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Online Journal of Bioinformatics ©
Volume 14 (1): 9-14, 2013.
In silico prediction and conservancy analysis of promiscuous epitopes in a novel adenovirus HAdV-65
Rezaul Islam MD1, Lamia Khan1, Amran Gazi MD1, Motaher Hossain1, Farhana Shafrin2, Aubhishek Zaman3, Ahsan Habib Polash2
1Department of Biochemistry and Molecular Biology, 2Molecular Biology Laboratory, 3Department of Genetic Engineering and Biotechnology, University of Dhaka, Bangladesh.
Islam R, Khan L, Gazi A, Hossain M, Shafrin F, Zaman A, Polash AH., In silico prediction and conservancy analysis of promiscuous epitopes in a novel adenovirus HAdV-65, Online J Bioinform., 14 (1):9-14, 2013. Human adenovirus-65 has been associated with infantile gastroenteritis in Bangladesh. In Silico promiscuous epitopes for antigenic capsid proteins and core components of HAdV-65 followed by conservancy analysis in 3 randomly selected genotypes 1, 2 and 3 from NCBI database from different regions were determined. A total of 191,056 candidate promiscuous epitopes for MHC-I molecules based on their binding affinity to different MHC-I alleles were predicted. Epitopes having an IC50 score ≤ 50 nM were selected from TAP, proteasomal, IC50 scores, and number of interactions with epitopes interacting with ≥ 3 MHC-I alleles. From this data, a catalogue of epitopes was created. Hexon protein had most (26.14%), T cell promiscuous epitopes of all the viral antigenic proteins. A total of 219 T cell epitopes were predicted to be promiscuous binders against 51 MHC-II alleles and 23 epitopes were predicted to bind with all of the subjected MHC-II alleles. A considerable number of predicted epitopes having higher affinity for both MHC-I and MHC-II alleles were found to be conserved in other adenovirus genotypes and may be potential candidates for design of epitope vaccines. To our knowledge, this study is the first in silico method to predict promiscuous epitopes for antigenic proteins in HAdV-65 and must be validated by In-vitro tests.
Keywords: Adenovirus; in silico; epitope based vaccine; promiscuous T cell epitopes