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



Mohammad Tuhin ali1*, Mohammed Monzur Morshed1, Md. Amran Gazi2, Md. Abu Musa2, Md Golam Kibria2, Md Jashim Uddin2, Md. Anik Ashfaq Khan3 & Shihab Hasan4,5*



1Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh; 2Laboratory Science Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh; 3Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh; 4Bioinformatics Lab, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia; 5School of Medicine, The University of Queensland (UQ), Brisbane, Queensland, Australia


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Received June 23, 2014; Revised July 07, 2014; Accepted July 08, 2014; Published August 30, 2014



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 MERS-CoV 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.



Epitope, HLA ligand, MERS-CoV, Receptor Binding Domain, Spike glycoprotein.



Tuhin ali et al. Bioinformation 10(8): 533-538 (2014)

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P Kangueane






Biomedical Informatics



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