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.

Structural Basis and Designing of Peptide Vaccine using PE-PGRS Family Protein of Mycobacterium ulcerans – An Integrated Vaccinomics Approach

“…Furthermore, the vaccine-TLR2 complex was found to be stable during MD simulation where protein backbone undergone some microscale-changes (⁓7.67 Å) and mild fluctuations in their side-chain residues that can occur due to the flexible regions Pandey, Bhatt, and Prajapati 2018). These results are in line with the previous study where stabilization of vaccinereceptor complex was achieved within similar time-scale (M. Ali et al 2017;Mirza et al 2016). The hydrogen bond helps in molecular recognition by providing specificity and directionality to the interaction (Hubbard and Kamran Haider 2010).…”

“…Ali et al 2019;M. Ali et al 2017;Ikram et al 2018;Mirza et al 2016;Yasmin and Nabi 2016). Conceptually, multi-epitope vaccines have some advantages over classical (i.e., live and attenuated) and single-epitope vaccines (Lin et al 2016;Lu et al 2017;Saadi, Karkhah, and Nouri 2017).…”

Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: an in silico study

“…Bepipred for linear epitope prediction uses both hidden Markov model and amino acid propensity scales methods. Kolaskar and Tongaonkar evaluate the protein for B cell epitopes using the physicochemical properties of the amino acids and their frequencies of occurrence in recognized B cell epitopes (Kolaskar & Tongaonkar, 1990;Mirza et al, 2016).…”

In Vitro Antidiabetic, Anti-Obesity and Antioxidant Analysis of Ocimum basilicum Aerial Biomass and in Silico Molecular Docking Simulations with Alpha-Amylase and Lipase Enzymes

“…In-silico molecular docking is a rapidly emerging field to understand and predict possible mode of interaction between a ligand and a target biomolecule [14][15][16][17][18], while molecular dynamics simulations presented a plausible way to estimate the dynamic stability and interaction energetics of a protein-ligand complex [18][19][20][21][22][23][24]. It was, therefore, planned to conduct docking analysis of the major constituents of O. basilicum, linalool and estragole, with alpha-amylase and lipase together with their inhibitors.…”