Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach
Identifieur interne : 001084 ( Main/Exploration ); précédent : 001083; suivant : 001085Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach
Auteurs : Arafat Rahman Oany [Bangladesh] ; Tahmina Sharmin [Bangladesh] ; Afrin Sultana Chowdhury [Bangladesh] ; Tahmina Pervin Jyoti [Bangladesh] ; Md. Anayet Hasan [Bangladesh]Source :
- In Silico Pharmacology [ 2193-9616 ] ; 2015.
Abstract
Ebola virus (EBOV) is such kind of virus which is responsible for 23,825 cases and 9675 deaths worldwide only in 2014 and with an average diseases fatality rate between 25 % and 90 %. Although, medical technology has tried to handle the problems, there is no Food and Drug Administration (FDA)-approved therapeutics or vaccines available for the prevention, post exposure, or treatment of Ebola virus disease (EVD).
In the present study, we used the immunoinformatics approach to design a potential epitope-based vaccine against the RNA-dependent RNA polymerase-L of EBOV. BioEdit v7.2.3 sequence alignment editor, Jalview v2 and CLC Sequence Viewer v7.0.2 were used for the initial sequence analysis for securing the conservancy from the sequences. Later the Immune Epitope Database and Analysis Resource (IEDB-AR) was used for the identification of T-cell and B-cellepitopes associated with type I and II major histocompatibility complex molecules analysis. Finally, the population coverage analysis was employed.
The core epitope “FRYEFTAPF” was found to be the most potential one, with 100 % conservancy among all the strains of EBOV. It also interacted with both type I and II major histocompatibility complex molecules and is considered as nonallergenic in nature. Finally, with impressive cumulative population coverage of 99.87 % for the both MHC-I and MHC-II class throughout the world population was found for the proposed epitope.
To end, the projected peptide gave us a solid stand to propose for vaccine consideration and that might be experimented for its potency in eliciting immunity through humoral and cell mediated immune responses
The online version of this article (doi:10.1186/s40203-015-0011-4) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s40203-015-0011-4
PubMed: 26820892
PubMed Central: 4529428
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach</title><author><name sortKey="Oany, Arafat Rahman" sort="Oany, Arafat Rahman" uniqKey="Oany A" first="Arafat Rahman" last="Oany">Arafat Rahman Oany</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh</nlm:aff><country xml:lang="fr">Bangladesh</country><wicri:regionArea>Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902</wicri:regionArea><wicri:noRegion>Tangail-1902</wicri:noRegion></affiliation></author><author><name sortKey="Sharmin, Tahmina" sort="Sharmin, Tahmina" uniqKey="Sharmin T" first="Tahmina" last="Sharmin">Tahmina Sharmin</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh</nlm:aff><country xml:lang="fr">Bangladesh</country><wicri:regionArea>Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902</wicri:regionArea><wicri:noRegion>Tangail-1902</wicri:noRegion></affiliation></author><author><name sortKey="Chowdhury, Afrin Sultana" sort="Chowdhury, Afrin Sultana" uniqKey="Chowdhury A" first="Afrin Sultana" last="Chowdhury">Afrin Sultana Chowdhury</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong-4331, Bangladesh</nlm:aff><country xml:lang="fr">Bangladesh</country><wicri:regionArea>Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong-4331</wicri:regionArea><wicri:noRegion>Chittagong-4331</wicri:noRegion></affiliation></author><author><name sortKey="Jyoti, Tahmina Pervin" sort="Jyoti, Tahmina Pervin" uniqKey="Jyoti T" first="Tahmina Pervin" last="Jyoti">Tahmina Pervin Jyoti</name><affiliation wicri:level="1"><nlm:aff id="Aff3">Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna-9208, Bangladesh</nlm:aff><country xml:lang="fr">Bangladesh</country><wicri:regionArea>Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna-9208</wicri:regionArea><wicri:noRegion>Khulna-9208</wicri:noRegion></affiliation></author><author><name sortKey="Hasan, Md Anayet" sort="Hasan, Md Anayet" uniqKey="Hasan M" first="Md. 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Anayet Hasan</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong-4331, Bangladesh</nlm:aff><country xml:lang="fr">Bangladesh</country><wicri:regionArea>Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong-4331</wicri:regionArea><wicri:noRegion>Chittagong-4331</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26820892</idno><idno type="pmc">4529428</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529428</idno><idno type="RBID">PMC:4529428</idno><idno type="doi">10.1186/s40203-015-0011-4</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000266</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000266</idno><idno type="wicri:Area/Pmc/Curation">000266</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000266</idno><idno type="wicri:Area/Pmc/Checkpoint">000566</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000566</idno><idno type="wicri:Area/Ncbi/Merge">000589</idno><idno type="wicri:Area/Ncbi/Curation">000589</idno><idno type="wicri:Area/Ncbi/Checkpoint">000589</idno><idno type="wicri:Area/Main/Merge">001086</idno><idno type="wicri:Area/Main/Curation">001084</idno><idno type="wicri:Area/Main/Exploration">001084</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach</title><author><name sortKey="Oany, Arafat Rahman" sort="Oany, Arafat Rahman" uniqKey="Oany A" first="Arafat Rahman" last="Oany">Arafat Rahman Oany</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh</nlm:aff><country xml:lang="fr">Bangladesh</country><wicri:regionArea>Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902</wicri:regionArea><wicri:noRegion>Tangail-1902</wicri:noRegion></affiliation></author><author><name sortKey="Sharmin, Tahmina" sort="Sharmin, Tahmina" uniqKey="Sharmin T" first="Tahmina" last="Sharmin">Tahmina Sharmin</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh</nlm:aff><country xml:lang="fr">Bangladesh</country><wicri:regionArea>Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902</wicri:regionArea><wicri:noRegion>Tangail-1902</wicri:noRegion></affiliation></author><author><name sortKey="Chowdhury, Afrin Sultana" sort="Chowdhury, Afrin Sultana" uniqKey="Chowdhury A" first="Afrin Sultana" last="Chowdhury">Afrin Sultana Chowdhury</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong-4331, Bangladesh</nlm:aff><country xml:lang="fr">Bangladesh</country><wicri:regionArea>Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong-4331</wicri:regionArea><wicri:noRegion>Chittagong-4331</wicri:noRegion></affiliation></author><author><name sortKey="Jyoti, Tahmina Pervin" sort="Jyoti, Tahmina Pervin" uniqKey="Jyoti T" first="Tahmina Pervin" last="Jyoti">Tahmina Pervin Jyoti</name><affiliation wicri:level="1"><nlm:aff id="Aff3">Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna-9208, Bangladesh</nlm:aff><country xml:lang="fr">Bangladesh</country><wicri:regionArea>Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna-9208</wicri:regionArea><wicri:noRegion>Khulna-9208</wicri:noRegion></affiliation></author><author><name sortKey="Hasan, Md Anayet" sort="Hasan, Md Anayet" uniqKey="Hasan M" first="Md. Anayet" last="Hasan">Md. Anayet Hasan</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong-4331, Bangladesh</nlm:aff><country xml:lang="fr">Bangladesh</country><wicri:regionArea>Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong-4331</wicri:regionArea><wicri:noRegion>Chittagong-4331</wicri:noRegion></affiliation></author></analytic><series><title level="j">In Silico Pharmacology</title><idno type="eISSN">2193-9616</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Purpose</title><p>Ebola virus (EBOV) is such kind of virus which is responsible for 23,825 cases and 9675 deaths worldwide only in 2014 and with an average diseases fatality rate between 25 % and 90 %. Although, medical technology has tried to handle the problems, there is no Food and Drug Administration (FDA)-approved therapeutics or vaccines available for the prevention, post exposure, or treatment of Ebola virus disease (EVD).</p></sec><sec><title>Methods</title><p>In the present study, we used the immunoinformatics approach to design a potential epitope-based vaccine against the RNA-dependent RNA polymerase-L of EBOV. BioEdit v7.2.3 sequence alignment editor, Jalview v2 and CLC Sequence Viewer v7.0.2 were used for the initial sequence analysis for securing the conservancy from the sequences. Later the Immune Epitope Database and Analysis Resource (IEDB-AR) was used for the identification of T-cell and B-cellepitopes associated with type I and II major histocompatibility complex molecules analysis. Finally, the population coverage analysis was employed.</p></sec><sec><title>Results</title><p>The core epitope “FRYEFTAPF” was found to be the most potential one, with 100 % conservancy among all the strains of EBOV. It also interacted with both type I and II major histocompatibility complex molecules and is considered as nonallergenic in nature. Finally, with impressive cumulative population coverage of 99.87 % for the both MHC-I and MHC-II class throughout the world population was found for the proposed epitope.</p></sec><sec><title>Conclusion</title><p>To end, the projected peptide gave us a solid stand to propose for vaccine consideration and that might be experimented for its potency in eliciting immunity through humoral and cell mediated immune responses <italic>in vitro</italic> and <italic>in vivo</italic>.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s40203-015-0011-4) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Apweiler, R" uniqKey="Apweiler R">R Apweiler</name></author><author><name sortKey="Bairoch, A" uniqKey="Bairoch A">A Bairoch</name></author><author><name sortKey="Wu, Ch" uniqKey="Wu C">CH 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sortKey="Sidney, J" uniqKey="Sidney J">J Sidney</name></author><author><name sortKey="Kim, Y" uniqKey="Kim Y">Y Kim</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ward, Jj" uniqKey="Ward J">JJ Ward</name></author><author><name sortKey="Mcguffin, Lj" uniqKey="Mcguffin L">LJ McGuffin</name></author><author><name sortKey="Bryson, K" uniqKey="Bryson K">K Bryson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Waterhouse, Am" uniqKey="Waterhouse A">AM Waterhouse</name></author><author><name sortKey="Procter, Jb" uniqKey="Procter J">JB Procter</name></author><author><name sortKey="Martin, Dm" uniqKey="Martin D">DM Martin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wilson, Cc" uniqKey="Wilson C">CC Wilson</name></author><author><name sortKey="Mckinney, D" uniqKey="Mckinney D">D McKinney</name></author><author><name sortKey="Anders, M" uniqKey="Anders M">M Anders</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Bangladesh</li></country></list><tree><country name="Bangladesh"><noRegion><name sortKey="Oany, Arafat Rahman" sort="Oany, Arafat Rahman" uniqKey="Oany A" first="Arafat Rahman" last="Oany">Arafat Rahman Oany</name></noRegion><name sortKey="Chowdhury, Afrin Sultana" sort="Chowdhury, Afrin Sultana" uniqKey="Chowdhury A" first="Afrin Sultana" last="Chowdhury">Afrin Sultana Chowdhury</name><name sortKey="Hasan, Md Anayet" sort="Hasan, Md Anayet" uniqKey="Hasan M" first="Md. Anayet" last="Hasan">Md. Anayet Hasan</name><name sortKey="Jyoti, Tahmina Pervin" sort="Jyoti, Tahmina Pervin" uniqKey="Jyoti T" first="Tahmina Pervin" last="Jyoti">Tahmina Pervin Jyoti</name><name sortKey="Sharmin, Tahmina" sort="Sharmin, Tahmina" uniqKey="Sharmin T" first="Tahmina" last="Sharmin">Tahmina Sharmin</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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