Introduction MRSA is a multi-drug-resistant bacteria responsible for severe infections that has become a major health concern. Due to constraints of traditional methods, there is a need for developing a new approach to prevent the MRSA-related infections by targeting key pathogens. Methods Initially, the subtractive genomics was applied to the MRSA proteome to identify non-homologous, essential, and virulence targets using comparative BLAST-based screening. Further, immunoinformatic tools were employed for B- and T-cell epitope prediction and vaccine construction with appropriate adjuvants and linkers, followed by immune simulation and molecular docking with immune receptors. Results Comparative metabolic pathway analysis identified 294 MRSA pathway proteins, with acetolactate synthase (ALS) as a non-homologous, essential, and virulent protein that is involved in the branched amino acid biosynthesis pathway. The constructed ALS vaccine consists of 3 B-cell and 19 T-cell epitopes exhibited stable immunological features with 97.55% global population coverage. Molecular docking revealed that ALS exhibited a superior binding affinity with the TLR4 receptor (−1,438.7 kcal/mol) than the TLR2 receptor (−1,103.5 kcal/mol), which was further confirmed by high structural stability and compactness analysis. Immune simulations also exhibited elevated IgM, IgG subtypes, and cytokine productions, suggesting a robust humoral and cellular immunity. Discussion Identified ALS highlights its biological relevance in MRSA survival. The stability predictions with TLR4 suggested effective activation of innate immunity that may enhance antigen presentation and downstream adaptive immunity. The validation of the ALS vaccine’s safety and immunogenicity further requires comprehensive in vitro and in vivo examinations. Conclusion Thus, ALS is recognized as a promising MRSA vaccine candidate and has the potential to activate immune responses effectively.

During antiviral immunity, MHC‑I molecules display endogenous peptides to CD8+ T‑cell receptors, prompting cytotoxic elimination of infected cells. The present study focused on dominant epitopes derived from the nucleocapsid protein (NP) of Hantaan virus (HTNV) and revealed their high affinity for the HLA‑I and H‑2 superfamilies. Through immunogenicity and conservation analyses, four selective epitopes were precisely identified. Molecular docking validated the binding characteristics of selective epitopes with MHC‑I molecules. Bidirectional hierarchical clustering analysis uncovered complex interaction patterns between NP 9‑mer peptides and MHC‑I haplotypes. Moreover, in‑depth investigation of 11 HTNV variants revealed three amino acid substitutions (I241S, E242A and F384I) within the four selective epitopes; however, these substitutions did not significantly affect the pan‑HLA‑I immunoreactivity of these epitopes. Safety assessments highlighted the potential of four selective epitopes for practical applications. Utilizing ELISpot, ELISA and flow cytometry, the immunogenicity of these selective epitopes was comprehensively confirmed. In summary, the present study thoroughly evaluated the pan‑MHC‑I immunoreactivity of HTNV NP, providing a robust foundation for developing effective epitope vaccines for population immunity.

Syphilis, caused by Treponema pallidum, remains a major global health burden. Given the key role of T cell-mediated immunity in T. pallidum clearance, this study evaluates a Tp0136-derived T-cell epitope (Tp0136T1) delivered via two platforms: lipid nanoparticle-encapsulated nucleoside-modified mRNA (LNP-mRNA) and Pyrococcus furiosus thioredoxin (PfTrx). In BALB/c mice, both platforms elicited robust Th1-type responses, with increased IL-2 and IFN-γ secretion and activation of Th1 CD4⁺ T cell. Only LNP-mRNA-Tp0136T1 induced strong CD8⁺ cytotoxic responses, marked by elevated perforin⁺ and granzyme B⁺ expression. In New Zealand White rabbits challenged intradermally with T. pallidum, complete ulcer prevention was achieved with the PfTrx-Tp0136T1, while LNP-mRNA-Tp0136T1 significantly reduced ulceration. Both vaccines suppressed RPR titers and lowered treponemal load. These findings demonstrate that epitope-specific T cell-based vaccines elicit potent cellular immunity, control treponemes, prevent ulcers, and may reduce secondary sexually transmitted infections by preserving mucosal integrity.

Evaluation of a tilapia epitopes vaccine against Streptococcus agalactiae based on phage display technology.

Human metapneumovirus (HMPV) is a respiratory viral pathogen classified within the Paramyxoviridae family and is a significant cause of acute respiratory tract infections. The vaccine construct maintains stable binding affinity with targeted receptors anaffects young children, the elderly, and immunocompromised individuals. HMPV was recognized initially in 2001. HMPV exhibits characteristics similar to respiratory syncytial virus (RSV) and generally causes symptoms ranging from mild, cold-like signs to more severe issues such as pneumonia and bronchiolitis. This study employs reverse vaccinology and bioinformatics approaches to screen potential vaccine targets and design epitope vaccine constructs. Following immunoinformatics analysis, six proteins, including >YP_009513265.1 nucleoprotein, >YP_009513266.1 phosphoprotein, >YP_009513268.1 fusion protein, >YP_009513269.1 matrix protein 2–1, >YP_009513272.1 attachment glycoprotein, and >YP_009513273.1 RNA-dependent RNA polymerase, were selected for further analysis. These proteins underwent B-cell epitope prediction, and the identified B-cell epitopes were used in T cell epitope prediction. Both MHC-I and MHC-II epitopes were predicted, with lower percentile scores prioritized. The selected epitopes- SLGKIKNNK, IPQNQRPSA, IPSEPKLAW, FPEDQNVAL, KLKNKNRLR, ELSSIKTRR, and QEKKLVPVY- were further screened through immunoinformatics analysis. These epitopes were connected with a GPGPG linker to form a linear sequence, and an EAAAK linker was used to attach the adjuvant to this sequence, which was then processed for structural modeling. Effective vaccines must bind to receptors on immune cells to activate the immune system. The vaccine-TLR-4 docked complex, predicted using Cluspro 2. 2.0 web server, showed that cluster 4 had the lowest binding energy score of − 1175. 3, indicating potential effectiveness in eliciting an immune response via TLR-4 activation. Similarly, for the vaccine- MHC-I complex, cluster 2 exhibited the lowest energy score of − 1087. 4 kcal/mol, suggesting a stable binding interaction. For the vaccine-MHC-II complex, cluster 2 showed the most stable binding with a lowest energy score of − 1189. 1 kcal/mol. To validate these docking results, molecular dynamics simulations analyze the stability of the complexes. The RMSD from the simulations indicated that the vaccine- MHC-I complex stabilized around 10 to 12 (Å). The vaccine-MHC-II complex stabilized after 60 ns, while the vaccine-TLR-4 complex initially showed a lower RMSD of approximately 5 (Å), which gradually increased to 12–15 (Å), reflecting conformational stability and binding affinity. In addition, in silico immune simulations suggested activation of both humoral and cellular immunity, indicating that the vaccine construct could effectively induce immune responses against HMPV.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-28522-4.

Public health emergencies pose significant threats to both human and environmental health, and the rapid control of emerging diseases often remains challenging due to their unknown characteristics. In this context, vaccines have historically been instrumental in the fight against major diseases, with epitope vaccines emerging as a preferred approach due to their precision and efficacy. In previous studies, we developed a strategy for peptide vaccine design based on simulated epitopes for tilapia lake virus (TiLV). To further improve vaccine immunogenicity and capitalize on the significance of antibodies for epitope screening, this study presents a structural modification strategy based on antigen-antibody docking for reverse vaccinology in conjunction with single amino acid mutagenesis inducing a robust immune response in tilapia. We believe that our findings are highly relevant to the field and contribute to the ongoing efforts to combat public health threats.

Viral antigen glycosylation is a central strategy for immune evasion. This review summarizes how viruses utilize glycosylation to form a "glycan shield" that occludes critical epitopes and to achieve molecular mimicry by imitating host "self" signals, thereby avoiding immune recognition. The article focuses on analyzing the challenges glycosylation poses to vaccine design, including heterogeneity, epitope masking, and dynamic evolution, as well as the obstacles it creates for antibody drugs, such as steric hindrance and drug resistance. Finally, it outlines future directions for overcoming this "glycan fortress" through cutting-edge analytical technologies, innovative intervention strategies, and artificial intelligence, offering insights for developing effective prevention and treatment strategies.

BackgroundAlveolar Echinococcosis (AE) is a serious infectious disease caused by Echinococcus multilocularis (E.multilocularis,Em) in the highlands of northwestern China and vaccination is currently the most effective means of preventing E. multilocularis infection. However, current vaccines are not sufficiently effective in preventing and controlling Alveolar Echinococcosis.MethodsIn this study, an oral M-cell targeted Lactococcus lactis (L. lactis) vaccine (LL-plSAM-GILE) was constructed by adding SAM gene sequence to the epitope vaccine GILE for E. multilocularis constructed in our previous study. Mice were orally immunized with LL-plSAM-GILE and their serum antibody levels (ELISA), lymphocyte proliferation (MTS), IFN-γ levels (ELISpot), IL-4 levels (flow cytometry, FCM), T cells (FCM), growth of hepatic cysts (Ultrasound), and weights were measured to evaluate the protective effect of LL-plSAM-GILE.ResultsThe L.lactis expression plasmid pNZ8148-SAM-GILE was successfully constructed and electroporated into L.lactis NZ9000, and the recombinant protein was approximately 45 KD. SAM-GILE was expressed on the surface of recombinant L.lactis. LL-plSAM-GILE is effective in targeting Microfold cells. Mice immunized with LL-plSAM-GILE exhibited significantly elevated levels of specific IgG antibodies. Lymphocyte proliferation was enhanced compared to the control group and the NZ9000 group. LL-plSAM-GILE stimulated the production of CD4+ and CD8+ T cells. Mice immunized with LL-plSAM-GILE secreted more IFN-γ and IL-4. For both primary and secondary infections, oral immunization with LL-plSAM-GILE led to a significant decrease in the diameter and weight of hepatic cysts.ConclusionsAn oral M-cell targeted L.lactis vaccine LL-plSAM-GILE with excellent immunogenic and immunoprotective properties has been successfully constructed. This study may provide important theoretical and experimental bases for the prevention and treatment of E. multilocularis infection.

The focus of this study was to explore phage display systems employing bacteriophage lambda (λ) gene fusions to its capsid decoration protein gpD as reagent tools for tackling disease. The biological activity of gpD-fusions was examined by testing for the retained antimicrobial toxicity of cathelicidins or defensins fused to gpD. Our previous finding that only COOH fusions of either cathelicidins or defensins to gpD were toxigenic was expanded to show that only the reduced form of fused defensin antimicrobial polypeptides was found to be toxigenic. Compared in review are gene-fusion lytic display systems (where the fusion-display gene is integrated within the viral genome) with a surrogate system, employed herein, that exogenously provides the fusion-display protein for addition to phage capsid. It is easily possible to produce fully coated lambda display particles (LDP) serving as single epitope vaccines (SEV), or antimicrobials, or to produce partially coated LDP without any complex bacteriophage genetic engineering, making the system available to all. The potential to build vaccine vector phage particles (LDNAP) comprising essentially sheathed DNA vaccines encapsulated within an environmentally protective capsid is described. LDNAP are produced by introducing a cassette into the phage genome either by phage–plasmid recombination or cloning. The cassette carries a high-level eukaryotic expression promoter driving transcription of the vaccine candidate gene and is devoid of plasmid resistance elements.

A Novel Aβ B-cell epitope Vaccine, Aβ1-10 with carrier protein OVA and KLH reduce Aβ-induced neuroinflammation mediated neuropathology in mouse model of Alzheimer's disease.

A BSTRACT Objectives: Enterococcus faecalis is a facultative anaerobe, and in recent years, it has emerged as an important cause of nosocomial infections. Among various virulent factors, a new cell wall-specific, surface anchor protein EF3314 contributes to the pathogenesis of the organism in the establishment of many recalcitrant infections. The aim of this study is thus to analyze the frequency of EF3314 by molecular methods and to predict the immune-dominant peptides from the EF3314 using an immune-informatics approach. Materials and Methods: Clinical strains of E. faecalis were characterized from the dental caries specimens, assessed for its multidrug resistance (MDR) property based on CLSI guidelines, and the presence of EF3314 by polymerase chain reaction (PCR). The protein sequence of the EF3314 protein from E. faecalis was further retrieved from UniProt and was subjected to assess allergenicity, secondary structure, antigenicity, stability predictions, physico-chemical analysis, and identification of major histocompatibility complex (MHC) Class II binders. Final selection of B-cell epitopes was done with the Immune Epitope Database B-cell epitope tool. Results: From the caries specimens, E. faecalis was isolated from 5 specimens (25%), with 3 MDR strains and 2 strains positive for EF3314 gene. Based on the combinatorial scores, the epitope peptide MILVFIVYF was suggested to be a promising vaccine candidate from EF3314 of E. faecalis . Conclusion: The study warrants the need for the periodical surveillance of the virulent and resistant traits of E. faecalis in dental health care settings. For the targeted therapeutic approach, immune-informatics is a suitable approach to design novel vaccine epitopes to treat infections caused by E. faecalis . However, the predicted epitope peptide needs further preclinical trials for its immunological response and memory against E. faecalis .

Canine parvovirus (CPV) poses a severe threat to canine health, necessitating the development of safer and more effective vaccines. While traditional vaccines carry risks of virulence reversion and environmental contamination, subunit vaccines-especially neutralizing epitope vaccines-offer promising alternatives by eliciting targeted immune responses with enhanced safety. We employed bacterial display technology to express 11 overlapping CPV VP2 gene fragments on the periplasmic membrane of E. coli. Key neutralizing antigenic epitopes of CPV VP2 were mapped using four neutralizing single-chain antibodies in combination with FCM. The identified epitopes were concatenated via GS linkers and expressed as a recombinant VP2D protein. Then, animal experiments were conducted to evaluate the immunogenicity of the epitope-based vaccine in mice. The data shows that the antigenic epitopes of the four single-chain antibodies are located in V2-V3, V8, V10 and V11 respectively. After linking five antigenic epitope fragments, we constructed a novel chimeric antigen protein, VP2D, and achieved the efficient expression of VP2D. Animal immunization evaluation results demonstrated that the VP2D vaccine exhibited superior immunological properties compared to both the VP2 vaccine and the commercial vaccine. The VP2D vaccine significantly enhanced the host's capacity to mount both humoral and cellular immune responses. Notably, the antibody titers in the VP2D vaccine group were consistently 1.2- to 1.5-fold higher than those in the VP2 vaccine group throughout the experimental period. Furthermore, the proportions of CD4⁺ T cells and F4/80⁺ cells were increased by up to 12% and 8%, respectively, in the VP2D group. Additionally, both the protein levels and mRNA transcription of inflammatory cytokines were elevated in the VP2D vaccine group relative to both the VP2 and commercial vaccine groups, indicating a consistently enhanced inflammatory response. Identified CPV-VP2 neutralizing antigenic epitopes (70-150, 410-440, 510-585 aa), and an effective candidate vaccine for the prevention of CPV was provided.

Salmonella enterica subsp. enterica serotype Typhi (Salmonella typhi) is the cause of typhoid fever, a severe public health issue in impoverished countries with inadequate sanitation. Despite the availability of therapies, infection rates remain high, underscoring the critical need for an effective and long-lasting vaccine. In this study, we used an integrated in silico strategy to develop a multi-epitope vaccine for 122 S. Typhi strains. A core proteome study identified 2,637 conserved proteins, while subtractive proteomics discovered three non-homologous, virulent, antigenic, and non-allergenic proteins: major curlin subunit, outer membrane protein A, and a hypothetical protein. Four B-cell and ten T-cell epitopes (four HTL and six CTL) were predicted and chosen for vaccine development using immunoinformatics methods. In order to improve immunogenicity, these epitopes were adjuvanted with human beta-defensin-2 and linked by suitable linkers in the final vaccine design. Molecular docking demonstrated binding energies of -305.76 kcal/mol (TLR4), -254.28 kcal/mol (MHC-I), and − 270.85 kcal/mol (MHC-II), confirming stable interactions of the vaccine with TLR4 and MHC class I and II molecules. Molecular dynamics simulations showed that the vaccine-receptor complexes were structurally stable and compact. A robust and long-lasting immune response was also suggested by an immunological simulation study, which showed increased numbers of memory B and T cells, IL-2, and IFN-γ. Together, these results show how computational pipelines can speed up the development of bacterial vaccines and support the multi-epitope vaccine’s potential as a viable option for typhoid fever prevention.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-15254-8.

Humans, as natural carriers of Staphylococcus aureus (SA), have developed nonprotective immune imprints that can be reactivated by SA antigen vaccination and that contribute to the failure of SA vaccine trials. To test whether an epitope-focused vaccine strategy can overcome this issue, we explored the protective epitope of the notable SA antigen MntC. A surface loop of MntC (Loop101) was found to be essential for SA to absorb manganese(II) ion and survive oxidative stress. Our Loop101-deficient versus -competent MntC-based differential screening identified a Loop101-specific human monoclonal antibody (Hm0686). Hm0686 blocked SA from absorbing manganese(II) ion and exhibited a strong opsonophagocytic activity, suggesting that Hm0686-targeted Loop101 may be a protective epitope. A Loop101 epitope vaccine but not the whole MntC antigen protected against SA infection in mice with prior exposure-induced nonprotective imprints. Thus, this effective protective epitope-based vaccine strategy may be explored to overcome nonprotective immune imprints in humans.

Dual Aβ/tau epitope vaccines: a poorly explored strategy for Alzheimer's disease immunotherapy.

The interdisciplinary field of immunoinformatics, which combines immunology with computational biology, is revolutionising vaccine development and epitope identification. This paper explores recent advancements, tools and methodologies in immunoinformatics, highlighting their potential applications in creating vaccines for diseases such as COVID-19, influenza, malaria, tuberculosis, dengue and pneumonia. We discuss how tools such as BepiPred 3.0, SVMTrip, IFNepitope, VaxiJen, immune epitope database, NetCTL and PEP-FOLD can enhance the precision and efficiency of vaccine design. In addition, we address the challenges and future directions in the field, emphasising the need for improved computational models, better data integration and rigorous experimental validation to bridge the gap between in silico predictions and real-world applications.

BackgroundAs the HIV-based complication is still going on with the high infection and mortality rate, it requires a novel strategy to combat this infection due to the unavailability of proper therapeutic. Therefore, we utilize integrated immuno and bioinformatics approaches in this study to design a peptide vaccine against HIV infection by targeting its complete genome.MethodsThe complete genome sequence was analyzed, and the potential B and T cells were predicted. Among the predicted epitopes, the promising ones were selected and further used with the adjuvant and linker to formulate a vaccine candidate. The vaccine was modeled, and its activity and stability towards the TLRs were analyzed via docking and dynamics (500ns). The vaccine-generated immune activity and expression via in-silico cloning were also evaluated.ResultsA total of 6 B cells, 7 CTL, and 6 HTL were identified as an immunodominant epitope and used for vaccine formulation. These epitopes were fused together via linkers, and their efficiency and constancy were enhanced with Adjuvant, PADRE epitope, and His-tag. Further, the formulated vaccine shows high population coverage and stable features based on the 2D and 3D assessments. The docking investigation demonstrated the strong activity of the vaccine towards the TLR2 and TLR3, having binding affinity − 10.8 kcal/mol-1 and − 15.8 kcal/mol-1, and also disclosed remarkable constancy based on the 500ns simulation period. The vaccine-assisted immune simulation and expression level in the vector revealed a robust immune response towards the host based on the vaccination and a significant expression level.ConclusionsBased on the integrated approach and validation steps, the overall finding suggests that the formulated vaccine may have strongly immunodominant properties and could combat the infection.

In 2022, the World Health Organisation (WHO) announced new cases of the developing Monkeypox Virus (MPXV), a zoonotic orthopoxvirus viral infection that mimics smallpox signs. Despite the ongoing infection, no proper medication is available to completely overcome this infection. The study aims to construct a multi-epitope vaccine targeting Monkeypox Virus (MPXV) membrane glycoprotein to provoke robust immune responses. To construct a potential immuno-dominant epitope vaccine to combat MPXV. The target sequence, sourced from the UAE-to-India travel case, was analyzed to identify potential B-cell and T-cell epitopes (MHC-I and MHC-II). Immunodominant epitopes were selected and fused with β-defensin-I and PADRE to increase immunogenicity. The vaccine was modeled, docked with TLR3, and subjected to a 500 ns molecular dynamics simulation for stability analysis. Immune responses and bacterial expression were also evaluated. The vaccine, comprising 230 amino acids, demonstrated antigenicity (0.6620), non-allergenicity, and broad population coverage. Selected epitopes included 3 B-cells, 4 MHC-I, and 2 MHC-II, ensuring a potent immunodominant profile. Docking with TLR3 revealed a binding affinity of -17.2 kcal/mol, while simulations confirmed their stability. Cloning (pET28a (+)) and immune response analyses showed a strong immunogenic profile, including elevated IgG1, IgM, and antigen levels, supported by a Codon Adaptation Index (CAI) of 1.0. The proposed multi-epitope vaccine shows promise against MPXV. However, further in vivo and in vitro investigations are essential to confirm its immune efficacy.

Staphylococcus warneri is a pathogenic bacterium that causes multiple life-threatening diseases, such as urinary tract and skin infections globally, with approximately one million new cases reported each day. The World Health Organization (WHO) has classified it as a "superbug," and no licensed vaccine is currently assessable. In this study, we designed a vaccine employing B and T-cell epitopes from two highly antigenic membrane proteins of S. warneri. We found activation of the immune response using an advanced immunoinformatic approach. Immunoinformatic approaches were utilized to predict epitopes, and only those exhibiting non-toxic profiles, antigenicity, non-allergenic characteristics, and immunogenicity were considered. The vaccine was constructed using B and T-cell epitopes predicted through advanced immunoinformatics, ensuring that only those with non-toxic, antigenic, non-allergenic, and immunogenic profiles were selected. These selected epitopes were linked together to create a multi-epitope vaccination utilizing the linkers AAY and GPGPG, which were subsequently combined with the 50S ribosomal protein L7/L12 to boost the antigenicity of the vaccine. The immunogenic ability of this multi-epitope vaccine was determined by its binding affinity of the vaccine with the essential Toll-like receptor 5 (TLR-5), through molecular docking. Molecular docking simulations showed favorable binding of the vaccine construct to Toll-like receptor 5 (TLR5), with a binding affinity of - 989.3kcal/mol, suggesting strong potential for immune activation. The global population coverage of the vaccine epitopes was predicted to be 99.47%. Simulation studies were performed to calculate stability of the docking complex over the time. Therefore, there is an urgent need to test the safety and efficacy of the developed model both in vitro and in vivo.

Mycoplasma genitalium is increasingly recognized for its role in severe health conditions, including sexually transmitted infections, ovarian and prostate cancer. The adhesion protein plays a crucial role in the pathogen's ability to attach to and invade host cells, making it a key target for vaccine development. The need to develop a vaccine against M. genitalium stems from its rising antibiotic resistance, limited treatments and effectiveness. This study focuses on the design and computational evaluation of adhesion protein-based epitope vaccine. Through an immunoinformatic approach, multiple novel cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), and linear B-cell epitopes were identified from the adhesion protein, demonstrating strong antigenic, non-allergenic, and immunogenic properties. The vaccine construct's 3D structure was validated using Ramachandran plot analysis, ProSA, and ERRAT servers, confirming its stability and suitability. Molecular docking studies revealed a high binding affinity of the vaccine with the TLR-2 receptor, further supported by 100ns molecular dynamics (MD) simulations that confirmed the structural stability and robust interaction of the vaccine with immune receptors. In silico immune simulations using the C-ImmSim server demonstrated the vaccine's potential to elicit strong humoral and cell-mediated immune responses. Codon optimization for expression in E. coli using the pET-29a(+) vector predicted efficient production of the vaccine. The comprehensive computational analysis, underscores the potential of this epitope-based vaccine as a promising candidate against M. genitalium infections. However, the study emphasizes the necessity of in vitro and in vivo experiments to validate the vaccine's efficacy and safety before advancing to clinical trials.