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Multi-target Parallel Processing Approach for Gene-to-structure Determination of the Influenza Polymerase PB2 Subunit
Published on: June 28, 2013
Computational structural dynamics and immunoinformatic analysis of EIEC IpaH4.5 targeting immunoprophylaxis design
Pinkan Sadhukhan1, Nibedita Mahata2
1Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, 713209, India.
Insights
A novel nasal vaccine candidate targeting bacillary dysentery was identified using the EIEC IpaH4.5 protein. This peptide-based vaccine shows potential for broad population coverage and activates both humoral and cellular immunity.
Area of Science:
- Immunology and Vaccinology
- Microbial Pathogenesis
- Computational Biology
Background:
- Bacillary dysentery remains a significant global health issue, particularly affecting infants in developing countries.
- The absence of a licensed vaccine and the rise of antimicrobial resistance necessitate alternative immunoprophylactic strategies.
- The Entero-invasive Escherichia coli (EIEC) IpaH4.5 protein is a virulence-associated factor conserved across Shigella species.
Purpose of the Study:
- To identify and characterize a nasal subunit vaccine candidate against bacillary dysentery.
- To investigate the immunogenic potential of a specific peptide derived from the EIEC IpaH4.5 protein.
Main Methods:
- Selection of the EIEC IpaH4.5 protein as an antigenic source and identification of a 29-mer protective antigenic peptide (PAP).
- In silico analysis including epitope mapping, HLA-binding prediction, T-cell epitope screening (IFN-γ, IL-4, IL-10 induction), and population coverage assessment.
- Structural modeling (ab-initio and homology modeling), molecular dynamics simulations, and binding energy calculations (MM/PBSA, MM/GBSA) of the IpaH4.5-TLR4 complex.
- In silico cloning for theoretical expression feasibility.
Main Results:
- A 29-mer PAP containing B-cell, CTL, and HTL epitopes was identified within the EIEC IpaH4.5 N-terminal region.
- Screened T-cell epitopes exhibited strong HLA-binding potential and induced key cytokine responses (IFN-γ, IL-4, IL-10), with high global population coverage (99.68%).
- Molecular dynamics simulations confirmed a stable and energetically favorable interaction between IpaH4.5 and human Toll-like receptor 4 (TLR4).
- In silico analysis predicted activation of both humoral and cellular immunity, and theoretical expression feasibility.
Conclusions:
- The identified PAP from EIEC IpaH4.5 shows significant promise as a nasal subunit vaccine candidate against bacillary dysentery.
- The in silico findings suggest broad applicability due to high population coverage and robust immune activation.
- Further experimental validation is crucial to confirm the protective immunogenicity of this vaccine candidate.
Abstract:
Bacillary dysentery continues as a latent global health challenge, mainly affecting infants in developing nations. The lack of a licensed vaccine and spread of antimicrobial resistance, underlines the need for an alternative immunoprophylactic management. The present study was to identify a nasal subunit vaccine candidate against bacillary dysentery. For this, the virulence-associated EIEC IpaH4.5 protein, also conserved across pathogenic Shigella species, was selected as the antigenic source. A 29-mer protective antigenic peptide (PAP) (44TTTENRIQAVRLLKICLDTREPVLNLSLL72) was identified within its N-terminal region, consisted of overlapping two B-cell, one CTL, and seven HTL epitopes. Both, T-cell epitopes were screened for strong HLA-binding potential (IC50 < 500 nM). Screened HTL epitopes positively induced IFN-γ, IL-4, and IL-10 and were non-homologous to human. Epitope clustering underscored the PAP region, having 99.68% world-wide population coverage. The 3D model of EIEC IpaH4.5 was predicted using ab-initio method (c-score: 0.44). Whereas, homology modelling was utilized to model the extracellular human Toll-like receptors (TLR1/2/4/5/6) corresponding to pulmonary macrophages. A 100 ns molecular dynamics simulation revealed a stable RMSD (Backbone) plot with an average fluctuation of 0.92 ± 0.05 nm for IpaH4.5 and TLR 4 complex. MM/PBSA analysis yielded an average ∆G: - 76.65 ± 8.12 kcal/mol, while MM/GBSA analysis produced a value of - 52.40 ± 6.45 kcal/mol, indicating an energetically favourable complex. In-silico immune titers of the IpaH4.5, was seen to activate both humoral and cellular immunity. Finally, in-silico cloning aided theoretical expression feasibility of the EIEC IpaH4.5. However, real-world experimental validation would be needed for evaluating its protective immunogenicity.
