proteins. The best energy binding values for S protein were, in kcal/mol: -19.22 for glycyrrhizin, -17.84 for gitoxin, -12.05 for dicumarol, -10.75 for diosgenin, and -8.12 for delphinidin. For Mpro were, in kcal/mol: -9.36 for spirostan, -8.75 for N-(3-acetylglycyrrhetinoyl)-2-amino-propanol, -8.41 for α-amyrin, -8.35 for oleanane, -8.11 for taraxasterol, and -8.03 for glycyrrhetinic acid. In addition, the synthetic drugs umifenovir, chloroquine, and hydroxychloroquine were used as controls for S protein, while atazanavir and nelfinavir were used for Mpro. Key hydrogen bonds and hydrophobic interactions between natural compounds and the respective viral proteins were identified, allowing us to explain the great affinity obtained in those compounds with the lowest binding energies. These results suggest that these natural compounds could potentially be useful as drugs to be experimentally evaluated against COVID-19.
DOI: 10.1016/j.scitotenv.2021.146400
PubMed: 33794459
PubMed Central: PMC7967396
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Electronic address: vbrajal@gmail.com.</nlm:affiliation></affiliation></author><author><name sortKey="Irazusta, Ver Nica Patricia" sort="Irazusta, Ver Nica Patricia" uniqKey="Irazusta V" first="Ver Nica Patricia" last="Irazusta">Ver Nica Patricia Irazusta</name><affiliation><nlm:affiliation>Instituto de Investigaciones para la Industria Química (INIQUI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad Nacional de Salta (UNSa), Av. 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Bolivia 5150, 4400 Salta, Argentina; Facultad de Ciencias Naturales, UNSa, Salta, Argentina.</nlm:affiliation></affiliation></author><author><name sortKey="Goytia, Matias Rivero" sort="Goytia, Matias Rivero" uniqKey="Goytia M" first="Matías Rivero" last="Goytia">Matías Rivero Goytia</name><affiliation><nlm:affiliation>Silentium Apps, Salta, Argentina; Facultad de Economía y Administración, Universidad Católica de Salta (UCASAL), Salta, Argentina.</nlm:affiliation></affiliation></author><author><name sortKey="Poma, Hugo Ramiro" sort="Poma, Hugo Ramiro" uniqKey="Poma H" first="Hugo Ramiro" last="Poma">Hugo Ramiro Poma</name><affiliation><nlm:affiliation>Instituto de Investigaciones para la Industria Química (INIQUI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad Nacional de Salta (UNSa), Av. Bolivia 5150, 4400 Salta, Argentina.</nlm:affiliation></affiliation></author><author><name sortKey="Rajal, Ver Nica Beatriz" sort="Rajal, Ver Nica Beatriz" uniqKey="Rajal V" first="Ver Nica Beatriz" last="Rajal">Ver Nica Beatriz Rajal</name><affiliation><nlm:affiliation>Instituto de Investigaciones para la Industria Química (INIQUI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad Nacional de Salta (UNSa), Av. Bolivia 5150, 4400 Salta, Argentina; Facultad de Ingeniería, UNSa, Salta, Argentina; Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore. Electronic address: vbrajal@gmail.com.</nlm:affiliation></affiliation></author><author><name sortKey="Irazusta, Ver Nica Patricia" sort="Irazusta, Ver Nica Patricia" uniqKey="Irazusta V" first="Ver Nica Patricia" last="Irazusta">Ver Nica Patricia Irazusta</name><affiliation><nlm:affiliation>Instituto de Investigaciones para la Industria Química (INIQUI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad Nacional de Salta (UNSa), Av. Bolivia 5150, 4400 Salta, Argentina; Facultad de Ciencias Naturales, UNSa, Salta, Argentina.</nlm:affiliation></affiliation></author></analytic><series><title level="j">The Science of the total environment</title><idno type="eISSN">1879-1026</idno><imprint><date when="2021" type="published">2021</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The new SARS-CoV-2, responsible for the COVID-19 pandemic, has been threatening public health worldwide for more than a year. The aim of this work was to evaluate compounds of natural origin, mainly from medicinal plants, as potential SARS-CoV-2 inhibitors through docking studies. The viral spike (S) glycoprotein and the main protease M<sup>pro</sup>, involved in the recognition of virus by host cells and in viral replication, respectively, were the main molecular targets in this study. Molecular docking was performed using AutoDock, which allowed us to select the plant actives with the highest affinity towards the viral targets and to identify the interaction molecular sites with the SARS-CoV2 proteins. The best energy binding values for S protein were, in kcal/mol: -19.22 for glycyrrhizin, -17.84 for gitoxin, -12.05 for dicumarol, -10.75 for diosgenin, and -8.12 for delphinidin. For M<sup>pro</sup> were, in kcal/mol: -9.36 for spirostan, -8.75 for N-(3-acetylglycyrrhetinoyl)-2-amino-propanol, -8.41 for α-amyrin, -8.35 for oleanane, -8.11 for taraxasterol, and -8.03 for glycyrrhetinic acid. In addition, the synthetic drugs umifenovir, chloroquine, and hydroxychloroquine were used as controls for S protein, while atazanavir and nelfinavir were used for M<sup>pro</sup>. Key hydrogen bonds and hydrophobic interactions between natural compounds and the respective viral proteins were identified, allowing us to explain the great affinity obtained in those compounds with the lowest binding energies. These results suggest that these natural compounds could potentially be useful as drugs to be experimentally evaluated against COVID-19.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">33794459</PMID><DateRevised><Year>2021</Year><Month>05</Month><Day>20</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1879-1026</ISSN><JournalIssue CitedMedium="Internet"><Volume>781</Volume><PubDate><Year>2021</Year><Month>Mar</Month><Day>17</Day></PubDate></JournalIssue><Title>The Science of the total environment</Title><ISOAbbreviation>Sci Total Environ</ISOAbbreviation></Journal><ArticleTitle>Virtual screening of plant-derived compounds against SARS-CoV-2 viral proteins using computational tools.</ArticleTitle><Pagination><MedlinePgn>146400</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S0048-9697(21)01468-6</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.scitotenv.2021.146400</ELocationID><Abstract><AbstractText>The new SARS-CoV-2, responsible for the COVID-19 pandemic, has been threatening public health worldwide for more than a year. The aim of this work was to evaluate compounds of natural origin, mainly from medicinal plants, as potential SARS-CoV-2 inhibitors through docking studies. The viral spike (S) glycoprotein and the main protease M<sup>pro</sup>, involved in the recognition of virus by host cells and in viral replication, respectively, were the main molecular targets in this study. Molecular docking was performed using AutoDock, which allowed us to select the plant actives with the highest affinity towards the viral targets and to identify the interaction molecular sites with the SARS-CoV2 proteins. The best energy binding values for S protein were, in kcal/mol: -19.22 for glycyrrhizin, -17.84 for gitoxin, -12.05 for dicumarol, -10.75 for diosgenin, and -8.12 for delphinidin. For M<sup>pro</sup> were, in kcal/mol: -9.36 for spirostan, -8.75 for N-(3-acetylglycyrrhetinoyl)-2-amino-propanol, -8.41 for α-amyrin, -8.35 for oleanane, -8.11 for taraxasterol, and -8.03 for glycyrrhetinic acid. In addition, the synthetic drugs umifenovir, chloroquine, and hydroxychloroquine were used as controls for S protein, while atazanavir and nelfinavir were used for M<sup>pro</sup>. Key hydrogen bonds and hydrophobic interactions between natural compounds and the respective viral proteins were identified, allowing us to explain the great affinity obtained in those compounds with the lowest binding energies. These results suggest that these natural compounds could potentially be useful as drugs to be experimentally evaluated against COVID-19.</AbstractText><CopyrightInformation>Copyright © 2021 Elsevier B.V. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zígolo</LastName><ForeName>María Antonela</ForeName><Initials>MA</Initials><AffiliationInfo><Affiliation>Instituto de Investigaciones para la Industria Química (INIQUI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad Nacional de Salta (UNSa), Av. Bolivia 5150, 4400 Salta, Argentina; Facultad de Ciencias Naturales, UNSa, Salta, Argentina.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Goytia</LastName><ForeName>Matías Rivero</ForeName><Initials>MR</Initials><AffiliationInfo><Affiliation>Silentium Apps, Salta, Argentina; Facultad de Economía y Administración, Universidad Católica de Salta (UCASAL), Salta, Argentina.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Poma</LastName><ForeName>Hugo Ramiro</ForeName><Initials>HR</Initials><AffiliationInfo><Affiliation>Instituto de Investigaciones para la Industria Química (INIQUI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad Nacional de Salta (UNSa), Av. Bolivia 5150, 4400 Salta, Argentina.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rajal</LastName><ForeName>Verónica Beatriz</ForeName><Initials>VB</Initials><AffiliationInfo><Affiliation>Instituto de Investigaciones para la Industria Química (INIQUI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad Nacional de Salta (UNSa), Av. Bolivia 5150, 4400 Salta, Argentina; Facultad de Ingeniería, UNSa, Salta, Argentina; Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore. Electronic address: vbrajal@gmail.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Irazusta</LastName><ForeName>Verónica Patricia</ForeName><Initials>VP</Initials><AffiliationInfo><Affiliation>Instituto de Investigaciones para la Industria Química (INIQUI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad Nacional de Salta (UNSa), Av. Bolivia 5150, 4400 Salta, Argentina; Facultad de Ciencias Naturales, UNSa, Salta, Argentina.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2021</Year><Month>03</Month><Day>17</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Sci Total Environ</MedlineTA><NlmUniqueID>0330500</NlmUniqueID><ISSNLinking>0048-9697</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">3-Chymotrypsin-like protease</Keyword><Keyword MajorTopicYN="N">Antiviral activity</Keyword><Keyword MajorTopicYN="N">Docking</Keyword><Keyword MajorTopicYN="N">SARS-CoV-2</Keyword><Keyword MajorTopicYN="N">Spike glycoprotein</Keyword></KeywordList><CoiStatement>Declaration of competing interest The authors declare no conflict of interests.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>10</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2021</Year><Month>02</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2021</Year><Month>03</Month><Day>05</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2021</Year><Month>4</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2021</Year><Month>4</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2021</Year><Month>4</Month><Day>1</Day><Hour>20</Hour><Minute>15</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">33794459</ArticleId><ArticleId IdType="pii">S0048-9697(21)01468-6</ArticleId><ArticleId 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