Search Results (99)

This study aimed to design a multi-epitope vaccine (MEV) against Pasteurella multocida (Pm) using immunoinformatics approaches. Based on four conserved outer membrane proteins (OmpA; OmpH; PlpEand LolA), 15 immunodominant epitopes were identified, including 8 CTL epitopes, 3 HTL epitopes, and 4 B-cell epitopes. A vaccine construct was developed by incorporating RGD and PADRE adjuvant sequences. Computational analyses indicated that the vaccine possesses favorable physicochemical properties and structural stability. The molecular docking and normal mode analyses reveal a potential binding interface between the basis and TLR2/TLR4, with a computed binding energy of −10.1 kcal/mol for TLR4, suggesting a possible preferential interaction. Immune simulation predicted the vaccine could effectively elicit responses from B cells, T cells, and key cytokines such as IFN-γ. Additionally, the vaccine sequence was successfully cloned into the pET-28a (+) expression vector, facilitating future recombinant expression. This study provides a theoretical foundation for developing a safe and effective subunit vaccine against Pm. Full article

As SARS-CoV-2 continues to evolve with increased transmissibility and immune evasion, the need for vaccines that provide broader and more durable protection has become increasingly urgent. The extensive research spurred by the pandemic has accelerated the development of diverse vaccine platforms, including mRNA, DNA, virus-like particles (VLPs), recombinant proteins, and mosaic mono- and polyvalent vaccines. While several of these platforms have reached regulatory approval and widespread clinical employment, others remain under evaluation or in various stages of clinical development. These vaccines have significantly reduced infection rates, severe disease, and hospitalizations, particularly among high-risk group. Nevertheless, the ongoing emergence of novel variants and subvariants has challenged the efficacy of both existing and newly developed vaccines. This evolving landscape underscores the urgent need for a universal SARS-CoV-2 vaccine platform capable of providing comprehensive and long-lasting immunity. In this review, we evaluate current and emerging strategies for SARS-CoV-2 universal vaccine development, with a focus on antigen design, breadth of immune protection, and clinical feasibility. Attention is given to various universal vaccine platforms such as the mosaic polyvalent spike construct, multi-epitope vaccines targeting the receptor-binding domain (RBD), and approaches centered on the conserved S2 subunit of the spike protein. We also discuss strategies leveraging additional conserved viral proteins and T helper (Th) and cytotoxic T lymphocyte (CTL) epitopes from across coronaviruses. By highlighting the advances in these areas, this review provides a framework to guide the rational design of next-generation universal vaccines capable of delivering broad and durable protection against SARS-CoV-2 variants. Full article

Mycoplasma pneumoniae (M. pneumoniae) is the crucial factor of global acquired respiratory infections. Currently, there are no specific disease modification treatments or vaccines available, and the vaccine development for this pathogen lags behind due to the complexity and variability of its antigens. A novel vaccine with broad-spectrum characteristics is essential to provide comprehensive protection against continuously evolving wild-type strains. Here, a broad-spectrum muti-epitope vaccine against M. pneumoniae had been designed through immunoinformatics methods. To ensure its broad-spectrum, we generated consistent sequences from all the antigen proteins of different strains, and then identified potential T cell epitopes. The multi-epitope vaccine (MEV) of M. pneumoniae incorporated 16 CTLs and 7 HTLs from the HMW1–3 and p1 adhesin proteins, which comprised 458 amino acids with adjuvant. The vaccine evaluation showed that the MEV had ideal physicochemical properties, high antigenicity, high immunogenicity, and was non-toxic. Furthermore, there was a strong and stable binding interaction between this vaccine and the toll-like receptors, which could be supported by the normal mode analysis. Finally, codon optimization resulted in the optimal GC content and higher CAI value. The vaccine candidate is expected to induce strong cellular immune responses and may provide protective immunity against the pathogen. We provided a novel in silico vaccine design strategy for vaccine design, which could provide a technical framework for the development of vaccines against other pathogens. Full article

Influenza’s pandemic threat is driven by antigenic drift, which limits the efficacy of conventional vaccines. To address this challenge, we established a clinical serum-anchored computational design pipeline for a broad-spectrum multi-epitope mRNA vaccine (MEMV), bridging the gap between pure in silico design and clinical applicability. Using 36 longitudinal sera (d0/d28/d365) from 12 well-characterized human cohorts (6 vaccine recipients and 6 influenza patients) and high-density antibody-peptide microarrays, we empirically identified 12 immunodominant B-cell linear epitopes from the nucleoprotein (NP) of influenza A (H1N1/H3N2) and B viruses. These experimentally validated epitopes were combined with in silico-predicted conserved helper T-lymphocyte (HTL)/cytotoxic T-lymphocyte (CTL) epitopes (from NP/HA/NA) to construct MEMVs candidates, ensuring high antigenicity, non-toxicity, and 95.63% global HLA coverage. Molecular docking and 100 ns molecular dynamics (MD) simulations confirmed favorable conformational compatibility between MEMVs and Toll-like receptor 3 (TLR3) in silico immunization via C-ImmSim predicted robust B/T-cell responses and protective cytokine (IFN-γ/IL-10) production. Collectively, this pipeline shortens the preliminary design cycle for influenza vaccines, provides a standard epitope-combination strategy, and offers direct targets for follow-up in vitro/in vivo experiments. Full article

Salmonellosis remains a persistent threat to global food safety and poultry productivity, compounded by rising antimicrobial resistance. Here, we report the in silico design and immunoinformatic validation of a broad-spectrum, edible multi-epitope vaccine targeting conserved adhesion and biofilm-associated proteins (FimH, AgfA, SefA, SefD, and MrkD) of Salmonella spp. Two constructs were engineered by integrating cytotoxic (CTL) and helper (HTL) epitopes with β-defensin-3 (HBD-3) or lipopolysaccharide (LPS) adjuvants, optimized for expression in Chlorella vulgaris. Structural modeling confirmed native-like folding (z-scores −2.58 and −5.22) and high stability indices. Molecular docking and dynamics revealed that the LPS-adjuvanted construct (Construct 2) forms a highly stable complex with Toll-like receptor 3 (HADDOCK score −63.4; desolvation energy −50.2 kcal/mol), indicating potent innate immune activation. Immune simulations predicted strong IgM-to-IgG class switching and durable humoral responses, consistent with effective antigen clearance. Codon optimization achieved high adaptability for algal expression (CAI = 0.93; GC ≈ 65%), supporting scalable microalgae-based production. Compared with current parenteral vaccines, offering a low-cost, non-invasive way to curb Salmonella in poultry, this edible vaccine platform reduces dependence on antibiotics. Our approach, which combines computational vaccinology with a safe-by-design sustainable biomanufacturing perspective, outlines a One Health framework for advancing antimicrobial stewardship and food safety. Full article

Background: Chromobacterium violaceum is an emerging multidrug-resistant (MDR) Gram-negative bacterium associated with severe septicemia, abscess formation, and high mortality, particularly in immunocompromised individuals. Increasing antimicrobial resistance and the absence of approved vaccines underscore the urgent need for alternative preventive strategies. Traditional vaccine approaches are often inadequate against genetically diverse MDR pathogens, prompting the use of computational immunology and reverse vaccinology for vaccine design. Objectives: This study aimed to design and characterize a novel multi-epitope subunit vaccine (MEV) candidate against C. violaceum using a comprehensive pangenome-guided subtractive proteomics and immunoinformatics pipeline to identify conserved antigenic targets capable of eliciting strong immune responses. Methods: Comparative genomic analysis across eight C. violaceum strains identified 3144 core genes. Subtractive proteomics filtering yielded two essential, non-homologous, surface-accessible, and antigenic proteins—penicillin-binding protein 1A (Pbp1A) and organic solvent tolerance protein (LptD)—as vaccine targets. Cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and B-cell epitopes were predicted and integrated into a 272-amino-acid MEV construct adjuvanted with human β-defensin-4A using optimal linkers. The construct was evaluated through structural modeling, molecular docking with TLR4, molecular dynamics simulation, immune simulation, and in silico cloning into the pET-28a(+) vector. Results: The MEV construct exhibited strong antigenicity, non-allergenicity, and non-toxicity, with stable tertiary structure and favorable physicochemical properties. Docking and dynamics simulations demonstrated high binding affinity and stability with TLR4 (ΔG = −16.2 kcal/mol), while immune simulations predicted durable humoral and cellular immune responses with broad population coverage (≈89%). Codon optimization confirmed high expression potential in E. coli K12. Conclusions: The pangenome-guided immunoinformatics approach enabled the identification of conserved antigenic proteins and rational design of a promising multi-epitope vaccine candidate against MDR C. violaceum. The construct exhibits favorable immunogenic and structural features, supporting its potential for experimental validation and future development as a preventive immunotherapeutic against emerging MDR pathogens. Full article

Background: Tuberculosis (TB) remains a pressing global health crisis. The inadequate efficacy of the BCG vaccine against adult pulmonary TB underscores the urgent need for novel, effective vaccines. This study aimed to design a novel mRNA vaccine candidate against TB using a rational immunoinformatics approach. Methods: From 13 antigens, >12,000 epitopes were filtered to select 60 optimal peptides (36 CTL, 16 HTL, 8 B-cell), assembled into 25 scaffolds with 49 TLR2/4 agonist configurations. EP9158H underwent structural modeling, 100 ns molecular dynamics, docking, immune simulation, RNAfold, and conservation analysis across 76 strains. Results: EP9158H, encoding 15 CTL, 9 HTL, and 8 B-cell epitopes flanked by TLR2 agonist ESAT-6 and TLR4 agonist HBHA, emerged as the optimal candidate. All 32 constituent epitopes showed >81% conservation, with 81.25% exhibiting perfect identity across MTBC lineages. The scaffold demonstrated high solubility (0.531), broad population coverage (73.76% MHC-I, 88.91% MHC-II), optimal TLR2/4 docking scores (−1359.7 and −1348.3), and robust structural stability (ProSA Z-score −6.18; RMSD 22–27 Å). Immune simulation predicted strong Th1-biased T-cell responses and high levels of antibody titers. RNAfold analysis revealed stable mRNA secondary structures (MFE −1127.5 kcal/mol) supporting efficient translation. Conclusions: EP9158H integrates broad epitope coverage, dual TLR agonism, and validated stability. Compared to single-antigen vaccines, it offers superior strain coverage, enhanced innate activation, and mRNA advantages for CTL induction, warranting experimental validation. Full article

The diseases caused by genotype VII Newcastle disease virus (NDV), H9N2 avian influenza virus (AIV), and fowl adenovirus serotype 4 (FAdV-4) continue to threaten the global poultry industry. However, no broad-spectrum vaccines provide simultaneous protection against these three pathogens. This study employed bioinformatics and immunoinformatics approaches to design a multi-epitope vaccine, named NFAF, which consists of B-cell, cytotoxic T lymphocyte (CTL) epitopes, and helper T lymphocyte (HTL) epitopes derived from hemagglutinin-neuraminidase (HN) and fusion (F) proteins of genotype VII NDV, hemagglutinin (HA) protein of H9N2, and Fiber2 protein of FAdV-4. The vaccine candidate was predicted to have non-allergenic properties, non-toxicity, high antigenicity, and favorable solubility. Each of its constituent antigenic epitopes has a high degree of conservation. Molecular docking demonstrated stable binding between NFAF and chicken Toll-like receptor (TLRs) and major histocompatibility complex (MHC) molecules. NFAF was expressed in soluble form in Escherichia coli and purified. Polyclonal antibodies against all three target viruses showed specific binding to NFAF. In vitro experiments revealed that NFAF effectively stimulated chicken peripheral blood mononuclear cells (PBMCs) and induced Th1, Th2, and pro-inflammatory cytokine production, confirming its immunogenicity, and increased the mRNA expression of the key signaling molecules MyD88 and NF-κB. These results suggested that NFAF could therefore be an efficacious multi-epitope vaccine against genotype VII NDV, H9N2, and FAdV-4 infections. Full article

Background: The minimized pan-coronavirus (CoV) vaccine-1 developed by our laboratory contained pDNA sequences of feline coronavirus serotype-1 (FCoV1) and SARS-CoV2 (SCoV2) spike B-cell epitopes plus FCoV/SCoV2-conserved, CoV-specific polymerase cytotoxic T-lymphocyte (CTL) epitopes formulated in lipid nanoparticle (LNP). Only FCoV2 infects feline cell lines needed for developing native challenge inoculum that causes feline infectious peritonitis (FIP). Hence, Pilot Study 1 evaluated the therapeutic efficacy and safety of the pan-CoV vaccine-1 in feline immunodeficiency virus (FIV)-infected cats, with or without FCoV1 coinfection. Pilot Study 2 evaluated the cross-protective effect of pan-CoV vaccines in specific-pathogen-free (SPF) cats against intranasal challenge with FIP virus serotype 2 (FIPV2). Methods: In Study 1, we vaccinated two FIV-infected cats (one negative and another positive for FCoV1 coinfection) intramuscularly twice with CTL epitopes-LNP vaccine and later twice with pan-CoV vaccine-1. Controls included two unvaccinated FIV-infected cats with or without FCoV1 coinfection. Study 2 assessed the sequential vaccinations of three pan-CoV vaccines in four SPF cats. The first two vaccinations were with pan-CoV vaccine-2, followed by pan-CoV vaccine-3 (twice), and lastly with pan-CoV vaccine-1 (once). Three SPF controls included two cats immunized with LNP and one lacking any immunization. Pan-CoV vaccine-2 contained pDNAs with modified FCoV1/SCoV2 B-cell epitopes plus CTL epitopes in LNP. Pan-CoV vaccine-3 contained only pDNAs with FCoV1 B-cell epitopes plus CTL epitopes in LNP. Results: Study 1 demonstrated no adverse effect with 25 μg and 50 μg CTL epitopes-LNP vaccine and 50 μg pan-CoV vaccine-1. However, 100 μg pan-CoV vaccine-1 caused fever 24 h later, which was resolved by a single Meloxicam treatment. Both vaccinees developed cross-FCoV2 neutralizing antibodies (XNAbs), immunoblot binding antibodies (bAbs) to FCoV1 receptor-binding domain (RBD), and T-cell responses to FCoV1 RBD, whereas one vaccinee also developed bAbs to SCoV2 RBD. Study 2 demonstrated no adverse effects after each vaccination. Three vaccinees developed low-titer XNAbs and bAbs to FCoV2 spike-2 by the fourth vaccination. Upon challenge, all cats developed FCoV2 NAbs and bAbs to FCoV2 nucleocapsid and RBD. High vaccine-induced T-cell responses to FCoV1 RBD and T-cell mitogen responses declined with an increase in responses to FCoV2 RBD at three weeks post-challenge. Two of the three controls died from FIP, whereas one vaccinee, with the lowest vaccine-induced immunity, died from skin vasculitis lesions and detection of FIPV2 infection by semi-nested RT-snPCR in feces. Conclusions: In Pilot Study 1, the pan-CoV vaccine-LNP dose of 50 μg had no adverse effects, but adverse effects were observed at 100 μg dose. In Pilot Study 2, the FCoV1-based B-cell vaccine(s) induced low levels of XNAbs against FIPV2 and delayed challenge infection against high-dose FIPV2. The high-dose FIPV2 infections in the vaccinated and control cats started to clear, by single housing at 23–26 weeks post-challenge, whereas two cats in Pilot Study 1 cleared natural FCoV1 transmission by 26 weeks post-infection. Full article

Duck viral hepatitis (DVH), a highly contagious disease, is caused primarily by duck hepatitis A virus (DHAV). The viral genotypes exhibit significant diversity, creating a challenge as monovalent vaccines fail to provide cross-genotype protection in ducklings. This study aimed to design a multi-epitope peptide vaccine targeting different genotypes of DHAV. Using immunoinformatics approaches, we systematically identified key antigenic determinants, including linear B-cell epitopes, cytotoxic T-cell epitopes (CTL), and helper T-cell epitopes (HTL). Based on these, a novel vaccine candidate was developed. The vaccine construct was subjected to rigorous computational validation: (1) Molecular docking with Toll-like receptors (TLRs) predicted immune interaction potential. (2) Molecular dynamics simulations assessed complex stability. (3) In silico cloning ensured prokaryotic expression feasibility. Then, we conducted preliminary experimental validation for the actual effect of the vaccine candidate, including recombinant protein expression in E. coli, enzyme-linked immunosorbent assay (ELISA) quantification of humoral responses, and Western blot analysis of cross-reactivity. ELISA results demonstrated that the vaccine candidate could induce high-titer antibodies in immunized animals, with potency reaching up to 1:128,000, and the immune serum showed strong reactivity with recombinant VP proteins. Western blot analysis using duck sera confirmed epitope conservancy across genotypes. Collectively, the multi-epitope vaccine candidate developed in this study represents a highly promising broad-spectrum strategy against DHAV. The robust humoral immunity it elicits, coupled with its demonstrated cross-reactivity, constitutes compelling proof-of-concept, laying a solid foundation for advancing to subsequent challenge trials and translational applications. Full article

Background: Mammalian orthoreovirus is a ubiquitous double-stranded RNA virus that causes mild respiratory and enteric infections, primarily in infants and young children. Its significant environmental stability and association with conditions like celiac disease highlight an unmet medical need, as no licensed vaccine or antiviral treatment currently exist. Methods: An immunoinformatics-driven approach was employed to design a multi-epitope vaccine. The highly antigenic inner capsid protein Sigma-2 was used to predict cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), and linear B cell epitopes using NetCTL, NetMHCpan, NetMHCIIpan, and IEDB tools. Selected epitopes were fused with appropriate linkers. The construct’s antigenicity, allergenicity, and physicochemical properties were evaluated. The tertiary structure was predicted with AlphaFold2, refined, and validated. Molecular docking with TLR2 and TLR4 was performed using HDOCK, and immune response simulation was conducted with C-ImmSim. Finally, the sequence was codon-optimized for E. coli expression using JCat. Results: The final vaccine construct comprises one CTL, four HTLs, and one B cell epitope. It is antigenic (VaxiJen score: 0.5026), non-allergenic, and non-toxic and possesses favorable physicochemical properties, including stability (instability index: 32.28). Molecular docking revealed exceptionally strong binding to key immune receptors, particularly TLR2 (docking score: −324.37 kcal/mol). Immune simulations predicted robust antibody production (elevated IgM, IgG1, and IgG2) and lasting memory cell formation. Codon optimization yielded an ideal CAI value of 0.952 and a GC content of 57.15%, confirming high potential for recombinant expression. Conclusions: This study presents a novel multi-epitope vaccine candidate against reovirus, designed to elicit broad cellular and humoral immunity. Comprehensive in silico analyses confirm its structural stability, potent interaction with innate immune receptors, and high potential for expression. These findings provide a strong rationale for further wet-lab studies to validate its efficacy and advance it as a promising prophylactic candidate. Full article

Acquired Immunodeficiency Syndrome (AIDS) is caused by Human Immunodeficiency Virus (HIV), and continues to be responsible for a substantial number of deaths worldwide each year. Development of a robust and efficient HIV-1 vaccine remains a critical priority. Structural analysis of viral proteins provides a foundational approach to designing peptide-based immunogenic vaccines. In the current experiment, we used computational prediction approaches alongside molecular docking and molecular dynamics (MD) simulations to identify potential epitopes within gp120 and Nef proteins. The selected co-epitopes were fused with the HBsAg-binding protein (SBP), a 344-amino acid protein previously identified in our laboratory through screening of a human liver cDNA expression library against HBsAg, to facilitate efficient delivery to and uptake by dendritic cells (DCs), thereby enhancing antigen (Ag) presentation. Flexible linkers are used to connect B cells, Helper T Lymphocytes (HTLs), and Cytotoxic T Lymphocytes (CTLs) in a sequential manner. The assembled vaccine construct comprises 757 amino acids, corresponding to a recombinant protein of 83.64 kDa molecular weight. Structural analysis through docking studies, MD simulations, and 3D structure validation revealed that the designed protein exhibits high structural stability and potential for interaction with Toll-like receptors (TLRs). These findings support the vaccine’s ability to enhance cellular and humoral feedback, including the stimulation of T and B cells and induction of antibody (Ab) production. The results underscore the promise of this in silico designed co-epitope vaccine as a viable candidate for HIV-1 prevention and suggest that such constructs may serve as effective immunogens in future HIV-1 vaccine strategies. Full article

Background/Objectives: Influenza A viruses—including highly pathogenic H5N1—remain a global threat due to rapid evolution, zoonoses, and pandemic potential. Strain-specific vaccines targeting variable antigens often yield limited, short-lived immunity. The HA receptor-binding domain (RBD), a functionally constrained and immunologically relevant region, is a promising target for broad and subtype-focused vaccines. We aimed to design multiepitope constructs targeting conserved HA-RBD and adjacent domains to elicit robust, durable, cross-protective responses. Methods: Extensive sequence analyses (>20,000 H5N1 and >190,000 influenza A sequences) were used to derive consensus sequences. Three HA-based candidates were developed: (i) EpitoCore-HA-VX, a multi-epitope construct containing CTL, HTL, and B-cell epitopes from the H5N1 HA-RBD; (ii) StructiRBD-HA-VX, incorporating a conformationally preserved RBD segment; and (iii) FusiCon-HA-VX, targeting the conserved HA fusion peptide shared across subtypes. Two external HA comparators—a 400-aa HA fragment and the literature-reported HA-13–263-Fd-His—were analyzed under the same pipeline. The workflow predicted epitopes; evaluated antigenicity, allergenicity, toxicity, conservation, and HLA coverage; generated AlphaFold models; performed TLR2/TLR4 docking with pyDockWEB; and carried out interface analysis with PDBsum; and C-ImmSim simulations. Results: Models suggested stable, energetically favorable TLR2/TLR4 interfaces supported by substantial binding surfaces and complementary electrostatic/desolvation profiles. Distinct docking patterns indicated receptor-binding flexibility. Immune simulations predicted strong humoral responses with modeled memory formation and, for the H5N1-focused designs, cytotoxic T-cell activity. All candidates and comparators were predicted to be antigenic, non-allergenic, and non-toxic, with combined HLA coverage approaching global breadth. Conclusions: This study compares three design strategies within a harmonized framework—epitope collation, structure-preserved RBD, and fusion-peptide targeting—while benchmarking against two HA comparators. EpitoCore-HA-VX and StructiRBD-HA-VX showed promise against diverse H5N1 isolates, whereas FusiCon-HA-VX supported cross-subtype coverage. As these findings are model-based, they should be interpreted qualitatively; nonetheless, the integrated, structure-guided approach provides an adaptable path for advancing targeted H5N1 and broader influenza A vaccine concepts. Full article

Background: Helcococcus kunzii, a facultative anaerobe and Gram-positive coccus, has been documented as a cunning pathogen, mainly in immunocompromised individuals, as evidenced by recent clinical and microbiological reports. It has been associated with a variety of polymicrobial infections, comprising diabetic foot ulcers, prosthetic joint infections, osteomyelitis, endocarditis, and bloodstream infections. Despite its emerging clinical relevance, no licensed vaccine or targeted immunotherapy currently exists for H. kunzii, and its rising resistance to conventional antibiotics presents a growing public health concern. Objectives: In this study, we employed an integrated subtractive proteomics and immunoinformatics pipeline to design a multi-epitope subunit vaccine (MEV) candidate against H. kunzii. Initially, pan-proteome analysis identified non-redundant, essential, non-homologous, and virulent proteins suitable for therapeutic targeting. Methods/Results: From these, two highly conserved and surface-accessible proteins, cell division protein FtsZ and peptidoglycan glycosyltransferase FtsW, were selected as promising vaccine targets. Comprehensive epitope prediction identified nine cytotoxic T-lymphocyte (CTL), five helper T-lymphocyte (HTL), and two linear B-cell (LBL) epitopes, which were rationally assembled into a 397-amino-acid-long chimeric construct. The construct was designed using appropriate linkers and adjuvanted with the cholera toxin B (CTB) subunit (NCBI accession: AND74811.1) to enhance immunogenicity. Molecular docking and dynamics simulations revealed persistent and high-affinity ties amongst the MEV and essential immune receptors, indicating a durable ability to elicit an immune reaction. In silico immune dynamic simulations predicted vigorous B- and T-cell-mediated immune responses. Codon optimization and computer-aided cloning into the E. coli K12 host employing the pET-28a(+) vector suggested high translational efficiency and suitability for bacterial expression. Conclusions: Overall, this computationally designed MEV demonstrates favorable immunological and physicochemical properties, and presents a durable candidate for subsequent in vitro and in vivo validation against H. kunzii-associated infections. Full article

Background: Multi-epitope vaccines have become the preferred strategy for protection against infectious diseases by integrating multiple MHC-restricted T-cell and B-cell epitopes that elicit both humoral and cellular immune responses against pathogens. Computational methods address various aspects independently, yet their orchestration is technically challenging, as most bioinformatics tools are accessible through heterogeneous interfaces and lack interoperability features. The present work proposes a novel framework for rationalized multi-epitope vaccine design that streamlines end-to-end analyses through an integrated web-based environment. Results: VaccineDesigner is a comprehensive web-based framework that streamlines the design of protective epitope-based vaccines by seamlessly integrating computational methods for B-cell, CTL, and HTL epitope prediction. VaccineDesigner incorporates single-epitope prediction and evaluation as well as additional analyses, such as multi-epitope vaccine generation, estimation of population coverage, molecular mimicry, and proteasome cleavage. The functionalities are transparently integrated into a modular architecture, providing a single access point for rationalized, multi-epitope vaccine generation in a time- and cost-effective manner. Conclusions: VaccineDesigner is a web-based tool that identifies and evaluates candidate B-cell, CTL, and HTL epitopes and constructs a library of multi-epitope vaccines that combine strong immunogenic responses, safety, and broad population coverage. The source code is available under the academic license and freely accessible. Full article