Immunoinformatic approach to design CTL epitope based chimeric vaccine targeting multiple serotypes of dengue virus

Abstract

The dengue outbreak is one of the serious global public health concerns. The World Health Organization reported 3,80,171 cases and 113 deaths this year till March 2023, and the rate of infection is expected to increase in vulnerable parts of the world. The development of vaccines is the best approach to managing infectious diseases. All the approved vaccines against dengue are based on live-attenuated virus but they have been questioned for their effectiveness in some population categories. Additionally, random occurrence of four closely related serotypes of dengue virus in humans leading to antibody-dependent enhancement of the disease is yet another cause of vaccine ineffectiveness. Therefore, development of a therapeutic subunit-vaccine based on epitopes from all four serotypes may be expected to provide effective cross-protective cellular immunity. Towards this end, we designed a multi-epitope chimeric immunogen using envelop protein of dengue virus. The MHC-I binding T-cell epitopes were predicted based on their immunogenicity, allergenicity and antigenicity. NetMHCpan-EL4.1 prediction method was used to determine the binding ability of the epitopes with HLA alleles with population coverage of over 99%. The five most potent epitopes based on their immunogenicity, population coverage and prediction scores were selected for each serotype and a multi-epitope polypeptide was generated by merging peptides with AAY linker. The polypeptide was predicted to be an antigen and a non-allergen with a stable tertiary structure retaining a half-life of 4.4 hours in mammalian system. The polypeptide has the potential to elicit effective cellular immune response against all the dengue virus serotypes.

Unveiling a Shield of Hope: A Novel Multiepitope-Based Immunogen for Cross-Serotype Cellular Defense against Dengue Virus

“…The physicochemical properties of the recombinant protein were evaluated in silico, using the tools previously described [ 29 ]. Protein-Sol webserver was used to predict the solubility of the recombinant H2DVE across its three segments: the primary antigen, XCL1 fused with the primary antigen, and the whole H2DVE sequence (including Ig-κ chain, c-myc epitope and 6xHis tag).…”

“…However, the CB6F1 mouse, an F1-hybrid of female BALB/cAnNCrl and male C57BL/6NCrl strains, was chosen to address the Th2 or Th1 bias associated with these strains, respectively [ 30 ]. Further, the use of integrated prediction tools for proteasomal processing, TAP transport, and MHC-I binding ensured that the selected epitopes had substantial potential to elicit a robust T cell response [ 29 ].…”

“…The synthesis of both the codon-optimized nucleotide sequences encoding the antigen was carried out by GeneArt Gene Synthesis services (Thermofisher Scientific, Carlsbad, CA, USA). The physicochemical characterization of H2DVE was performed using in silico webtools, as previously described [ 29 ].…”

“…The proteomics and immunoinformatics study of the immunogen was performed, as described previously [29]. Briefly, the amino acid sequences of the envelope (E) protein of each DENV serotype group were retrieved from the Virus Variation-Dengue Virus Database hosted by the National Center for Biotechnology Information (NCBI) (https: //www.ncbi.nlm.nih.gov/genome/viruses/variation/, accessed on 3 December 2021) [31].…”

“…However, there is a lack of in vivo studies assessing the functionality of these vaccine models, specifically in terms of multivalent cellular response. In our prior research, the in silico evaluation of a multi-epitope chimera based on HLA Class I CTL epitopes displayed potential for eliciting a CD8-specific cellular immune response [ 29 ].…”