Multi-epitopes vaccine design for surface glycoprotein against SARS-CoV-2 using immunoinformatic approach

Arshad, Sarmad Frogh; Rehana, Rehana; Saleem, Muhammad Asif; Usman, Muhammad; Arshad, Hasan Junaid; Rizwana, Rizwana; Shakeela, Shakeela; Rukh, Asma Shah; Khan, Imran Ahmad; Hayssam, M. Ali; Anwar, Muhammad

doi:10.1016/j.heliyon.2024.e24186

Cited by 4 publications

(1 citation statement)

References 51 publications

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“…Importantly, these in-silico designed vaccine constructs have undergone experimental validation, confirming their potential efficacy in immunological responses ( 108 ). It is expected that the vaccination models developed in this work will exhibit advantageous properties, such as strong antigenicity combined with minimal allergenicity and toxicity ( 109 ). Predicted physicochemical characteristics indicate that the vaccine designs have increased hydrophilicity and stability ( 70 ).…”

Section: Discussionmentioning

confidence: 99%

Designing of a multi-epitopes based vaccine against Haemophilius parainfluenzae and its validation through integrated computational approaches

Ghaffar,

Tahir,

Muhammad

et al. 2024

Front. Immunol.

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Haemophilus parainfluenzae is a Gram-negative opportunist pathogen within the mucus of the nose and mouth without significant symptoms and has an ability to cause various infections ranging from ear, eye, and sinus to pneumonia. A concerning development is the increasing resistance of H. parainfluenzae to beta-lactam antibiotics, with the potential to cause dental infections or abscesses. The principal objective of this investigation is to utilize bioinformatics and immuno-informatic methodologies in the development of a candidate multi-epitope Vaccine. The investigation focuses on identifying potential epitopes for both B cells (B lymphocytes) and T cells (helper T lymphocytes and cytotoxic T lymphocytes) based on high non-toxic and non-allergenic characteristics. The selection process involves identifying human leukocyte antigen alleles demonstrating strong associations with recognized antigenic and overlapping epitopes. Notably, the chosen alleles aim to provide coverage for 90% of the global population. Multi-epitope constructs were designed by using suitable linker sequences. To enhance the immunological potential, an adjuvant sequence was incorporated using the EAAAK linker. The final vaccine construct, comprising 344 amino acids, was achieved after the addition of adjuvants and linkers. This multi-epitope Vaccine demonstrates notable antigenicity and possesses favorable physiochemical characteristics. The three-dimensional conformation underwent modeling and refinement, validated through in-silico methods. Additionally, a protein-protein molecular docking analysis was conducted to predict effective binding poses between the multi-epitope Vaccine and the Toll-like receptor 4 protein. The Molecular Dynamics (MD) investigation of the docked TLR4-vaccine complex demonstrated consistent stability over the simulation period, primarily attributed to electrostatic energy. The docked complex displayed minimal deformation and enhanced rigidity in the motion of residues during the dynamic simulation. Furthermore, codon translational optimization and computational cloning was performed to ensure the reliability and proper expression of the multi-Epitope Vaccine. It is crucial to emphasize that despite these computational validations, experimental research in the laboratory is imperative to demonstrate the immunogenicity and protective efficacy of the developed vaccine. This would involve practical assessments to ascertain the real-world effectiveness of the multi-epitope Vaccine.

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Section: Discussionmentioning

confidence: 99%

Designing of a multi-epitopes based vaccine against Haemophilius parainfluenzae and its validation through integrated computational approaches

Ghaffar,

Tahir,

Muhammad

et al. 2024

Front. Immunol.

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Immunoinformatics-Based Design of Broad-Spectrum Multi-Epitope Vaccines Targeting Mutations in Emerging SARS-CoV-2 Variants

Mei,

Xie,

Lin

et al. 2024

Preprint

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The ongoing COVID-19 pandemic, intensified by emerging SARS-CoV-2 mutations, highlights the urgent need for enhanced vaccines. Despite considerable efforts in vaccine design, improvements are still required in formulating vaccines targeting the novel coronavirus. This study, utilized immunoinformatics and reverse vaccinology to design multi-epitope vaccines targeting emerging variations. B and T cell epitopes were generated by analyzing the mutation sites of the prevalent variant strains, and two vaccines were designed by linking with two different adjuvants. Interaction of the model vaccines with four Toll-like receptors (TLR) revealed a relatively high affinity between vaccines and immune receptors. Codon optimization and computational cloning were conducted to validate the robustness of the multi-epitope vaccines and immunogenic simulations were performed to assess the antigenicity and antibody generation capability of the vaccine. The L455S mutation in the JN.1 variant and its adjacent F456L mutation on antibody effectiveness against the XBB variant revealed that 15 antibody structures maintained a certain level of binding affinity. This study offers an immunological evaluation from a mutation-centric perspective and integrates co-evolutionary analysis with immunoinformatics to design effective multi-epitope vaccines targeting various SARS-CoV-2 strains. The methodologies applied in this research can also be extended to the vaccine development for other pathogens.

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Exploring glutathione transferase and Cathepsin L-like proteinase for designing of epitopes-based vaccine against Fasciola hepatica by immunoinformatics and biophysics studies

Alhassan,

Ullah,

Niazy

et al. 2024

Front. Immunol.

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Fasciolosis is a zoonotic infection and is considered a developing deserted tropical illness threatening ruminant productivity and causing financial losses. Herein, we applied immunoinformatics and biophysics studies to develop an epitopes vaccine against Fasciola hepatica using glutathione transferase and Cathepsin L-like proteinase as possible vaccine candidates. Using the selected proteins, B- and T-cell epitopes were predicted. After epitopes prediction, the epitopes were clarified over immunoinformatics screening, and only five epitopes, EFGRWQQEKCTIDLD, RRNIWEKNVKHIQEH, FKAKYLTEMSRASDI, TDMTFEEFKAKYLTE, and YTAVEGQCR were selected for vaccine construction; selected epitopes were linked with the help of a GPGPG linker and attached with an adjuvant through another linker, EAAAK linker. Cholera toxin B subunit was used as an adjuvant. The ExPASy ProtParam tool server predicted 234 amino acids, 25.86257 kDa molecular weight, 8.54 theoretical pI, 36.86 instability index, and −0.424 grand average of hydropathicity. Molecular docking analysis predicted that the vaccine could activate the immune system against F. hepatica. We calculated negative binding energy values. A biophysics study, likely molecular docking molecular dynamic simulation, further validated the docking results. In molecular dynamic simulation analysis, the top hit docked compounds with the lowest binding energy values were subjected to MD simulation; the simulation analysis showed that the vaccine and immune cell receptors are stable and can activate the immune system. MMGBSA of −146.27 net energy (kcal/mol) was calculated for the vaccine–TLR2 complex, while vaccine–TLR4 of −148.11 net energy (kcal/mol) was estimated. Furthermore, the C-ImmSim bioinformatics tool predicted that the vaccine construct can activate the immune system against F. hepatica, eradicate the infection caused by F. hepatica, and reduce financial losses that need to be spent while protecting against infections of F. hepatica. The computational immune simulation unveils that the vaccine model can activate the immune system against F. hepatica; hence, the experimental scientist can validate the finding accomplished through computational approaches.

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Multi-epitopes vaccine design for surface glycoprotein against SARS-CoV-2 using immunoinformatic approach

Cited by 4 publications

References 51 publications

Designing of a multi-epitopes based vaccine against Haemophilius parainfluenzae and its validation through integrated computational approaches

Designing of a multi-epitopes based vaccine against Haemophilius parainfluenzae and its validation through integrated computational approaches

Immunoinformatics-Based Design of Broad-Spectrum Multi-Epitope Vaccines Targeting Mutations in Emerging SARS-CoV-2 Variants

Exploring glutathione transferase and Cathepsin L-like proteinase for designing of epitopes-based vaccine against Fasciola hepatica by immunoinformatics and biophysics studies

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