# In silico design of a multi-epitope vaccine targeting DENV-1 and DENV-3

## TL;DR

Researchers designed a potential vaccine targeting DENV-1 and DENV-3 using computational methods, focusing on immune responses and vaccine stability.

## Contribution

A novel in silico multi-epitope vaccine design targeting DENV-1 and DENV-3 co-infection using NS1 and E proteins.

## Key findings

- The vaccine construct showed favorable antigenicity, stability, and non-allergenic properties.
- Molecular docking and simulations confirmed strong binding and stable interactions with TLR3.
- Immune simulations predicted strong B and T cell memory responses with elevated IgG and cytokine levels.

## Abstract

The co-infection of DENV-1 and DENV-3 during endemic outbreaks can be potentially fatal and complicate the diagnostic process. In our study, we have focused on the development of a multiepitope vaccine against DENV-1 and DENV-3 co-infection, utilizing non-structural protein 1 (NS1) and envelope protein (E) as key antigens. B cell and T cell epitopes were predicted for their immunogenicity, antigenicity, and ability to elicit an IFN-γ response. The final construct showed predicted stability (Instability Index: 30.63), antigenicity (0.5509), non-allergenicity, and hydrophilic character (GRAVY: −0.226) based on computational assessments. Tertiary structural validation revealed 90.1% of residues in a favoured region. Molecular docking revealed a stronger binding of the DENV-TLR3 complex. The receptor and vaccine have stable interactions, according to molecular dynamics simulations and free energy estimations (-90 kJ/mol). Strong B and T cell memory responses were demonstrated by immune simulations, accompanied by increased levels of IgG, IFN-γ, and TGF-β. The codon-optimized sequence was successfully cloned into the pcDNA™3.1/V5-His-TOPO® expression vector for potential experimental validation. As a result of this in silico approach, a targeted vaccine for DENV-1 and DENV-3 co-infections is possible, which merits further experimental evaluation.

The online version contains supplementary material available at 10.1038/s41598-026-35678-0.