# Molecular insights into pangenome localization and constructs design for Hemophilus influenza vaccine

## TL;DR

This paper presents a new multiepitope vaccine candidate for Haemophilus influenza by combining pangenome analysis and immunoinformatics to target key virulence proteins.

## Contribution

The study introduces a novel vaccine design pipeline integrating pan-genome analysis and in silico methods for H. influenzae.

## Key findings

- Key virulence proteins like Protein E, PilA, and TolC were identified as vaccine targets.
- The MEV candidate showed structural stability and strong receptor affinity through simulations.
- The approach offers broad coverage against pathogenic and multidrug-resistant H. influenzae strains.

## Abstract

Haemophilus influenza, a major contributor to respiratory infections such as pneumonia, meningitis, sinusitis, chronic bronchitis, and acute otitis, poses a significant public health challenge, driven by rising antibiotic resistance particularly among the non-typeable H. influenza (NTHi) strains given their ability to evade immune surveillance. To address this, we employed a comprehensive immunoinformatics pipeline integrated with extensive pan-genome analysis of 59 strains of H. influenzae to design a novel multiepitope vaccine (MEV) candidate targeting most virulent and clinically significant proteins. Key surface exposed and virulence associated proteins, including Protein E, PilA, Protein D, P4, TolC, YadA, and HifC were prioritized based on their roles in bacterial adhesion, immune evasion, biofilm formation, and nutrient acquisition. Advanced in silico epitope prediction and verification strategies were utilized to map highly immunogenic regions across these proteins, followed by codon optimization to enhance expression efficiency in human systems. To further stabilize the vaccine construct, we performed disulfide engineering to enhance structural integrity and resilience. Comprehensive validation through in silico immune simulations, molecular dynamics (MD) simulations and binding free energy calculations confirmed the structural stability, immunogenic potential, and strong receptor affinity of the MEV candidate. Phylogenetic and virulence factor analysis further corroborated the broad coverage of the pathogenic relevance of the selected proteins. Together, our integrative approach presents a robust pipeline for rational vaccine design, offering a promising avenue toward combating multidrug resistant and immune evasive H. influenza strains.

The online version contains supplementary material available at 10.1038/s41598-025-03536-0.