Potential Broad Spectrum Inhibitors of the Coronavirus 3CLpro: A Virtual Screening and Structure-Based Drug Design Study.
Identifieur interne : 000D26 ( PubMed/Corpus ); précédent : 000D25; suivant : 000D27Potential Broad Spectrum Inhibitors of the Coronavirus 3CLpro: A Virtual Screening and Structure-Based Drug Design Study.
Auteurs : Michael Berry ; Burtram C. Fielding ; Junaid GamieldienSource :
- Viruses [ 1999-4915 ] ; 2015.
English descriptors
- KwdEn :
- Antiviral Agents (chemistry), Antiviral Agents (isolation & purification), Antiviral Agents (pharmacology), Coronavirus (drug effects), Cysteine Endopeptidases (chemistry), Cysteine Proteinase Inhibitors (chemistry), Cysteine Proteinase Inhibitors (isolation & purification), Cysteine Proteinase Inhibitors (pharmacology), Drug Design, Drug Evaluation, Preclinical (methods), Humans, Molecular Docking Simulation, Molecular Dynamics Simulation, Viral Proteins (antagonists & inhibitors), Viral Proteins (chemistry).
- MESH :
- chemical , antagonists & inhibitors : Viral Proteins.
- chemical , chemistry : Antiviral Agents, Cysteine Endopeptidases, Cysteine Proteinase Inhibitors, Viral Proteins.
- chemical , isolation & purification : Antiviral Agents, Cysteine Proteinase Inhibitors.
- chemical , pharmacology : Antiviral Agents, Cysteine Proteinase Inhibitors.
- drug effects : Coronavirus.
- methods : Drug Evaluation, Preclinical.
- Drug Design, Humans, Molecular Docking Simulation, Molecular Dynamics Simulation.
Abstract
Human coronaviruses represent a significant disease burden; however, there is currently no antiviral strategy to combat infection. The outbreak of severe acute respiratory syndrome (SARS) in 2003 and Middle East respiratory syndrome (MERS) less than 10 years later demonstrates the potential of coronaviruses to cross species boundaries and further highlights the importance of identifying novel lead compounds with broad spectrum activity. The coronavirus 3CL(pro) provides a highly validated drug target and as there is a high degree of sequence homology and conservation in main chain architecture the design of broad spectrum inhibitors is viable. The ZINC drugs-now library was screened in a consensus high-throughput pharmacophore modeling and molecular docking approach by Vina, Glide, GOLD and MM-GBSA. Molecular dynamics further confirmed results obtained from structure-based techniques. A highly defined hit-list of 19 compounds was identified by the structure-based drug design methodologies. As these compounds were extensively validated by a consensus approach and by molecular dynamics, the likelihood that at least one of these compounds is bioactive is excellent. Additionally, the compounds segregate into 15 significantly dissimilar (p < 0.05) clusters based on shape and features, which represent valuable scaffolds that can be used as a basis for future anti-coronaviral inhibitor discovery experiments. Importantly though, the enriched subset of 19 compounds identified from the larger library has to be validated experimentally.
DOI: 10.3390/v7122963
PubMed: 26694449
Links to Exploration step
pubmed:26694449Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Potential Broad Spectrum Inhibitors of the Coronavirus 3CLpro: A Virtual Screening and Structure-Based Drug Design Study.</title><author><name sortKey="Berry, Michael" sort="Berry, Michael" uniqKey="Berry M" first="Michael" last="Berry">Michael Berry</name><affiliation><nlm:affiliation>South African Medical Research Council Bioinformatics Capacity Development Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa. michael@sanbi.ac.za.</nlm:affiliation></affiliation></author><author><name sortKey="Fielding, Burtram C" sort="Fielding, Burtram C" uniqKey="Fielding B" first="Burtram C" last="Fielding">Burtram C. Fielding</name><affiliation><nlm:affiliation>Molecular Biology and Virology Laboratory, Department of Medical BioSciences, Faculty of Natural Sciences, University of the Western Cape, Western Cape, Bellville 7535, South Africa. bfielding@uwc.ac.za.</nlm:affiliation></affiliation></author><author><name sortKey="Gamieldien, Junaid" sort="Gamieldien, Junaid" uniqKey="Gamieldien J" first="Junaid" last="Gamieldien">Junaid Gamieldien</name><affiliation><nlm:affiliation>South African Medical Research Council Bioinformatics Capacity Development Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa. junaid@sanbi.ac.za.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:26694449</idno><idno type="pmid">26694449</idno><idno type="doi">10.3390/v7122963</idno><idno type="wicri:Area/PubMed/Corpus">000D26</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000D26</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Potential Broad Spectrum Inhibitors of the Coronavirus 3CLpro: A Virtual Screening and Structure-Based Drug Design Study.</title><author><name sortKey="Berry, Michael" sort="Berry, Michael" uniqKey="Berry M" first="Michael" last="Berry">Michael Berry</name><affiliation><nlm:affiliation>South African Medical Research Council Bioinformatics Capacity Development Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa. michael@sanbi.ac.za.</nlm:affiliation></affiliation></author><author><name sortKey="Fielding, Burtram C" sort="Fielding, Burtram C" uniqKey="Fielding B" first="Burtram C" last="Fielding">Burtram C. Fielding</name><affiliation><nlm:affiliation>Molecular Biology and Virology Laboratory, Department of Medical BioSciences, Faculty of Natural Sciences, University of the Western Cape, Western Cape, Bellville 7535, South Africa. bfielding@uwc.ac.za.</nlm:affiliation></affiliation></author><author><name sortKey="Gamieldien, Junaid" sort="Gamieldien, Junaid" uniqKey="Gamieldien J" first="Junaid" last="Gamieldien">Junaid Gamieldien</name><affiliation><nlm:affiliation>South African Medical Research Council Bioinformatics Capacity Development Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa. junaid@sanbi.ac.za.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Viruses</title><idno type="eISSN">1999-4915</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Antiviral Agents (chemistry)</term><term>Antiviral Agents (isolation & purification)</term><term>Antiviral Agents (pharmacology)</term><term>Coronavirus (drug effects)</term><term>Cysteine Endopeptidases (chemistry)</term><term>Cysteine Proteinase Inhibitors (chemistry)</term><term>Cysteine Proteinase Inhibitors (isolation & purification)</term><term>Cysteine Proteinase Inhibitors (pharmacology)</term><term>Drug Design</term><term>Drug Evaluation, Preclinical (methods)</term><term>Humans</term><term>Molecular Docking Simulation</term><term>Molecular Dynamics Simulation</term><term>Viral Proteins (antagonists & inhibitors)</term><term>Viral Proteins (chemistry)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="antagonists & inhibitors" xml:lang="en"><term>Viral Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Antiviral Agents</term><term>Cysteine Endopeptidases</term><term>Cysteine Proteinase Inhibitors</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="isolation & purification" xml:lang="en"><term>Antiviral Agents</term><term>Cysteine Proteinase Inhibitors</term></keywords><keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Antiviral Agents</term><term>Cysteine Proteinase Inhibitors</term></keywords><keywords scheme="MESH" qualifier="drug effects" xml:lang="en"><term>Coronavirus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Drug Evaluation, Preclinical</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Drug Design</term><term>Humans</term><term>Molecular Docking Simulation</term><term>Molecular Dynamics Simulation</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Human coronaviruses represent a significant disease burden; however, there is currently no antiviral strategy to combat infection. The outbreak of severe acute respiratory syndrome (SARS) in 2003 and Middle East respiratory syndrome (MERS) less than 10 years later demonstrates the potential of coronaviruses to cross species boundaries and further highlights the importance of identifying novel lead compounds with broad spectrum activity. The coronavirus 3CL(pro) provides a highly validated drug target and as there is a high degree of sequence homology and conservation in main chain architecture the design of broad spectrum inhibitors is viable. The ZINC drugs-now library was screened in a consensus high-throughput pharmacophore modeling and molecular docking approach by Vina, Glide, GOLD and MM-GBSA. Molecular dynamics further confirmed results obtained from structure-based techniques. A highly defined hit-list of 19 compounds was identified by the structure-based drug design methodologies. As these compounds were extensively validated by a consensus approach and by molecular dynamics, the likelihood that at least one of these compounds is bioactive is excellent. Additionally, the compounds segregate into 15 significantly dissimilar (p < 0.05) clusters based on shape and features, which represent valuable scaffolds that can be used as a basis for future anti-coronaviral inhibitor discovery experiments. Importantly though, the enriched subset of 19 compounds identified from the larger library has to be validated experimentally. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26694449</PMID><DateCompleted><Year>2016</Year><Month>09</Month><Day>29</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>25</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1999-4915</ISSN><JournalIssue CitedMedium="Internet"><Volume>7</Volume><Issue>12</Issue><PubDate><Year>2015</Year><Month>Dec</Month><Day>15</Day></PubDate></JournalIssue><Title>Viruses</Title><ISOAbbreviation>Viruses</ISOAbbreviation></Journal><ArticleTitle>Potential Broad Spectrum Inhibitors of the Coronavirus 3CLpro: A Virtual Screening and Structure-Based Drug Design Study.</ArticleTitle><Pagination><MedlinePgn>6642-60</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3390/v7122963</ELocationID><Abstract><AbstractText>Human coronaviruses represent a significant disease burden; however, there is currently no antiviral strategy to combat infection. The outbreak of severe acute respiratory syndrome (SARS) in 2003 and Middle East respiratory syndrome (MERS) less than 10 years later demonstrates the potential of coronaviruses to cross species boundaries and further highlights the importance of identifying novel lead compounds with broad spectrum activity. The coronavirus 3CL(pro) provides a highly validated drug target and as there is a high degree of sequence homology and conservation in main chain architecture the design of broad spectrum inhibitors is viable. The ZINC drugs-now library was screened in a consensus high-throughput pharmacophore modeling and molecular docking approach by Vina, Glide, GOLD and MM-GBSA. Molecular dynamics further confirmed results obtained from structure-based techniques. A highly defined hit-list of 19 compounds was identified by the structure-based drug design methodologies. As these compounds were extensively validated by a consensus approach and by molecular dynamics, the likelihood that at least one of these compounds is bioactive is excellent. Additionally, the compounds segregate into 15 significantly dissimilar (p < 0.05) clusters based on shape and features, which represent valuable scaffolds that can be used as a basis for future anti-coronaviral inhibitor discovery experiments. Importantly though, the enriched subset of 19 compounds identified from the larger library has to be validated experimentally. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Berry</LastName><ForeName>Michael</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>South African Medical Research Council Bioinformatics Capacity Development Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa. michael@sanbi.ac.za.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Molecular Biology and Virology Laboratory, Department of Medical BioSciences, Faculty of Natural Sciences, University of the Western Cape, Western Cape, Bellville 7535, South Africa. michael@sanbi.ac.za.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fielding</LastName><ForeName>Burtram C</ForeName><Initials>BC</Initials><AffiliationInfo><Affiliation>Molecular Biology and Virology Laboratory, Department of Medical BioSciences, Faculty of Natural Sciences, University of the Western Cape, Western Cape, Bellville 7535, South Africa. bfielding@uwc.ac.za.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gamieldien</LastName><ForeName>Junaid</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>South African Medical Research Council Bioinformatics Capacity Development Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa. junaid@sanbi.ac.za.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate 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