De novo design, retrosynthetic analysis and combinatorial synthesis of a hybrid antiviral (VTAR-01) to inhibit the interaction of SARS-CoV2 spike glycoprotein with human angiotensin-converting enzyme 2.
Identifieur interne : 001A53 ( Main/Exploration ); précédent : 001A52; suivant : 001A54De novo design, retrosynthetic analysis and combinatorial synthesis of a hybrid antiviral (VTAR-01) to inhibit the interaction of SARS-CoV2 spike glycoprotein with human angiotensin-converting enzyme 2.
Auteurs : Vishvanath Tiwari [Inde]Source :
- Biology open [ 2046-6390 ] ; 2020.
Descripteurs français
- KwdFr :
- Antiviraux (composition chimique), Antiviraux (pharmacologie), Betacoronavirus (métabolisme), Domaines protéiques (MeSH), Glycoprotéine de spicule des coronavirus (métabolisme), Humains (MeSH), Liaison aux protéines (effets des médicaments et des substances chimiques), Mort cellulaire (effets des médicaments et des substances chimiques), Peptidyl-Dipeptidase A (composition chimique), Peptidyl-Dipeptidase A (métabolisme), Simulation de docking moléculaire (MeSH), Techniques de chimie combinatoire (MeSH), Thermodynamique (MeSH).
- MESH :
- composition chimique : Antiviraux, Peptidyl-Dipeptidase A.
- effets des médicaments et des substances chimiques : Liaison aux protéines, Mort cellulaire.
- métabolisme : Betacoronavirus, Glycoprotéine de spicule des coronavirus, Peptidyl-Dipeptidase A.
- pharmacologie : Antiviraux.
- Domaines protéiques, Humains, Simulation de docking moléculaire, Techniques de chimie combinatoire, Thermodynamique.
English descriptors
- KwdEn :
- Angiotensin-Converting Enzyme 2 (MeSH), Antiviral Agents (chemistry), Antiviral Agents (pharmacology), Betacoronavirus (metabolism), Cell Death (drug effects), Combinatorial Chemistry Techniques (MeSH), Humans (MeSH), Molecular Docking Simulation (MeSH), Peptidyl-Dipeptidase A (chemistry), Peptidyl-Dipeptidase A (metabolism), Protein Binding (drug effects), Protein Domains (MeSH), SARS-CoV-2 (MeSH), Spike Glycoprotein, Coronavirus (metabolism), Thermodynamics (MeSH).
- MESH :
- chemical , chemistry : Antiviral Agents, Peptidyl-Dipeptidase A.
- chemical , metabolism : Peptidyl-Dipeptidase A, Spike Glycoprotein, Coronavirus.
- chemical , pharmacology : Antiviral Agents.
- chemical : Angiotensin-Converting Enzyme 2.
- drug effects : Cell Death, Protein Binding.
- metabolism : Betacoronavirus.
- Combinatorial Chemistry Techniques, Humans, Molecular Docking Simulation, Protein Domains, SARS-CoV-2, Thermodynamics.
Abstract
SARS-like coronavirus (SARS-CoV2) has emerged as a global threat to humankind and is rapidly spreading. The infectivity, pathogenesis and infection of this virus are dependent on the interaction of SARS-CoV2 spike protein with human angiotensin converting enzyme 2 (hACE2). Spike protein contains a receptor-binding domain (RBD) that recognizes hACE-2. In the present study, we are reporting a de novo designed novel hybrid antiviral 'VTAR-01' molecule that binds at the interface of RBD-hACE2 interaction. A series of antiviral molecules were tested for binding at the interface of RBD-hACE2 interaction. In silico screening, molecular mechanics and molecular dynamics simulation (MDS) analysis suggest ribavirin, ascorbate, lopinavir and hydroxychloroquine have strong interaction at the RBD-hACE2 interface. These four molecules were used for de novo fragment-based antiviral design. De novo designing, docking and MDS analysis identified a 'VTAR' hybrid molecule that has better interaction with this interface than all of the antivirals used to design it. We have further used retrosynthetic analysis and combinatorial synthesis to design 100 variants of VTAR molecules. Retrosynthetic analysis and combinatorial synthesis, along with docking and MDS, identified that VTAR-01 interacts with the interface of the RBD-ACE2 complex. MDS analysis confirmed its interaction with the RBD-ACE2 interface by involving Glu35 and Lys353 of ACE2, as well as Gln493 and Ser494 of RBD. Interaction of spike protein with ACE2 is essential for pathogenesis and infection of this virus; hence, this in silico designed hybrid antiviral molecule (VTAR-01) that binds at the interface of RBD-hACE2 may be further developed to control the infection of SARS-CoV2.
DOI: 10.1242/bio.054056
PubMed: 32878881
PubMed Central: PMC7595696
Affiliations:
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Ajmer 305817, India vishvanath@curaj.ac.in.</nlm:affiliation><country wicri:rule="url">Inde</country><wicri:regionArea>Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer 305817</wicri:regionArea><wicri:noRegion>Ajmer 305817</wicri:noRegion></affiliation></author></analytic><series><title level="j">Biology open</title><idno type="eISSN">2046-6390</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Angiotensin-Converting Enzyme 2 (MeSH)</term><term>Antiviral Agents (chemistry)</term><term>Antiviral Agents (pharmacology)</term><term>Betacoronavirus (metabolism)</term><term>Cell Death (drug effects)</term><term>Combinatorial Chemistry Techniques (MeSH)</term><term>Humans (MeSH)</term><term>Molecular Docking Simulation (MeSH)</term><term>Peptidyl-Dipeptidase A (chemistry)</term><term>Peptidyl-Dipeptidase A (metabolism)</term><term>Protein Binding (drug effects)</term><term>Protein Domains (MeSH)</term><term>SARS-CoV-2 (MeSH)</term><term>Spike Glycoprotein, Coronavirus (metabolism)</term><term>Thermodynamics (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Antiviraux (composition chimique)</term><term>Antiviraux (pharmacologie)</term><term>Betacoronavirus (métabolisme)</term><term>Domaines protéiques (MeSH)</term><term>Glycoprotéine de spicule des coronavirus (métabolisme)</term><term>Humains (MeSH)</term><term>Liaison aux protéines (effets des médicaments et des substances chimiques)</term><term>Mort cellulaire (effets des médicaments et des substances chimiques)</term><term>Peptidyl-Dipeptidase A (composition chimique)</term><term>Peptidyl-Dipeptidase A (métabolisme)</term><term>Simulation de docking moléculaire (MeSH)</term><term>Techniques de chimie combinatoire (MeSH)</term><term>Thermodynamique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" 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xml:lang="en"><term>Betacoronavirus</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Betacoronavirus</term><term>Glycoprotéine de spicule des coronavirus</term><term>Peptidyl-Dipeptidase A</term></keywords><keywords scheme="MESH" qualifier="pharmacologie" xml:lang="fr"><term>Antiviraux</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Combinatorial Chemistry Techniques</term><term>Humans</term><term>Molecular Docking Simulation</term><term>Protein Domains</term><term>SARS-CoV-2</term><term>Thermodynamics</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Domaines protéiques</term><term>Humains</term><term>Simulation de docking moléculaire</term><term>Techniques de chimie combinatoire</term><term>Thermodynamique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">SARS-like coronavirus (SARS-CoV2) has emerged as a global threat to humankind and is rapidly spreading. The infectivity, pathogenesis and infection of this virus are dependent on the interaction of SARS-CoV2 spike protein with human angiotensin converting enzyme 2 (hACE2). Spike protein contains a receptor-binding domain (RBD) that recognizes hACE-2. In the present study, we are reporting a <i>de novo</i> designed novel hybrid antiviral 'VTAR-01' molecule that binds at the interface of RBD-hACE2 interaction. A series of antiviral molecules were tested for binding at the interface of RBD-hACE2 interaction. <i>In silico</i> screening, molecular mechanics and molecular dynamics simulation (MDS) analysis suggest ribavirin, ascorbate, lopinavir and hydroxychloroquine have strong interaction at the RBD-hACE2 interface. These four molecules were used for <i>de novo</i> fragment-based antiviral design. <i>De novo</i> designing, docking and MDS analysis identified a 'VTAR' hybrid molecule that has better interaction with this interface than all of the antivirals used to design it. We have further used retrosynthetic analysis and combinatorial synthesis to design 100 variants of VTAR molecules. Retrosynthetic analysis and combinatorial synthesis, along with docking and MDS, identified that VTAR-01 interacts with the interface of the RBD-ACE2 complex. MDS analysis confirmed its interaction with the RBD-ACE2 interface by involving Glu35 and Lys353 of ACE2, as well as Gln493 and Ser494 of RBD. Interaction of spike protein with ACE2 is essential for pathogenesis and infection of this virus; hence, this <i>i</i><i>n s</i><i>ilico</i> designed hybrid antiviral molecule (VTAR-01) that binds at the interface of RBD-hACE2 may be further developed to control the infection of SARS-CoV2.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">32878881</PMID><DateCompleted><Year>2020</Year><Month>10</Month><Day>27</Day></DateCompleted><DateRevised><Year>2020</Year><Month>12</Month><Day>18</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2046-6390</ISSN><JournalIssue CitedMedium="Internet"><Volume>9</Volume><Issue>10</Issue><PubDate><Year>2020</Year><Month>10</Month><Day>15</Day></PubDate></JournalIssue><Title>Biology open</Title><ISOAbbreviation>Biol Open</ISOAbbreviation></Journal><ArticleTitle><i>De novo</i> design, retrosynthetic analysis and combinatorial synthesis of a hybrid antiviral (VTAR-01) to inhibit the interaction of SARS-CoV2 spike glycoprotein with human angiotensin-converting enzyme 2.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">bio054056</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1242/bio.054056</ELocationID><Abstract><AbstractText>SARS-like coronavirus (SARS-CoV2) has emerged as a global threat to humankind and is rapidly spreading. The infectivity, pathogenesis and infection of this virus are dependent on the interaction of SARS-CoV2 spike protein with human angiotensin converting enzyme 2 (hACE2). Spike protein contains a receptor-binding domain (RBD) that recognizes hACE-2. In the present study, we are reporting a <i>de novo</i> designed novel hybrid antiviral 'VTAR-01' molecule that binds at the interface of RBD-hACE2 interaction. A series of antiviral molecules were tested for binding at the interface of RBD-hACE2 interaction. <i>In silico</i> screening, molecular mechanics and molecular dynamics simulation (MDS) analysis suggest ribavirin, ascorbate, lopinavir and hydroxychloroquine have strong interaction at the RBD-hACE2 interface. These four molecules were used for <i>de novo</i> fragment-based antiviral design. <i>De novo</i> designing, docking and MDS analysis identified a 'VTAR' hybrid molecule that has better interaction with this interface than all of the antivirals used to design it. We have further used retrosynthetic analysis and combinatorial synthesis to design 100 variants of VTAR molecules. Retrosynthetic analysis and combinatorial synthesis, along with docking and MDS, identified that VTAR-01 interacts with the interface of the RBD-ACE2 complex. MDS analysis confirmed its interaction with the RBD-ACE2 interface by involving Glu35 and Lys353 of ACE2, as well as Gln493 and Ser494 of RBD. Interaction of spike protein with ACE2 is essential for pathogenesis and infection of this virus; hence, this <i>i</i><i>n s</i><i>ilico</i> designed hybrid antiviral molecule (VTAR-01) that binds at the interface of RBD-hACE2 may be further developed to control the infection of SARS-CoV2.</AbstractText><CopyrightInformation>© 2020. Published by The Company of Biologists Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tiwari</LastName><ForeName>Vishvanath</ForeName><Initials>V</Initials><Identifier Source="ORCID">0000-0003-1664-3871</Identifier><AffiliationInfo><Affiliation>Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer 305817, India vishvanath@curaj.ac.in.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>10</Month><Day>15</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Biol Open</MedlineTA><NlmUniqueID>101578018</NlmUniqueID><ISSNLinking>2046-6390</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D000998">Antiviral Agents</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D064370">Spike Glycoprotein, Coronavirus</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.4.15.1</RegistryNumber><NameOfSubstance UI="D007703">Peptidyl-Dipeptidase A</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.4.17.23</RegistryNumber><NameOfSubstance UI="C000705307">ACE2 protein, human</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.4.17.23</RegistryNumber><NameOfSubstance UI="D000085962">Angiotensin-Converting Enzyme 2</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000085962" MajorTopicYN="N">Angiotensin-Converting Enzyme 2</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000998" MajorTopicYN="N">Antiviral Agents</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000494" MajorTopicYN="Y">pharmacology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D000073640" MajorTopicYN="N">Betacoronavirus</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016923" MajorTopicYN="N">Cell Death</DescriptorName><QualifierName UI="Q000187" MajorTopicYN="N">drug effects</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020650" MajorTopicYN="Y">Combinatorial Chemistry Techniques</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D062105" MajorTopicYN="N">Molecular Docking Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D007703" MajorTopicYN="N">Peptidyl-Dipeptidase A</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011485" MajorTopicYN="N">Protein Binding</DescriptorName><QualifierName UI="Q000187" MajorTopicYN="N">drug effects</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D000072417" MajorTopicYN="N">Protein Domains</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000086402" MajorTopicYN="N">SARS-CoV-2</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D064370" MajorTopicYN="N">Spike Glycoprotein, Coronavirus</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013816" MajorTopicYN="N">Thermodynamics</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Angiotensin converting enzyme 2</Keyword><Keyword MajorTopicYN="Y">De novo designing</Keyword><Keyword MajorTopicYN="Y">Hybrid antiviral molecule</Keyword><Keyword MajorTopicYN="Y">Molecular dynamics simulation</Keyword><Keyword MajorTopicYN="Y">Retrosynthetic analysis</Keyword><Keyword MajorTopicYN="Y">SARS-CoV2 spike glycoprotein</Keyword></KeywordList><CoiStatement>Competing interestsThe authors declare no competing or financial interests.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>9</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>10</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>9</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32878881</ArticleId><ArticleId IdType="pii">bio.054056</ArticleId><ArticleId IdType="doi">10.1242/bio.054056</ArticleId><ArticleId 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IdType="pubmed">26492219</ArticleId></ArticleIdList></Reference><Reference><Citation>Clin Immunol. 2020 Aug;217:108480</Citation><ArticleIdList><ArticleId IdType="pubmed">32461193</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Inde</li></country></list><tree><country name="Inde"><noRegion><name sortKey="Tiwari, Vishvanath" sort="Tiwari, Vishvanath" uniqKey="Tiwari V" first="Vishvanath" last="Tiwari">Vishvanath Tiwari</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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