Towards peptide vaccines against Zika virus: Immunoinformatics combined with molecular dynamics simulations to predict antigenic epitopes of Zika viral proteins

MU Mirza, S Rafique, A Ali, M Munir, N Ikram, A Manan, Outi Salo-Ahen, M Idrees

Research output: Contribution to journalArticleScientificpeer-review

98 Citations (Scopus)


The recent outbreak of Zika virus (ZIKV) infection in Brazil has developed to a global health concern due to its likely association with birth defects (primary microcephaly) and neurological complications. Consequently, there is an urgent need to develop a vaccine to prevent or a medicine to treat the infection. In this study, immunoinformatics approach was employed to predict antigenic epitopes of Zika viral proteins to aid in development of a peptide vaccine against ZIKV. Both linear and conformational B-cell epitopes as well as cytotoxic T-lymphocyte (CTL) epitopes were predicted for ZIKV Envelope (E), NS3 and NS5 proteins. We further investigated the binding interactions of altogether 15 antigenic CTL epitopes with three class I major histocompatibility complex (MHC I) proteins after docking the peptides to the binding groove of the MHC I proteins. The stability of the resulting peptide-MHC I complexes was further studied by molecular dynamics simulations. The simulation results highlight the limits of rigid-body docking methods. Some of the antigenic epitopes predicted and analyzed in this work might present a preliminary set of peptides for future vaccine development against ZIKV.

Original languageUndefined/Unknown
Pages (from-to)1–17
JournalScientific Reports
Publication statusPublished - 2016
MoE publication typeA1 Journal article-refereed


  • Zika virus
  • immunoinformatics
  • bioinformatics
  • epitope prediction
  • peptide vaccine

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