title: Towards peptide vaccines against Zika virus: Immunoinformatics combined with molecular dynamics simulations to predict antigenic epitopes of Zika viral proteins.
abstract: 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.
authors.affiliation: Center for Research in Molecular Medicine (CRiMM), The University of Lahore, Pakistan.
authors.forename: Muhammad Usman
authors.initials: MU
authors.lastname: Mirza
authors.affiliation: Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan.
authors.forename: Shazia
authors.initials: S
authors.lastname: Rafique
authors.affiliation: Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan.
authors.forename: Amjad
authors.initials: A
authors.lastname: Ali
authors.affiliation: Division of Science and Technology, University of Education Lahore, Pakistan.
authors.forename: Mobeen
authors.initials: M
authors.lastname: Munir
authors.affiliation: Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, Pakistan.
authors.forename: Nazia
authors.initials: N
authors.lastname: Ikram
authors.affiliation: Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, Pakistan.
authors.forename: Abdul
authors.initials: A
authors.lastname: Manan
authors.affiliation: Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku, Finland.|Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, Turku, Finland.
authors.forename: Outi M H
authors.initials: OM
authors.lastname: Salo-Ahen
authors.affiliation: Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan.|Vice Chancellor Hazara University, Mansehra, Pakistan.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Idrees
mesh_terms: D000595:Amino Acid Sequence; D001402:B-Lymphocytes / Q000276:immunology; D019295:Computational Biology / Q000379:methods*; D015195:Drug Design; D000939:Epitopes / Q000737:chemistry / Q000276:immunology*; D006801:Humans; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D013601:T-Lymphocytes / Q000276:immunology; D013602:T-Lymphocytes, Cytotoxic / Q000276:immunology; D022223:Vaccines, Subunit / Q000008:administration & dosage / Q000276:immunology*; D014764:Viral Proteins / Q000737:chemistry / Q000276:immunology* / Q000378:metabolism; D000071244:Zika Virus / Q000276:immunology* / Q000378:metabolism / Q000502:physiology; D000071243:Zika Virus Infection / Q000276:immunology* / Q000517:prevention & control / Q000821:virology
chemical_list: D000939:Epitopes; D022223:Vaccines, Subunit; D014764:Viral Proteins