Immunoinformatic Identification of Potential Epitopes

Desai, Priti; Tarwadi, Divya; Pandya, Bhargav; Yagnik, Bhrugu

doi:10.1007/978-1-0716-0389-5_14

Cited by 3 publications

(1 citation statement)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Moreover, it is essential to predict epitopes that can trigger both B and T cells accurately and incorporate them into the vaccine construction. The HTL epitopes to be selected must be capable of producing IFN-γ, IL-4, and IL-10 cytokines, which play key functions against pathogens (Desai et al, 2020 ). All immune cells die once the infections is eradicated, apart from memory cells.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of the whole proteome to design a novel mRNA-based vaccine against multidrug-resistant Serratia marcescens

et al. 2022

View full text Add to dashboard Cite

Serratia marcescens, a Gram-negative bacterium, is one of the known disease-causing pathogens. It is resistant to ampicillin, macrolides, cephalosporins, cefotaxime, and ceftazidime. The only antibiotic that has been proven to be effective against S. marcescens is gentamicin. By causing epigenetic alterations, bacteria can also become resistant to all antibiotics. Many epigenetically related proteins were studied, and four proteins were selected in this regard for epitope evaluation and their subsequent use in the development of a messenger ribonucleic acid (mRNA) vaccine. A series of immune-informatics tools used to build this mRNA vaccine elicited cellular and humoral immunity. Molecular docking between epitopes and alleles of the major histocompatibility complex (MHC) was performed. The vaccine was developed using 37 epitopes, an adjuvant that is a TLR-4 agonist known as resuscitation-promoting factor E (RpfE), subcellular trafficking structures, secretion boosters, and linkers. This proposed architecture was found to cover 99.6% of the population during testing. During testing, it was proven that it was both effective and safe. To confirm our idea, we performed an in silico immunological simulation of vaccination. The codon was also optimized to ensure that the mRNA reached the cytoplasm of a human host and underwent efficient translation. TLR-4 and TLR-3 were also docked against the secondary and tertiary structures of the vaccine peptide. Furthermore, the vaccine's stability was confirmed by molecular dynamics simulation. In summary, this vaccine construct can be a potential candidate against S. marcescens and is suitable for in vitro analyses to validate its effectiveness.

show abstract

Section: Discussionmentioning

confidence: 99%

Evaluation of the whole proteome to design a novel mRNA-based vaccine against multidrug-resistant Serratia marcescens

et al. 2022

View full text Add to dashboard Cite

show abstract

Immunoinformatics-Driven Multiepitope Vaccine Targeting Streptococcus mutans for Dental Caries Prevention

Pangabam,

Naorem,

Teli

et al. 2023

Preprint

View full text Add to dashboard Cite

Streptococcus mutans is a major causative agent of dental caries and associated infections, posing significant challenges in oral healthcare. To develop an effective vaccine against S. mutans, we employed an immunoinformatics approach to identify potential vaccine candidates and design a multiepitope vaccine. The genomes of S. mutans were analyzed, and five core-proteins (PBP2X, PBP2b, MurG, ATP-F, and AGPAT) were selected as vaccine candidates based on antigenicity and conservation. Linear B-cell and T-cell epitopes were predicted from these proteins, and four B-cell epitopes and ten T-cell epitopes were chosen for vaccine construction. The multiepitope vaccine comprised 10 CTL epitopes, 5 HTL epitopes, and 5 linear B-cell epitopes linked with appropriate linkers. A 50S ribosomal L7/L12 protein was used as an adjuvant at the N-terminal. The final vaccine construct exhibited high antigenicity, solubility, and stability. The tertiary structure was modeled using AlphaFold v.2 and refined with GalaxyRefine. The refined 3D model had improved quality scores and structural stability. Molecular docking simulations revealed strong interactions between the vaccine and Toll-Like Receptors (TLRs). In silico immune simulation demonstrated the vaccine's ability to trigger both humoral and cell-mediated immune responses. The vaccine design strategy presented here provides a promising platform for developing a potential multiepitope vaccine against S. mutans, offering a novel approach to combat dental caries and associated infections. Further, experimental evaluations should be performed to validate its efficacy and safety as a potential vaccine candidate for dental health.

show abstract

Immunoinformatics Design of a Multiepitope Vaccine (MEV) Targeting Streptococcus mutans: A Novel Computational Approach

Naorem,

Pangabam,

Bora

et al. 2024

Pathogens

View full text Add to dashboard Cite

Dental caries, a persistent oral health challenge primarily linked to Streptococcus mutans, extends its implications beyond dental decay, affecting over 4 billion individuals globally. Despite its historical association with childhood, dental caries often persists into adulthood with prevalence rates ranging from 60 to 90% in children and 26 to 85% in adults. Currently, there is a dearth of multiepitope vaccines (MEVs) specifically designed to combat S. mutans. To address this gap, we employed an immunoinformatics approach for MEV design, identifying five promising vaccine candidates (PBP2X, PBP2b, MurG, ATP-F, and AGPAT) based on antigenicity and conservation using several tools including CELLO v.2.5, Vaxign, v2.0, ANTIGENpro, and AllerTop v2.0 tools. Subsequent identification of linear B-cell and T-cell epitopes by SVMTrip and NetCTL/NetMHC II tools, respectively, guided the construction of a MEV comprising 10 Cytotoxic T Lymphocyte (CTL) epitopes, 5 Helper T Lymphocyte (HTL) epitopes, and 5 linear B-cell epitopes, interconnected by suitable linkers. The resultant MEV demonstrated high antigenicity, solubility, and structural stability. In silico immune simulations showcased the MEV’s potential to elicit robust humoral and cell-mediated immune responses. Molecular docking studies revealed strong interactions between the MEV construct and Toll-Like Receptors (TLRs) and Major Histocompatibility Complex (MHC) molecules. Remarkably, the MEV–TLR-4 complexes exhibited a low energy score, high binding affinity, and a low dissociation constant. The Molecular Dynamic (MD) simulation analysis suggested that MEV–TLR-4 complexes had the highest stability and minimal conformational changes indicating equilibrium within 40 nanosecond time frames. Comprehensive computational analyses strongly support the potential of the proposed MEV to combat dental caries and associated infections. The study’s computational assays yielded promising results, but further validation through in vitro and in vivo experiments is needed to assess its efficacy and safety.

show abstract

Immunoinformatic Identification of Potential Epitopes

Cited by 3 publications

References 30 publications

Evaluation of the whole proteome to design a novel mRNA-based vaccine against multidrug-resistant Serratia marcescens

Evaluation of the whole proteome to design a novel mRNA-based vaccine against multidrug-resistant Serratia marcescens

Immunoinformatics-Driven Multiepitope Vaccine Targeting Streptococcus mutans for Dental Caries Prevention

Immunoinformatics Design of a Multiepitope Vaccine (MEV) Targeting Streptococcus mutans: A Novel Computational Approach

Contact Info

Product

Resources

About