Rational Design of Peptide Vaccines for the Highly Lethal Nipah and Hendra Viruses

Abstract

9The Nipah virus disease is a lethal infection that has led to 40% to 75% fatalities in Malaysia, 10 Bangladesh and India. The reports of human-to-human transmission documented in Bangladesh 11 has raised the specter of pandemic potential and has caused the World Health Organization to list 12 the Nipah virus as one of the pathogens to be considered for development of drugs and vaccines 13 on urgent basis, neither of which exist against the Nipah virus as of now, although many 14 proposals have been made and trials initiated. Given that there are established country-specific 15 differences in the virus' effects and fatalities, meeting the sudden need for a vaccine in case of an 16 epidemic will require design, development and preparation for a peptide vaccine. Thus, we 17 propose a protocol for creating peptide vaccines that can be tailor-made for these specific 18 countries, an approach which is being advocated for the first time. Here, we analyze the surface 19 proteins, Fusion protein and Glycoprotein, of the strains currently affecting the three countries on 20 a large scale and determine the specific country-based epitope differences. 21

New Computational Approach for Peptide Vaccine Design Against SARS-COV-2

“…The comparison shows that all the regions we predicted were present among the published results in Dey et al (2018) Final shortlist for G protein of Hendra virus as per the new method Final shortlists obtained for G protein of Hendra virus for each of the three affected countries as per Dey et al (2018) been highlighted in star in Table 12. Considering the 5 grouped peptide zones obtained, we now performed the IEDB-AR study with the help of the MHC II DRB and DP/DQ alleles as mentioned in Paul et al (2015), which can cover a majority of world population.…”

“…The final shortlist of candidates obtained have been matched with an already established set of results given for the Zika virus E protein in Dey et al (2017). In the same way, for Hendra virus, the surface situated G glycoprotein was chosen and thereby, suitable peptide vaccine stretches obtained using our analysis were compared with similar established results for the G glycoprotein given in Dey et al (2018). Consequently, a majority of the stretches matched with the published results for both the cases, showing that this method, overall, can be utilized for peptide vaccine design for any virus in general.…”

“…2 ASA and PV profiles of the full-length sequence of spike glycoprotein of SARS-CoV-2: The components shown in the figure are: ASA profile (blue), PV profile (red), predicted peptide stretches using the new approach (green) and peptide stretches determined using eyeestimation (black). (Color figure online) 15 full-length sequences of G glycoprotein that were analysed in Dey et al (2018) for obtaining the suiable peptides regions. Therefore, in this analysis, we have used the exact same 15 sequences to determine similar peptide candidates before they are being compared.…”

“…This means, these 5 zones had high solvent accessibility, high conservation from mutation and a broad span, thus making them suitable for vaccine design. These 5 regions have Table 11 Comparison of the final shortlist for peptide candidates for G protein of Hendra virus obtained from the new approach with that given in Dey et al (2018), after the IEDB-AR and BLAST analyses…”

“…In this context, different mathematical models and computational algorithms are used to study the appropriate proteins for their solvent exposure, their extent of mutation and other attributes. In our previous studies as in Dey et al (2017Dey et al ( , 2018Dey et al ( , 2016 and Ghosh et al (2012), graphical plots and manual observations have been relied upon to identify the regions of the virus, which have high surface exposure and low mutation probability i.e., more conserved. But there is need for a more robust and automated mathematical or computational approach that bypasses manual interventions so that the most highly conserved and surface accessible peptides can be figured out precisely through mathematical descriptors.…”