Immunoinformatics and reverse vaccinomic approaches for effective design

Parihar, Arpana; Malviya, Shivani; Khan, Raju

doi:10.1016/b978-0-323-91172-6.00004-2

Cited by 4 publications

(1 citation statement)

References 61 publications

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“…Reverse vaccinology (RV), which analyses the complete viral genome using computer software to detect pathogen antigens/epitopes, is the most practical use of bioinformatics in vaccine production that can best benefit the emergence of newer mRNA vaccines. [30,31] Advances in immune profiling technologies, such as flow cytometry mass cytometry (CyTOF) and high-throughput and high-dimensional sequencing, have enabled in-depth analyses of immune responses at the single-cell level. [32] These technologies allow researchers to identify and quantify specific T-cell subsets, cytokine profiles, and immune activation markers associated with protection.…”

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confidence: 99%

mRNA Vaccines: A Prospective Analysis of Long-term, Multi-target, and Autoimmune Disorders

Niazi

2023

Preprint

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The new class of mRNA vaccines is studied extensively, leading to many novel prospects based on the pivotal success of vaccines against the SARS-Cov-2 virus. Many novel mechanisms of immune response discovered have led to the possibility of mutation-resistant vaccines by combining multiple conserved epitopes as antigens to manipulate the T-cell and B-cell responses; these antigens can also come from different organisms, providing protection against numerous diseases and of most tremendous significance is the utility of mRNA vaccines in preventing and treating more than 100 autoimmune disorders. This is a significant humanitarian breakthrough given the ease and faster and low cost of mRNA vaccines, being a chemical entity. This paper provides a prospective analysis of mRNA vaccines with much broader applications than anticipated when these vaccines entered treating SARS-Cov-2 infections.

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confidence: 99%

mRNA Vaccines: A Prospective Analysis of Long-term, Multi-target, and Autoimmune Disorders

Niazi

2023

Preprint

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In silico design of an epitope-based vaccine against PspC in Streptococcus pneumoniae using reverse vaccinology

Nahian,

Shahab,

Mazumder

et al. 2023

Journal of Genetic Engineering and Biotechnology

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Background Streptococcus pneumoniae is a major pathogen that poses a significant hazard to global health, causing a variety of infections including pneumonia, meningitis, and sepsis. The emergence of antibiotic-resistant strains has increased the difficulty of conventional antibiotic treatment, highlighting the need for alternative therapies such as multi-epitope vaccines. In this study, immunoinformatics algorithms were used to identify potential vaccine candidates based on the extracellular immunogenic protein Pneumococcal surface protein C (PspC). Method The protein sequence of PspC was retrieved from NCBI for the development of the multi-epitope vaccine (MEV), and potential B cell and T cell epitopes were identified. Linkers including EAAAK, AAY, and CPGPG were used to connect the epitopes. Through molecular docking, molecular dynamics, and immunological simulation, the affinity between MEV and Toll-like receptors was determined. After cloning the MEV construct into the PET28a ( +) vector, SnapGene was used to achieve expression in Escherichia coli. Result The constructed MEV was discovered to be stable, non-allergenic, and antigenic. Microscopic interactions between ligand and receptor are confirmed by molecular docking and molecular dynamics simulation. The use of an in-silico cloning approach guarantees the optimal expression and translation efficiency of the vaccine within an expression vector. Conclusion Our study demonstrates the potential of in silico approaches for designing effective multi-epitope vaccines against S. pneumoniae. The designated vaccine exhibits the required physicochemical, structural, and immunological characteristics of a successful vaccine against SPN. However, laboratory validation is required to confirm the safety and immunogenicity of the proposed vaccine design.

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Designing novel multiepitope mRNA vaccine targeting Hendra virus (HeV): An integrative approach utilizing immunoinformatics, reverse vaccinology, and molecular dynamics simulation

Mahdeen,

Hossain,

Masum

et al. 2024

PLoS ONE

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Human and animal health is threatened by Hendra virus (HeV), which has few treatments. This in-silico vaccine design study focuses on HeV G (glycoprotein), F (fusion protein), and M (matrix protein). These proteins were computationally assessed for B and T-cell epitopes after considering HeV strain conservation, immunogenicity, and antigenicity. To improve vaccination immunogenicity, these epitopes were selectively ligated into a multiepitope construct. To improve vaccination longevity and immunological response, adjuvants and linkers were ligated. G, F, and M epitopes were used to create an mRNA HeV vaccine. Cytotoxic, helper, and linear B-lymphocytes’ epitopes are targeted by this vaccine. The population coverage analysis demonstrates that multi-epitope vaccination covers 91.81 percent of CTL and 98.55 percent of HTL epitopes worldwide. GRAVY evaluated the vaccine’s well-characterized physicochemical properties -0.503, indicating solubility and functional stability. Structure analysis showed well-stabilized 2° and 3° structures in the vaccine, with alpha helix, beta sheet, and coil structures (Ramachandran score of 88.5% and Z score of -3.44). There was a strong affinity as shown by docking tests with TLR-4 (central score of -1139.4 KJ/mol) and TLR-2 (center score of -1277.9 KJ/mol). The coupled V-apo, V-TLR2, and V-TLR4 complexes were tested for binding using molecular dynamics simulation where extremely stable complexes were found. The predicted mRNA structures provided significant stability. Codon optimization for Escherichia. coli synthesis allowed the vaccine to attain a GC content of 46.83% and a CAI score of 1.0, which supports its significant expression. Immunological simulations indicated vaccine-induced innate and adaptive immune reactions. Finally, this potential HeV vaccine needs more studies to prove its efficacy and safety.

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Immunoinformatics and reverse vaccinomic approaches for effective design

Cited by 4 publications

References 61 publications

mRNA Vaccines: A Prospective Analysis of Long-term, Multi-target, and Autoimmune Disorders

mRNA Vaccines: A Prospective Analysis of Long-term, Multi-target, and Autoimmune Disorders

In silico design of an epitope-based vaccine against PspC in Streptococcus pneumoniae using reverse vaccinology

Designing novel multiepitope mRNA vaccine targeting Hendra virus (HeV): An integrative approach utilizing immunoinformatics, reverse vaccinology, and molecular dynamics simulation

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