Vaccine Design from the Ensemble of Surface Glycoprotein Epitopes of SARS-CoV-2: An Immunoinformatics Approach.
Identifieur interne : 000281 ( Main/Exploration ); précédent : 000280; suivant : 000282Vaccine Design from the Ensemble of Surface Glycoprotein Epitopes of SARS-CoV-2: An Immunoinformatics Approach.
Auteurs : Noor Rahman [Pakistan] ; Fawad Ali [Pakistan] ; Zarrin Basharat [Pakistan] ; Muhammad Shehroz [Pakistan] ; Muhammad Kazim Khan [Pakistan] ; Philippe Jeandet [France] ; Eugenie Nepovimova [République tchèque] ; Kamil Kuca [République tchèque] ; Haroon Khan [Pakistan]Source :
- Vaccines [ 2076-393X ] ; 2020.
Abstract
The present study aimed to work out a peptide-based multi-epitope vaccine against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We predicted different B-cell and T-cell epitopes by using the Immune Epitopes Database (IEDB). Homology modeling of the construct was done using SWISS-MODEL and then docked with different toll-like-receptors (TLR4, TLR7, and TLR8) using PatchDock, HADDOCK, and FireDock, respectively. From the overlapped epitopes, we designed five vaccine constructs C1-C5. Based on antigenicity, allergenicity, solubility, different physiochemical properties, and molecular docking scores, we selected the vaccine construct 1 (C1) for further processing. Docking of C1 with TLR4, TLR7, and TLR8 showed striking interactions with global binding energy of -43.48, -65.88, and -60.24 Kcal/mol, respectively. The docked complex was further simulated, which revealed that both molecules remain stable with minimum RMSF. Activation of TLRs induces downstream pathways to produce pro-inflammatory cytokines against viruses and immune system simulation shows enhanced antibody production after the booster dose. In conclusion, C1 was the best vaccine candidate among all designed constructs to elicit an immune response SARS-CoV-2 and combat the coronavirus disease (COVID-19).
DOI: 10.3390/vaccines8030423
PubMed: 32731461
Affiliations:
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Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.</nlm:affiliation><country xml:lang="fr">Pakistan</country><wicri:regionArea>H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270</wicri:regionArea><wicri:noRegion>Karachi 75270</wicri:noRegion></affiliation></author><author><name sortKey="Ali, Fawad" sort="Ali, Fawad" uniqKey="Ali F" first="Fawad" last="Ali">Fawad Ali</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, Hazara University, Mansehra 21120, Pakistan.</nlm:affiliation><country xml:lang="fr">Pakistan</country><wicri:regionArea>Department of Biochemistry, Hazara University, Mansehra 21120</wicri:regionArea><wicri:noRegion>Mansehra 21120</wicri:noRegion></affiliation></author><author><name sortKey="Basharat, Zarrin" sort="Basharat, Zarrin" uniqKey="Basharat Z" first="Zarrin" last="Basharat">Zarrin Basharat</name><affiliation wicri:level="1"><nlm:affiliation>Jamil-ur-Rahman Center for Genome Research, PCMD, ICCBS, University of Karachi, Karachi 75270, Pakistan.</nlm:affiliation><country xml:lang="fr">Pakistan</country><wicri:regionArea>Jamil-ur-Rahman Center for Genome Research, PCMD, ICCBS, University of Karachi, Karachi 75270</wicri:regionArea><wicri:noRegion>Karachi 75270</wicri:noRegion></affiliation></author><author><name sortKey="Shehroz, Muhammad" sort="Shehroz, Muhammad" uniqKey="Shehroz M" first="Muhammad" last="Shehroz">Muhammad Shehroz</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biotechnology, Virtual University of Pakistan, Lahore 54000, Pakistan.</nlm:affiliation><country xml:lang="fr">Pakistan</country><wicri:regionArea>Department of Biotechnology, Virtual University of Pakistan, Lahore 54000</wicri:regionArea><wicri:noRegion>Lahore 54000</wicri:noRegion></affiliation></author><author><name sortKey="Khan, Muhammad Kazim" sort="Khan, Muhammad Kazim" uniqKey="Khan M" first="Muhammad Kazim" last="Khan">Muhammad Kazim Khan</name><affiliation wicri:level="1"><nlm:affiliation>Centre for Applied Molecular Biology, University of the Punjab, Lahore 53700, Pakistan.</nlm:affiliation><country xml:lang="fr">Pakistan</country><wicri:regionArea>Centre for Applied Molecular Biology, University of the Punjab, Lahore 53700</wicri:regionArea><wicri:noRegion>Lahore 53700</wicri:noRegion></affiliation></author><author><name sortKey="Jeandet, Philippe" sort="Jeandet, Philippe" uniqKey="Jeandet P" first="Philippe" last="Jeandet">Philippe Jeandet</name><affiliation wicri:level="3"><nlm:affiliation>Faculty of Sciences, University of Reims Champagne-Ardenne, CEDEX 2, 51687 Reims, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Faculty of Sciences, University of Reims Champagne-Ardenne, CEDEX 2, 51687 Reims</wicri:regionArea><placeName><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Champagne-Ardenne</region><settlement type="city">Reims</settlement></placeName></affiliation></author><author><name sortKey="Nepovimova, Eugenie" sort="Nepovimova, Eugenie" uniqKey="Nepovimova E" first="Eugenie" last="Nepovimova">Eugenie Nepovimova</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50005 Hradec Kralove, Czech Republic.</nlm:affiliation><country xml:lang="fr">République tchèque</country><wicri:regionArea>Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50005 Hradec Kralove</wicri:regionArea><wicri:noRegion>50005 Hradec Kralove</wicri:noRegion></affiliation></author><author><name sortKey="Kuca, Kamil" sort="Kuca, Kamil" uniqKey="Kuca K" first="Kamil" last="Kuca">Kamil Kuca</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50005 Hradec Kralove, Czech Republic.</nlm:affiliation><country xml:lang="fr">République tchèque</country><wicri:regionArea>Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50005 Hradec Kralove</wicri:regionArea><wicri:noRegion>50005 Hradec Kralove</wicri:noRegion></affiliation></author><author><name sortKey="Khan, Haroon" sort="Khan, Haroon" uniqKey="Khan H" first="Haroon" last="Khan">Haroon Khan</name><affiliation wicri:level="1"><nlm:affiliation>Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan.</nlm:affiliation><country xml:lang="fr">Pakistan</country><wicri:regionArea>Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan 23200</wicri:regionArea><wicri:noRegion>Mardan 23200</wicri:noRegion></affiliation></author></analytic><series><title level="j">Vaccines</title><idno type="ISSN">2076-393X</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The present study aimed to work out a peptide-based multi-epitope vaccine against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We predicted different B-cell and T-cell epitopes by using the Immune Epitopes Database (IEDB). Homology modeling of the construct was done using SWISS-MODEL and then docked with different toll-like-receptors (TLR4, TLR7, and TLR8) using PatchDock, HADDOCK, and FireDock, respectively. From the overlapped epitopes, we designed five vaccine constructs C1-C5. Based on antigenicity, allergenicity, solubility, different physiochemical properties, and molecular docking scores, we selected the vaccine construct 1 (C1) for further processing. Docking of C1 with TLR4, TLR7, and TLR8 showed striking interactions with global binding energy of -43.48, -65.88, and -60.24 Kcal/mol, respectively. The docked complex was further simulated, which revealed that both molecules remain stable with minimum RMSF. Activation of TLRs induces downstream pathways to produce pro-inflammatory cytokines against viruses and immune system simulation shows enhanced antibody production after the booster dose. In conclusion, C1 was the best vaccine candidate among all designed constructs to elicit an immune response SARS-CoV-2 and combat the coronavirus disease (COVID-19).</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32731461</PMID><DateRevised><Year>2020</Year><Month>07</Month><Day>31</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Print">2076-393X</ISSN><JournalIssue CitedMedium="Print"><Volume>8</Volume><Issue>3</Issue><PubDate><Year>2020</Year><Month>Jul</Month><Day>28</Day></PubDate></JournalIssue><Title>Vaccines</Title><ISOAbbreviation>Vaccines (Basel)</ISOAbbreviation></Journal><ArticleTitle>Vaccine Design from the Ensemble of Surface Glycoprotein Epitopes of SARS-CoV-2: An Immunoinformatics Approach.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">E423</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.3390/vaccines8030423</ELocationID><Abstract><AbstractText>The present study aimed to work out a peptide-based multi-epitope vaccine against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We predicted different B-cell and T-cell epitopes by using the Immune Epitopes Database (IEDB). Homology modeling of the construct was done using SWISS-MODEL and then docked with different toll-like-receptors (TLR4, TLR7, and TLR8) using PatchDock, HADDOCK, and FireDock, respectively. From the overlapped epitopes, we designed five vaccine constructs C1-C5. Based on antigenicity, allergenicity, solubility, different physiochemical properties, and molecular docking scores, we selected the vaccine construct 1 (C1) for further processing. Docking of C1 with TLR4, TLR7, and TLR8 showed striking interactions with global binding energy of -43.48, -65.88, and -60.24 Kcal/mol, respectively. The docked complex was further simulated, which revealed that both molecules remain stable with minimum RMSF. Activation of TLRs induces downstream pathways to produce pro-inflammatory cytokines against viruses and immune system simulation shows enhanced antibody production after the booster dose. In conclusion, C1 was the best vaccine candidate among all designed constructs to elicit an immune response SARS-CoV-2 and combat the coronavirus disease (COVID-19).</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Rahman</LastName><ForeName>Noor</ForeName><Initials>N</Initials><Identifier Source="ORCID">0000-0002-7062-2302</Identifier><AffiliationInfo><Affiliation>H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ali</LastName><ForeName>Fawad</ForeName><Initials>F</Initials><Identifier Source="ORCID">0000-0002-5331-7816</Identifier><AffiliationInfo><Affiliation>Department of Biochemistry, Hazara University, Mansehra 21120, Pakistan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Basharat</LastName><ForeName>Zarrin</ForeName><Initials>Z</Initials><Identifier Source="ORCID">0000-0003-1785-3803</Identifier><AffiliationInfo><Affiliation>Jamil-ur-Rahman Center for Genome Research, PCMD, ICCBS, University of Karachi, Karachi 75270, Pakistan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shehroz</LastName><ForeName>Muhammad</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Biotechnology, Virtual University of Pakistan, Lahore 54000, Pakistan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Khan</LastName><ForeName>Muhammad Kazim</ForeName><Initials>MK</Initials><AffiliationInfo><Affiliation>Centre for Applied Molecular Biology, University of the Punjab, Lahore 53700, Pakistan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jeandet</LastName><ForeName>Philippe</ForeName><Initials>P</Initials><Identifier Source="ORCID">0000-0003-3023-4871</Identifier><AffiliationInfo><Affiliation>Faculty of Sciences, University of Reims Champagne-Ardenne, CEDEX 2, 51687 Reims, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nepovimova</LastName><ForeName>Eugenie</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50005 Hradec Kralove, Czech Republic.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kuca</LastName><ForeName>Kamil</ForeName><Initials>K</Initials><Identifier Source="ORCID">0000-0001-9664-1109</Identifier><AffiliationInfo><Affiliation>Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50005 Hradec Kralove, Czech Republic.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Khan</LastName><ForeName>Haroon</ForeName><Initials>H</Initials><Identifier Source="ORCID">0000-0002-1736-4404</Identifier><AffiliationInfo><Affiliation>Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>faculty of science VT209-2021</GrantID><Agency>UHK</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>07</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Vaccines (Basel)</MedlineTA><NlmUniqueID>101629355</NlmUniqueID><ISSNLinking>2076-393X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">allergenicity</Keyword><Keyword MajorTopicYN="N">antigenicity</Keyword><Keyword MajorTopicYN="N">coronavirus</Keyword><Keyword MajorTopicYN="N">multi-epitopes</Keyword><Keyword MajorTopicYN="N">pneumonia</Keyword><Keyword MajorTopicYN="N">vaccine</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>06</Month><Day>07</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>07</Month><Day>09</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>07</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>8</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>8</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>8</Month><Day>1</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32731461</ArticleId><ArticleId IdType="pii">vaccines8030423</ArticleId><ArticleId IdType="doi">10.3390/vaccines8030423</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>France</li><li>Pakistan</li><li>République tchèque</li></country><region><li>Champagne-Ardenne</li><li>Grand Est</li></region><settlement><li>Reims</li></settlement></list><tree><country name="Pakistan"><noRegion><name sortKey="Rahman, Noor" sort="Rahman, Noor" uniqKey="Rahman N" first="Noor" last="Rahman">Noor Rahman</name></noRegion><name sortKey="Ali, Fawad" sort="Ali, Fawad" uniqKey="Ali F" first="Fawad" last="Ali">Fawad Ali</name><name sortKey="Basharat, Zarrin" sort="Basharat, Zarrin" uniqKey="Basharat Z" first="Zarrin" last="Basharat">Zarrin Basharat</name><name sortKey="Khan, Haroon" sort="Khan, Haroon" uniqKey="Khan H" first="Haroon" last="Khan">Haroon Khan</name><name sortKey="Khan, Muhammad Kazim" sort="Khan, Muhammad Kazim" uniqKey="Khan M" first="Muhammad Kazim" last="Khan">Muhammad Kazim Khan</name><name sortKey="Shehroz, Muhammad" sort="Shehroz, Muhammad" uniqKey="Shehroz M" first="Muhammad" last="Shehroz">Muhammad Shehroz</name></country><country name="France"><region name="Grand Est"><name sortKey="Jeandet, Philippe" sort="Jeandet, Philippe" uniqKey="Jeandet P" first="Philippe" last="Jeandet">Philippe Jeandet</name></region></country><country name="République tchèque"><noRegion><name sortKey="Nepovimova, Eugenie" sort="Nepovimova, Eugenie" uniqKey="Nepovimova E" first="Eugenie" last="Nepovimova">Eugenie Nepovimova</name></noRegion><name sortKey="Kuca, Kamil" sort="Kuca, Kamil" uniqKey="Kuca K" first="Kamil" last="Kuca">Kamil Kuca</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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