MersV1, Main, Exploration, bibRecord, 001D13

Computer aided prediction and identification of potential epitopes in the receptor binding domain (RBD) of spike (S) glycoprotein of MERS-CoV

Identifieur interne : 001D13 ( Main/Exploration ); précédent : 001D12; suivant : 001D14

Computer aided prediction and identification of potential epitopes in the receptor binding domain (RBD) of spike (S) glycoprotein of MERS-CoV

Auteurs : Mohammad Tuhin Ali [Bangladesh] ; Mohammed Monzur Morshed [Bangladesh] ; Md. Amran Gazi [Bangladesh] ; Md. Abu Musa [Bangladesh] ; Md Golam Kibria [Bangladesh] ; Md Jashim Uddin [Bangladesh] ; Md. Anik Ashfaq Khan [Bangladesh] ; Shihab Hasan [Australie]

Source :

Bioinformation [ 0973-8894 ] ; 2014.

RBID : PMC:4166774

Abstract

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) belongs to the coronaviridae family. In spite of several outbreaks in the very recent years, no vaccine against this deadly virus is developed yet. In this study, the receptor binding domain (RBD) of Spike (S) glycoprotein of MERS-CoV was analyzed through Computational Immunology approach to identify the antigenic determinants (epitopes). In order to do so, the sequences of S glycoprotein that belong to different geographical regions were aligned to observe the conservancy of MERS-CoV RBD. The immune parameters of this region were determined using different in silico tools and Immune Epitope Database (IEDB). Molecular docking study was also employed to check the affinity of the potential epitope towards the binding cleft of the specific HLA allele. The N-terminus RBD (S367-S606) of S glycoprotein was found to be conserved among all the available strains of MERS-CoV. Based on the lower IC₅₀ value, a total of eight potential T-cell epitopes and 19 major histocompatibility complex (MHC) class-I alleles were identified for this conserved region. A 9-mer epitope CYSSLILDY displayed interactions with the maximum number of MHC class-I molecules and projected the highest peak in the B-cell antigenicity plot which concludes that it could be a better choice for designing an epitope based peptide vaccine against MERSCoV considering that it must undergo further in vitro and in vivo experiments. Moreover, in molecular docking study, this epitope was found to have a significant binding affinity of -8.5 kcal/mol towards the binding cleft of the HLA-C*12:03 molecule.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166774

DOI: 10.6026/97320630010533
PubMed: 25258490
PubMed Central: 4166774

Affiliations:

Australie, Bangladesh

Le document en format XML

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<series><title level="j">Bioinformation</title>
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<front><div type="abstract" xml:lang="en"><p>Middle East Respiratory Syndrome Coronavirus (MERS-CoV) belongs to the coronaviridae family. In spite of several outbreaks in
the very recent years, no vaccine against this deadly virus is developed yet. In this study, the receptor binding domain (RBD) of
Spike (S) glycoprotein of MERS-CoV was analyzed through Computational Immunology approach to identify the antigenic
determinants (epitopes). In order to do so, the sequences of S glycoprotein that belong to different geographical regions were
aligned to observe the conservancy of MERS-CoV RBD. The immune parameters of this region were determined using different <italic>in
silico</italic> tools and Immune Epitope Database (IEDB). Molecular docking study was also employed to check the affinity of the potential
epitope towards the binding cleft of the specific HLA allele. The N-terminus RBD (S367-S606) of S glycoprotein was found to be
conserved among all the available strains of MERS-CoV. Based on the lower IC<sub>50</sub> value, a total of eight potential T-cell epitopes and
19 major histocompatibility complex (MHC) class-I alleles were identified for this conserved region. A 9-mer epitope CYSSLILDY
displayed interactions with the maximum number of MHC class-I molecules and projected the highest peak in the B-cell
antigenicity plot which concludes that it could be a better choice for designing an epitope based peptide vaccine against MERSCoV
considering that it must undergo further <italic>in vitro</italic>
 and <italic>in vivo</italic> experiments. Moreover, in molecular docking study, this epitope
was found to have a significant binding affinity of -8.5 kcal/mol towards the binding cleft of the HLA-C*12:03 molecule.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Coleman, Cm" uniqKey="Coleman C">CM Coleman</name>
</author>
<author><name sortKey="Frieman, Mb" uniqKey="Frieman M">MB Frieman</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Assiri, A" uniqKey="Assiri A">A Assiri</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Petrovsky, N" uniqKey="Petrovsky N">N Petrovsky</name>
</author>
<author><name sortKey="Brusic, V" uniqKey="Brusic V">V Brusic</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rota, Pa" uniqKey="Rota P">PA Rota</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Spaan, W" uniqKey="Spaan W">W Spaan</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Raj, Vs" uniqKey="Raj V">VS Raj</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jiang, S" uniqKey="Jiang S">S Jiang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Weiss, Sr" uniqKey="Weiss S">SR Weiss</name>
</author>
<author><name sortKey="Navas Martin, S" uniqKey="Navas Martin S">S Navas-Martin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Du, L" uniqKey="Du L">L Du</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wang, N" uniqKey="Wang N">N Wang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Du, L" uniqKey="Du L">L Du</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sievers, F" uniqKey="Sievers F">F Sievers</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Larsen, Mv" uniqKey="Larsen M">MV Larsen</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Larsen, Mv" uniqKey="Larsen M">MV Larsen</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Peters, B" uniqKey="Peters B">B Peters</name>
</author>
<author><name sortKey="Sette, A" uniqKey="Sette A">A Sette</name>
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</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Tenzer, S" uniqKey="Tenzer S">S Tenzer</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Peters, B" uniqKey="Peters B">B Peters</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bui, H H" uniqKey="Bui H">H-H Bui</name>
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</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Singh, H" uniqKey="Singh H">H Singh</name>
</author>
<author><name sortKey="Raghava, G" uniqKey="Raghava G">G Raghava</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rammensee, H G" uniqKey="Rammensee H">H-G Rammensee</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Morris, Gm" uniqKey="Morris G">GM Morris</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Trott, O" uniqKey="Trott O">O Trott</name>
</author>
<author><name sortKey="Olson, Aj" uniqKey="Olson A">AJ Olson</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kolaskar, A" uniqKey="Kolaskar A">A Kolaskar</name>
</author>
<author><name sortKey="Tongaonkar, Pc" uniqKey="Tongaonkar P">PC Tongaonkar</name>
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</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhou, J" uniqKey="Zhou J">J Zhou</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
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<affiliations><list><country><li>Australie</li>
<li>Bangladesh</li>
</country>
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<tree><country name="Bangladesh"><noRegion><name sortKey="Ali, Mohammad Tuhin" sort="Ali, Mohammad Tuhin" uniqKey="Ali M" first="Mohammad Tuhin" last="Ali">Mohammad Tuhin Ali</name>
</noRegion>
<name sortKey="Gazi, Md Amran" sort="Gazi, Md Amran" uniqKey="Gazi M" first="Md. Amran" last="Gazi">Md. Amran Gazi</name>
<name sortKey="Khan, Md Anik Ashfaq" sort="Khan, Md Anik Ashfaq" uniqKey="Khan M" first="Md. Anik Ashfaq" last="Khan">Md. Anik Ashfaq Khan</name>
<name sortKey="Kibria, Md Golam" sort="Kibria, Md Golam" uniqKey="Kibria M" first="Md Golam" last="Kibria">Md Golam Kibria</name>
<name sortKey="Morshed, Mohammed Monzur" sort="Morshed, Mohammed Monzur" uniqKey="Morshed M" first="Mohammed Monzur" last="Morshed">Mohammed Monzur Morshed</name>
<name sortKey="Musa, Md Abu" sort="Musa, Md Abu" uniqKey="Musa M" first="Md. Abu" last="Musa">Md. Abu Musa</name>
<name sortKey="Uddin, Md Jashim" sort="Uddin, Md Jashim" uniqKey="Uddin M" first="Md Jashim" last="Uddin">Md Jashim Uddin</name>
</country>
<country name="Australie"><noRegion><name sortKey="Hasan, Shihab" sort="Hasan, Shihab" uniqKey="Hasan S" first="Shihab" last="Hasan">Shihab Hasan</name>
</noRegion>
<name sortKey="Hasan, Shihab" sort="Hasan, Shihab" uniqKey="Hasan S" first="Shihab" last="Hasan">Shihab Hasan</name>
</country>
</tree>
</affiliations>
</record>

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Serveur d'exploration MERS

Computer aided prediction and identification of potential epitopes in the receptor binding domain (RBD) of spike (S) glycoprotein of MERS-CoV

Computer aided prediction and identification of potential epitopes in the receptor binding domain (RBD) of spike (S) glycoprotein of MERS-CoV

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Abstract

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