A computational approach for the screening of potential antiviral compounds against SARS-CoV-2 protease: Ionic liquid vs herbal and natural compounds.
Identifieur interne : 000418 ( Main/Curation ); précédent : 000417; suivant : 000419A computational approach for the screening of potential antiviral compounds against SARS-CoV-2 protease: Ionic liquid vs herbal and natural compounds.
Auteurs : Juhi Saraswat [Inde] ; Prashant Singh [Inde] ; Rajan Patel [Inde]Source :
- Journal of molecular liquids [ 0167-7322 ] ; 2021.
Abstract
The current scenario across the globe shows unprecedented healthcare and an economic crisis due to the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Recently, the World Health Organization (WHO) has declared a pandemic stage worldwide because of the high mortality and morbidity rate caused by novel infection disease. There have been several clinical trials and identification underway to find a treatment of this novel virus. For the treatment of severe infection involves the blocking of the replication of its CoV-2 protein. Hydroxychloroquine and remdesivir has been used on an emergency basis for its treatment. The uncontrolled infection and increasing death rate underline the emergence to develop the antiviral drug. In our study, the blind docking of various classes of compounds including control antiviral drugs (abacavir, acyclovir, quinoline, hydroxyquinoline), antimicrobial drugs (levofloxacin, amoxicillin, cloxacin, ofloxacin), natural compounds (lycorine, saikosaponins, myricetin, amentaflavone), herbal compounds (silymarin, palmatine, curcumin, eugenin) available in Indian Ayurveda was done. Besides, we have also performed the blind docking of various ionic liquids (ILs) such as pyrrolidinium, piperidinium, pyridinium, imidazolium based ILs against CoV-2 protease as they have recently emerged as a potential antimicrobial agent. Further, the pharmacokinetic properties and cytotoxicity of the compounds were determined computationally. The docking results showed successful binding to the active site or near a crucial site. The present computational approach was found helpful to predict the best possible inhibitor of protease and may result in an effective therapeutic agent against COVID-19.
DOI: 10.1016/j.molliq.2021.115298
PubMed: 33518856
PubMed Central: PMC7832122
Links toward previous steps (curation, corpus...)
- to stream Main, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000418
Links to Exploration step
pubmed:33518856Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A computational approach for the screening of potential antiviral compounds against SARS-CoV-2 protease: Ionic liquid vs herbal and natural compounds.</title><author><name sortKey="Saraswat, Juhi" sort="Saraswat, Juhi" uniqKey="Saraswat J" first="Juhi" last="Saraswat">Juhi Saraswat</name><affiliation wicri:level="1"><nlm:affiliation>Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025</wicri:regionArea></affiliation></author><author><name sortKey="Singh, Prashant" sort="Singh, Prashant" uniqKey="Singh P" first="Prashant" last="Singh">Prashant Singh</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi</wicri:regionArea></affiliation></author><author><name sortKey="Patel, Rajan" sort="Patel, Rajan" uniqKey="Patel R" first="Rajan" last="Patel">Rajan Patel</name><affiliation wicri:level="1"><nlm:affiliation>Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2021">2021</date><idno type="RBID">pubmed:33518856</idno><idno type="pmid">33518856</idno><idno type="doi">10.1016/j.molliq.2021.115298</idno><idno type="pmc">PMC7832122</idno><idno type="wicri:Area/Main/Corpus">000418</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000418</idno><idno type="wicri:Area/Main/Curation">000418</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000418</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">A computational approach for the screening of potential antiviral compounds against SARS-CoV-2 protease: Ionic liquid vs herbal and natural compounds.</title><author><name sortKey="Saraswat, Juhi" sort="Saraswat, Juhi" uniqKey="Saraswat J" first="Juhi" last="Saraswat">Juhi Saraswat</name><affiliation wicri:level="1"><nlm:affiliation>Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025</wicri:regionArea></affiliation></author><author><name sortKey="Singh, Prashant" sort="Singh, Prashant" uniqKey="Singh P" first="Prashant" last="Singh">Prashant Singh</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi</wicri:regionArea></affiliation></author><author><name sortKey="Patel, Rajan" sort="Patel, Rajan" uniqKey="Patel R" first="Rajan" last="Patel">Rajan Patel</name><affiliation wicri:level="1"><nlm:affiliation>Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025</wicri:regionArea></affiliation></author></analytic><series><title level="j">Journal of molecular liquids</title><idno type="ISSN">0167-7322</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 current scenario across the globe shows unprecedented healthcare and an economic crisis due to the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Recently, the World Health Organization (WHO) has declared a pandemic stage worldwide because of the high mortality and morbidity rate caused by novel infection disease. There have been several clinical trials and identification underway to find a treatment of this novel virus. For the treatment of severe infection involves the blocking of the replication of its CoV-2 protein. Hydroxychloroquine and remdesivir has been used on an emergency basis for its treatment. The uncontrolled infection and increasing death rate underline the emergence to develop the antiviral drug. In our study, the blind docking of various classes of compounds including control antiviral drugs (<i>abacavir, acyclovir, quinoline, hydroxyquinoline</i>), antimicrobial drugs (<i>levofloxacin, amoxicillin, cloxacin, ofloxacin</i>), natural compounds (<i>lycorine, saikosaponins, myricetin, amentaflavone</i>), herbal compounds (<i>silymarin, palmatine, curcumin, eugenin</i>) available in <i>Indian Ayurveda</i> was done. Besides, we have also performed the blind docking of various ionic liquids (ILs) such as <i>pyrrolidinium, piperidinium, pyridinium, imidazolium based ILs</i> against CoV-2 protease as they have recently emerged as a potential antimicrobial agent. Further, the pharmacokinetic properties and cytotoxicity of the compounds were determined computationally. The docking results showed successful binding to the active site or near a crucial site. The present computational approach was found helpful to predict the best possible inhibitor of protease and may result in an effective therapeutic agent against COVID-19.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">33518856</PMID><DateRevised><Year>2021</Year><Month>03</Month><Day>03</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0167-7322</ISSN><JournalIssue CitedMedium="Print"><Volume>326</Volume><PubDate><Year>2021</Year><Month>Mar</Month><Day>15</Day></PubDate></JournalIssue><Title>Journal of molecular liquids</Title><ISOAbbreviation>J Mol Liq</ISOAbbreviation></Journal><ArticleTitle>A computational approach for the screening of potential antiviral compounds against SARS-CoV-2 protease: Ionic liquid vs herbal and natural compounds.</ArticleTitle><Pagination><MedlinePgn>115298</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.molliq.2021.115298</ELocationID><Abstract><AbstractText>The current scenario across the globe shows unprecedented healthcare and an economic crisis due to the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Recently, the World Health Organization (WHO) has declared a pandemic stage worldwide because of the high mortality and morbidity rate caused by novel infection disease. There have been several clinical trials and identification underway to find a treatment of this novel virus. For the treatment of severe infection involves the blocking of the replication of its CoV-2 protein. Hydroxychloroquine and remdesivir has been used on an emergency basis for its treatment. The uncontrolled infection and increasing death rate underline the emergence to develop the antiviral drug. In our study, the blind docking of various classes of compounds including control antiviral drugs (<i>abacavir, acyclovir, quinoline, hydroxyquinoline</i>), antimicrobial drugs (<i>levofloxacin, amoxicillin, cloxacin, ofloxacin</i>), natural compounds (<i>lycorine, saikosaponins, myricetin, amentaflavone</i>), herbal compounds (<i>silymarin, palmatine, curcumin, eugenin</i>) available in <i>Indian Ayurveda</i> was done. Besides, we have also performed the blind docking of various ionic liquids (ILs) such as <i>pyrrolidinium, piperidinium, pyridinium, imidazolium based ILs</i> against CoV-2 protease as they have recently emerged as a potential antimicrobial agent. Further, the pharmacokinetic properties and cytotoxicity of the compounds were determined computationally. The docking results showed successful binding to the active site or near a crucial site. The present computational approach was found helpful to predict the best possible inhibitor of protease and may result in an effective therapeutic agent against COVID-19.</AbstractText><CopyrightInformation>© 2021 Published by Elsevier B.V.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Saraswat</LastName><ForeName>Juhi</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Singh</LastName><ForeName>Prashant</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Patel</LastName><ForeName>Rajan</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2021</Year><Month>01</Month><Day>07</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>J Mol Liq</MedlineTA><NlmUniqueID>9882716</NlmUniqueID><ISSNLinking>0167-7322</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Antiviral drug</Keyword><Keyword MajorTopicYN="N">Herbal compounds</Keyword><Keyword MajorTopicYN="N">Ionic liquids</Keyword><Keyword MajorTopicYN="N">Natural compounds</Keyword><Keyword MajorTopicYN="N">SARS-CoV protease</Keyword></KeywordList><CoiStatement>The authors declare no competing financial interest.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>10</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>12</Month><Day>15</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2021</Year><Month>01</Month><Day>04</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2021</Year><Month>2</Month><Day>1</Day><Hour>5</Hour><Minute>51</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2021</Year><Month>2</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2021</Year><Month>2</Month><Day>2</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">33518856</ArticleId><ArticleId IdType="doi">10.1016/j.molliq.2021.115298</ArticleId><ArticleId IdType="pii">S0167-7322(21)00024-6</ArticleId><ArticleId IdType="pmc">PMC7832122</ArticleId></ArticleIdList><pmc-dir>pmcsd</pmc-dir>
<ReferenceList><Reference><Citation>J Colloid Interface Sci. 2007 Dec 15;316(2):803-14</Citation><ArticleIdList><ArticleId IdType="pubmed">17719598</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biomol Struct Dyn. 2020 Jun 12;:1-9</Citation><ArticleIdList><ArticleId IdType="pubmed">32462996</ArticleId></ArticleIdList></Reference><Reference><Citation>J Comput Chem. 2004 Oct;25(13):1605-12</Citation><ArticleIdList><ArticleId IdType="pubmed">15264254</ArticleId></ArticleIdList></Reference><Reference><Citation>J Adv Res. 2020 Mar 16;24:91-98</Citation><ArticleIdList><ArticleId IdType="pubmed">32257431</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biomol Struct Dyn. 2017 May;35(6):1367-1380</Citation><ArticleIdList><ArticleId IdType="pubmed">27141981</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biomol Struct Dyn. 2020 Apr 27;:1-9</Citation><ArticleIdList><ArticleId IdType="pubmed">32306854</ArticleId></ArticleIdList></Reference><Reference><Citation>Langmuir. 2017 Jul 5;33(26):6511-6520</Citation><ArticleIdList><ArticleId IdType="pubmed">28605906</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biomol Struct Dyn. 2020 May 13;:1-11</Citation><ArticleIdList><ArticleId IdType="pubmed">32362245</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biomol Struct Dyn. 2020 Jun 22;:1-15</Citation><ArticleIdList><ArticleId IdType="pubmed">32567995</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biomol Struct Dyn. 2020 Jun 9;:1-7</Citation><ArticleIdList><ArticleId IdType="pubmed">32448041</ArticleId></ArticleIdList></Reference><Reference><Citation>J Colloid Interface Sci. 2007 Mar 1;307(1):235-45</Citation><ArticleIdList><ArticleId IdType="pubmed">17184790</ArticleId></ArticleIdList></Reference><Reference><Citation>Langmuir. 2013 Feb 26;29(8):2536-45</Citation><ArticleIdList><ArticleId IdType="pubmed">23360222</ArticleId></ArticleIdList></Reference><Reference><Citation>J Mol Recognit. 2018 Nov;31(11):e2734</Citation><ArticleIdList><ArticleId IdType="pubmed">29920814</ArticleId></ArticleIdList></Reference><Reference><Citation>Curr Med Chem. 2019;26(32):5947-5967</Citation><ArticleIdList><ArticleId IdType="pubmed">29874988</ArticleId></ArticleIdList></Reference><Reference><Citation>ACS Omega. 2020 Mar 17;5(12):6376-6388</Citation><ArticleIdList><ArticleId IdType="pubmed">32258872</ArticleId></ArticleIdList></Reference><Reference><Citation>Phys Chem Chem Phys. 2016 May 21;18(19):13375-84</Citation><ArticleIdList><ArticleId IdType="pubmed">27121134</ArticleId></ArticleIdList></Reference><Reference><Citation>Antiviral Res. 2005 Jul;67(1):18-23</Citation><ArticleIdList><ArticleId IdType="pubmed">15885816</ArticleId></ArticleIdList></Reference><Reference><Citation>JAMA. 2020 Apr 14;323(14):1406-1407</Citation><ArticleIdList><ArticleId IdType="pubmed">32083643</ArticleId></ArticleIdList></Reference><Reference><Citation>Eur Rev Med Pharmacol Sci. 2020 Apr;24(8):4539-4547</Citation><ArticleIdList><ArticleId IdType="pubmed">32373993</ArticleId></ArticleIdList></Reference><Reference><Citation>Complement Ther Clin Pract. 2020 May;39:101165</Citation><ArticleIdList><ArticleId IdType="pubmed">32379692</ArticleId></ArticleIdList></Reference><Reference><Citation>Phytother Res. 2020 Dec;34(12):3124-3136</Citation><ArticleIdList><ArticleId IdType="pubmed">32468635</ArticleId></ArticleIdList></Reference><Reference><Citation>Front Microbiol. 2017 Aug 24;8:1608</Citation><ArticleIdList><ArticleId IdType="pubmed">28883814</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biomol Struct Dyn. 2020 May 2;:1-9</Citation><ArticleIdList><ArticleId IdType="pubmed">32362243</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biomol Struct Dyn. 2020 May 12;:1-10</Citation><ArticleIdList><ArticleId IdType="pubmed">32345140</ArticleId></ArticleIdList></Reference><Reference><Citation>Inform Med Unlocked. 2020;21:100458</Citation><ArticleIdList><ArticleId IdType="pubmed">33102687</ArticleId></ArticleIdList></Reference><Reference><Citation>Lancet. 2020 Feb 15;395(10223):507-513</Citation><ArticleIdList><ArticleId IdType="pubmed">32007143</ArticleId></ArticleIdList></Reference><Reference><Citation>J Pharm Sci. 2015 Mar;104(3):872-905</Citation><ArticleIdList><ArticleId IdType="pubmed">25546108</ArticleId></ArticleIdList></Reference><Reference><Citation>N Engl J Med. 2020 May 28;382(22):e75</Citation><ArticleIdList><ArticleId IdType="pubmed">32240580</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2018 Jul 2;46(W1):W257-W263</Citation><ArticleIdList><ArticleId IdType="pubmed">29718510</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/CovidChloroV1/Data/Main/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000418 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Curation/biblio.hfd -nk 000418 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= CovidChloroV1
|flux= Main
|étape= Curation
|type= RBID
|clé= pubmed:33518856
|texte= A computational approach for the screening of potential antiviral compounds against SARS-CoV-2 protease: Ionic liquid vs herbal and natural compounds.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Curation/RBID.i -Sk "pubmed:33518856" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Curation/biblio.hfd \
| NlmPubMed2Wicri -a CovidChloroV1
| This area was generated with Dilib version V0.6.38. |  |