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Search Results (265)

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Keywords = T-cell epitope-based vaccine

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15 pages, 462 KB  
Review
Advances in Neoantigen-Based Cancer Vaccines
by An-Chih Wu, Yusuke Nakamura and Kazuma Kiyotani
Cancers 2026, 18(1), 144; https://doi.org/10.3390/cancers18010144 - 31 Dec 2025
Abstract
Neoantigen-based immunotherapies harness somatic mutations as tumor-specific targets and represent a major advance in personalized cancer treatment. Since neoantigens are presented exclusively on cancer cells, they enable highly selective T-cell recognition with minimal off-tumor toxicity. Neoantigen vaccines are rapidly emerging as a versatile [...] Read more.
Neoantigen-based immunotherapies harness somatic mutations as tumor-specific targets and represent a major advance in personalized cancer treatment. Since neoantigens are presented exclusively on cancer cells, they enable highly selective T-cell recognition with minimal off-tumor toxicity. Neoantigen vaccines are rapidly emerging as a versatile class of personalized cancer immunotherapies designed to prime tumor-specific T cells by targeting somatic mutations unique to each patient’s tumor. Multiple types of neoantigen vaccines, using peptide, mRNA, and DNA, have shown feasibility, safety, and immunogenicity across diverse solid tumors. Emerging comparative data indicate that the vaccines using peptide-pulsed dendritic cells (DCs) elicit higher per-epitope CD8+ T cell responses than mRNA-based vaccines, likely due to more efficient class I presentation of synthetic peptides and ex vivo-loaded DCs. In contrast, mRNAs, despite their capacity of targeting multiple neoantigen peptides simultaneously, often induce CD4+-dominant responses due to immunodominance patterns during antigen processing. Recent clinical trials in melanoma, glioblastoma, pancreatic cancer, and other types of cancer have demonstrated not only robust immune activation but also encouraging relapse-free outcomes when administered in adjuvant settings. Treatment timing strongly influenced immune responsiveness; patients with early-stage disease or those vaccinated after surgical resection generally exhibit more preserved systemic immunity and greater vaccine-induced T cell expansion compared to those with advanced disease. Future progress will rely on improved neoantigen prediction, including incorporation of post-translationally modified antigenic targets and acceleration of manufacturing pipelines to ensure timely, personalized vaccine delivery. Collectively, neoantigen vaccines offer substantial promise for integration into next-generation cancer treatment strategies. Full article
(This article belongs to the Special Issue Neoantigen Vaccines for Cancer Therapy)
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32 pages, 3556 KB  
Article
Development and Immunogenicity Assessment of a Multi-Epitope Antigen Against Zika Virus: An In Silico and In Vivo Approach
by Lígia Rosa Sales Leal, Matheus Gardini Amâncio Marques de Sena, Maria da Conceição Viana Invenção, Ingrid Andrêssa de Moura, André Luiz Santos de Jesus, Georon Ferreira de Sousa, Bárbara Rafaela da Silva Barros, Cristiane Moutinho Lagos de Melo, Lindomar José Pena, Francesca Paolini, Aldo Venuti, Anna Jéssica Duarte Silva and Antonio Carlos de Freitas
Vaccines 2026, 14(1), 31; https://doi.org/10.3390/vaccines14010031 - 26 Dec 2025
Viewed by 169
Abstract
Background/Objectives: The Zika virus (ZIKV) represents an ongoing threat to public health due to its neurological and congenital complications. Even after 10 years since the first major outbreak, correlated with an increase in congenital ZIKV syndrome, there is still no vaccine or treatment [...] Read more.
Background/Objectives: The Zika virus (ZIKV) represents an ongoing threat to public health due to its neurological and congenital complications. Even after 10 years since the first major outbreak, correlated with an increase in congenital ZIKV syndrome, there is still no vaccine or treatment for this infection. Among the various existing platforms, DNA vaccines combined with the use of immunoinformatics tools allow for the efficient selection of immunogenic epitopes and immunostimulatory molecules with greater flexibility, in addition to being simple to manufacture and having a higher cost–benefit ratio in production. Methods: In this work, we conducted an integrated approach, combining in silico analyses and in vivo experimental validations, for the development of multi-epitope DNA vaccines against ZIKV. The computational analyses confirmed structural stability, adequate solubility, absence of toxicity, and immune induction potential for constructs based on epitopes from the Envelope (E) and NS1 proteins. Therefore, we evaluated DNA constructs containing the ENV + NS1 epitopes, both with and without fusion to the ssPGIP signal peptide, in BALB/c mice. Results: Both vaccines increased the population of CD4+ and CD8+ T lymphocytes, in addition to the production of IgG antibodies associated with the Th1 profile. The fusion with ssPGIP broadened the response, stimulating the release of Th1, Th2, and Th17 cytokines, as well as enhancing antibody formation. In contrast, its absence was associated with a slight increase in CD4+ and CD8+ T cells, accompanied by restricted cytokine production. Conclusions: These results indicate that epitope-targeted techniques offer a viable and safe method for inducing robust immune responses, demonstrating that combining immunoinformatics methods with early preclinical testing is an effective strategy for ZIKV vaccine development. Furthermore, although the present study focused on initial immunogenic characterization, future studies involving viral challenge in a suitable animal model will be essential to conclusively determine the protective efficacy of these vaccine candidates. Full article
(This article belongs to the Special Issue New Approaches to Vaccine Development and Delivery—2nd Edition)
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12 pages, 2309 KB  
Article
Complete Genome Sequences of Human Japanese Encephalitis Virus Genotype V Isolates in Korea Reveal Genotype-Specific Amino Acid Signatures
by Seung-Rye Cho, Ye-Ji Lee, Myung Guk Han and Heui Man Kim
Pathogens 2025, 14(12), 1279; https://doi.org/10.3390/pathogens14121279 - 12 Dec 2025
Viewed by 365
Abstract
Japanese encephalitis virus (JEV) is a mosquito-borne zoonotic flavivirus causing severe neurological disease across Asia, and genotype V (GV) is now predominant in Korea. Despite frequent detection of GV in mosquitoes, human-derived complete genome data remain scarce. To elucidate the molecular and antigenic [...] Read more.
Japanese encephalitis virus (JEV) is a mosquito-borne zoonotic flavivirus causing severe neurological disease across Asia, and genotype V (GV) is now predominant in Korea. Despite frequent detection of GV in mosquitoes, human-derived complete genome data remain scarce. To elucidate the molecular and antigenic characteristics of human GV infections, cerebrospinal fluid samples from unvaccinated patients positive for JEV RNA during 2018–2023 were subjected to virus isolation in LLC-MK2 cells (rhesus monkey kidney-derived epithelial cell line). Three human GV isolates (K18P80, K23P84, K23P88) were successfully obtained and their complete open reading frames (~10.3 kb) sequenced. Phylogenetic analysis with representative JEV strains (GI–GV) revealed that these isolates form a distinct lineage, clustering into two domestic clades (Clade I and II), suggesting endemic circulation and local evolution in Korea. Sequence identities with GIII-based vaccine strains were low (79% nucleotide, 91.1% amino acid), with notable divergence in nonstructural regions. Three consistent E protein substitutions (Q52E, S156T, D292E) near antigenic epitopes indicate possible immune escape. Additional clade-defining substitutions in NS3 (L31F) and NS5 (K269R, M330I) were shared with mosquito isolates, supporting human–vector molecular continuity. These findings provide fundamental genomic evidence of human JEV GV in Korea and highlight the need for genotype-specific surveillance and next-generation vaccine evaluation. Full article
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30 pages, 7254 KB  
Article
Pilot Studies Testing Novel Minimized Pan-Coronavirus (CoV) Vaccines in Feline Immunodeficiency Virus-Infected Cats With or Without Feline CoV Serotype-1 (FCoV1) Coinfection and in Specific-Pathogen-Free Cats Against Pathogenic FCoV2
by Pranaw Sinha, Marco B. Prevedello, Ananta P. Arukha, Valentina Stevenson, Karen F. Keisling, Taylor G. Nycum, Nina M. Beam, Elise D. Barras, Bikash Sahay and Janet K. Yamamoto
Vaccines 2025, 13(11), 1172; https://doi.org/10.3390/vaccines13111172 - 18 Nov 2025
Viewed by 664
Abstract
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 [...] Read more.
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
(This article belongs to the Special Issue Next-Generation Vaccines for Animal Infectious Diseases)
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19 pages, 1167 KB  
Review
mRNA-Based Neoantigen Vaccines in Pancreatic Ductal Adenocarcinoma (PDAC)—A Promising Avenue in Cancer Immunotherapy
by Jacek Kabut, Małgorzata Stopyra, Natalia Nafalska, Grzegorz J. Stępień, Michał Miciak, Marcin Jezierzański, Tomasz Furgoł, Krzysztof Feret and Iwona Gisterek-Grocholska
Int. J. Mol. Sci. 2025, 26(22), 10988; https://doi.org/10.3390/ijms262210988 - 13 Nov 2025
Viewed by 2062
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains one of the most aggressive malignancies, with 5-year survival rates consistently below 5% despite advances in surgery, chemotherapy, and targeted therapy. Worldwide, PDAC remains highly lethal, with 458,918 new cases and 432,242 deaths in 2018—about a 94% mortality-to-incidence [...] Read more.
Pancreatic ductal adenocarcinoma (PDAC) remains one of the most aggressive malignancies, with 5-year survival rates consistently below 5% despite advances in surgery, chemotherapy, and targeted therapy. Worldwide, PDAC remains highly lethal, with 458,918 new cases and 432,242 deaths in 2018—about a 94% mortality-to-incidence ratio. The limited therapeutic efficacy is largely attributed to the pronounced heterogeneity of the disease, late clinical presentation, and the strongly immunosuppressive tumor microenvironment. In recent years, mRNA-based vaccines encoding patient-specific neoantigens have emerged as a promising immunotherapeutic modality. By delivering tailored antigenic sequences, these vaccines are capable of eliciting potent cytotoxic T-cell responses against tumor-restricted epitopes, thereby enhancing tumor immunogenicity while minimizing off-target effects. This review summarizes the biological rationale underlying mRNA vaccination in PDAC, recent progress in preclinical and early clinical trials, and key obstacles related to antigen selection, delivery platforms, and the immunosuppressive stroma. The potential integration of neoantigen mRNA vaccines into multimodal therapeutic strategies, including immune checkpoint inhibition and chemotherapy, is also discussed, underscoring their prospective role in overcoming resistance mechanisms and improving clinical outcomes in PDAC. However, most current data come from early-phase trials, with long-term benefits yet unproven. Definitive conclusions on efficacy and survival await results from ongoing randomized studies expected by 2028–2029. Further progress in neoantigen identification, delivery systems, and combination strategies is crucial to fully harness mRNA vaccine potential in PDAC. Full article
(This article belongs to the Special Issue Molecular Research for Cancer Immunotherapy)
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20 pages, 3706 KB  
Article
A Highly Immunogenic and Cross-Reactive Multi-Epitope Vaccine Candidate Against Duck Hepatitis A Virus: Immunoinformatics Design and Preliminary Experimental Validation
by Yuanhe Yang, Xiaodong Chen, Anguo Liu, Jinxin He, Yunhe Cao and Pingli He
Int. J. Mol. Sci. 2025, 26(22), 10958; https://doi.org/10.3390/ijms262210958 - 12 Nov 2025
Viewed by 640
Abstract
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 [...] Read more.
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
(This article belongs to the Special Issue Advances in Vaccine Immunology)
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13 pages, 830 KB  
Article
Genomic Analysis of Glycosyltransferases Responsible for Galactose-α-1,3-Galactose Epitopes in Streptococcus pneumoniae: Implications for Broadly Protective Vaccination Strategy
by Xinjia Mai, Nian Wang, Chenxi Zhu, Yue Ma, Zhongrui Ma, Lan Yin and Dapeng Zhou
Vaccines 2025, 13(11), 1148; https://doi.org/10.3390/vaccines13111148 - 10 Nov 2025
Viewed by 567
Abstract
Background: The origin of natural anti-galactose-α-1,3-galactose (anti-Gal) antibodies in humans is only partially understood. The gut microbiome has been proposed as an important source of galactose-α-1,3-galactose (αGal) epitopes that drive the maturation of anti-Gal–reactive B cells. Certain bacteria expressing αGal epitopes, notably Escherichia [...] Read more.
Background: The origin of natural anti-galactose-α-1,3-galactose (anti-Gal) antibodies in humans is only partially understood. The gut microbiome has been proposed as an important source of galactose-α-1,3-galactose (αGal) epitopes that drive the maturation of anti-Gal–reactive B cells. Certain bacteria expressing αGal epitopes, notably Escherichia coli O86:B7, have been shown to elicit anti-Gal antibody responses in α1,3-galactosyltransferase knockout (α3GalT1 KO) mice. In this study, we investigated the interaction between currently widely used bacteria polysaccharide vaccine, the 23-valent pneumococcal polysaccharide vaccine (PPV23), which contains capsular polysaccharides (CPS) from multiple Streptococcus pneumoniae serotypes, and host anti-Gal antibodies. Methods: We conducted a genomic analysis to identify α1,3-galactosyltransferase (α3GalT1) genes in S. pneumoniae strains. Binding of PPV23 to anti-Gal monoclonal antibodies was evaluated by ELISA, and αGal epitope content in PPV23 was estimated using a four-parameter logistic (4PL) model fitted to the ELISA calibration data. To assess in vivo immunogenicity, we immunized α3GalT1 KO mice with PPV23 and measured serum anti-Gal IgG and IgM titers before and after vaccination. Results: Genomic analysis revealed the presence of α3GalT1 genes in S. pneumoniae strains. PPV23 showed specific binding to anti-Gal monoclonal antibodies as detected by ELISA. Quantitative modeling indicated that αGal epitopes are present at low abundance within PPV23, consistent with limited expression of αGal among a minority of included serotypes. Immunization of α3GalT1 KO mice with PPV23 induced a significant rise in anti-Gal IgG titers (mean value from 124 to 384), whereas anti-Gal IgM titers remained relatively unchanged (mean value at the range of 6500–7500). High baseline anti-Gal IgM levels observed in α3GalT1 KO mice are consistent with age-dependent induction by the gut microbiota. Conclusions: These results provide genetic and immunological evidence that αGal epitopes derived from S. pneumoniae are present in PPV23 and can engage pre-existing anti-Gal antibodies. Our findings underscore a complex interplay among bacterial glycosyltransferase genes, vaccine polysaccharide composition, and host anti-Gal antibody repertoires, which may influence vaccine immunogenicity. Consideration of host natural antibody profiles may therefore be important for interpreting responses to carbohydrate-based vaccines and for guiding vaccine design. Full article
(This article belongs to the Section Pathogens-Host Immune Boundaries)
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12 pages, 1559 KB  
Article
TCEPVDB: Artificial Intelligence-Based Proteome-Wide Screening of Antigens and Linear T-Cell Epitopes in the Poxviruses and the Development of a Repository
by Mansi Dutt, Anuj Kumar, Ali Toloue Ostadgavahi, David J. Kelvin and Gustavo Sganzerla Martinez
Proteomes 2025, 13(4), 58; https://doi.org/10.3390/proteomes13040058 - 6 Nov 2025
Viewed by 562
Abstract
Background: Poxviruses constitute a family of large dsDNA viruses that can infect a plethora of species including humans. Historically, poxviruses have caused a health burden in multiple outbreaks. The large genome of poxviruses favors reverse vaccinology approaches that can determine potential antigens and [...] Read more.
Background: Poxviruses constitute a family of large dsDNA viruses that can infect a plethora of species including humans. Historically, poxviruses have caused a health burden in multiple outbreaks. The large genome of poxviruses favors reverse vaccinology approaches that can determine potential antigens and epitopes. Here, we propose the modeling of a user-friendly database containing the predicted antigens and epitopes of a large cohort of poxvirus proteomes using the existing PoxiPred method for reverse vaccinology of poxviruses. Methods: In the present study, we obtained the whole proteomes of as many as 37 distinct poxviruses. We utilized each proteome to predict both antigenic proteins and T-cell epitopes of poxviruses with the aid of an Artificial Intelligence method, namely the PoxiPred method. Results: In total, we predicted 3966 proteins as potential antigen targets. Of note, we considered that this protein may exist in a set of proteoforms. Subsets of these proteins constituted a comprehensive repository of 54,291 linear T-cell epitopes. We combined the outcome of the predictions in the format of a web tool that delivers a database of antigens and epitopes of poxviruses. We also developed a comprehensive repository dedicated to providing access to end-users to obtain AI-based screened antigens and T-cell epitopes of poxviruses in a user-friendly manner. These antigens and epitopes can be utilized to design experiments for the development of effective vaccines against a plethora of poxviruses. Conclusions: The TCEPVDB repository, already deployed to the web under an open-source coding philosophy, is free to use, does not require any login, does not store any information from its users. Full article
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22 pages, 1292 KB  
Review
T-Cell-Based Universal Dengue Vaccine Design for Robust Protective Response
by Yi Fei Sun, Adeline Yeo Syin Lian and Meng Ling Moi
Vaccines 2025, 13(11), 1118; https://doi.org/10.3390/vaccines13111118 - 30 Oct 2025
Viewed by 1476
Abstract
Dengue virus remains a major global health threat due to the lack of a safe and broadly effective vaccine. Traditional antibody-based vaccines often show limited protection and can exacerbate disease severity in individuals without prior exposure. A new generation of T-cell epitope-based vaccines [...] Read more.
Dengue virus remains a major global health threat due to the lack of a safe and broadly effective vaccine. Traditional antibody-based vaccines often show limited protection and can exacerbate disease severity in individuals without prior exposure. A new generation of T-cell epitope-based vaccines offers a promising and safer approach by activating the cellular arm of the immune system to complement antibody responses. Instead of targeting only surface structural proteins, these vaccines focus on highly conserved peptide regions within non-structural proteins, particularly NS3 and NS5, that are shared across all four dengue virus serotypes. Peptides such as DTTPFGQQR, KPGTSGSPI, and MYFHRRDLRL have been identified as potent immunogenic targets capable of inducing strong cytotoxic and helper T-cell responses, promoting viral clearance and long-term immune memory. Advanced immunoinformatic enables precise prediction and selection of epitopes with high binding affinity to human leukocyte antigens and broad cross-serotype conservation. These peptides can be integrated into next-generation vaccine delivery systems, including messenger RNA and nanoparticle platforms, which enhance antigen presentation, improve molecular stability, and reduce the risk of antibody-dependent disease enhancement. Together, this integrative design represents a rational path toward a safer, cross-protective, and durable dengue vaccine that closely mimics the balanced cellular and humoral immunity observed after natural infection, offering renewed hope for effective global dengue prevention. Full article
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24 pages, 4523 KB  
Review
Artificial Intelligence Driven Framework for the Design and Development of Next-Generation Avian Viral Vaccines
by Muddapuram Deeksha Goud, Elisa Ramos, Abid Ullah Shah and Maged Gomaa Hemida
Microorganisms 2025, 13(10), 2361; https://doi.org/10.3390/microorganisms13102361 - 14 Oct 2025
Viewed by 1708
Abstract
The rapid emergence and evolution of avian viral pathogens present a major challenge to global poultry health and food security. Traditional vaccine development is often slow, costly, and limited by antigenic diversity. In this study, we present a comprehensive artificial intelligence (AI)-driven pipeline [...] Read more.
The rapid emergence and evolution of avian viral pathogens present a major challenge to global poultry health and food security. Traditional vaccine development is often slow, costly, and limited by antigenic diversity. In this study, we present a comprehensive artificial intelligence (AI)-driven pipeline for the rational design, modeling, and optimization of multi-epitope vaccines targeting economically important RNA and DNA viruses affecting poultry, including H5N1, NDV, IBV, IBDV, CAV, and FPV. We utilized advanced machine learning and deep learning tools for epitope prediction, antigenicity assessment, and structural modeling (via AlphaFold2), and codon optimization. B-cell and T-cell epitopes were selected based on binding affinity, conservation, and immunogenicity, while adjuvants and linker sequences enhanced construct stability and immune response. In silico immune simulations forecasted robust humoral and cellular responses, including cytokine production and memory cell activation. The study also highlights challenges such as data quality, model interpretability, and ethical considerations. Our work demonstrates the transformative potential of AI in veterinary vaccinology and offers a scalable model for rapid, data-driven vaccine development against avian diseases. Full article
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38 pages, 8212 KB  
Article
Immunoinformatic Prediction of HIV-1 Glycoprotein gp120 and Nef Epitopes Conjugated to HBsAg-Binding Protein (SBP) to Induce the Humoral and Cellular Immune Response
by Arslan Habib, Xinyi Xu, Jun Xie and Naishuo Zhu
Int. J. Mol. Sci. 2025, 26(19), 9828; https://doi.org/10.3390/ijms26199828 - 9 Oct 2025
Viewed by 1096
Abstract
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 [...] Read more.
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
(This article belongs to the Section Molecular Informatics)
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32 pages, 7470 KB  
Article
Consensus-Guided Construction of H5N1-Specific and Universal Influenza a Multiepitope Vaccines
by Marco Palma
Biology 2025, 14(10), 1327; https://doi.org/10.3390/biology14101327 - 25 Sep 2025
Viewed by 992
Abstract
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 [...] Read more.
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
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27 pages, 2108 KB  
Article
Integrating Reverse Vaccinology with Immunoinformatics for Rational Vaccine Target Discovery in Mycoplasma genitalium
by Jyoti Taneja, Ravi Kant and Daman Saluja
Venereology 2025, 4(3), 14; https://doi.org/10.3390/venereology4030014 - 22 Sep 2025
Viewed by 988
Abstract
Background: The increasing prevalence of antibiotic-resistant Mycoplasma genitalium poses a significant challenge to global public health, necessitating the exploration of alternative therapeutic strategies, including vaccine development. Methods: In this study, we employed an immuno-informatics-based reverse vaccinology approach augmented with artificial intelligence-driven [...] Read more.
Background: The increasing prevalence of antibiotic-resistant Mycoplasma genitalium poses a significant challenge to global public health, necessitating the exploration of alternative therapeutic strategies, including vaccine development. Methods: In this study, we employed an immuno-informatics-based reverse vaccinology approach augmented with artificial intelligence-driven tools, to identify and characterize potential B-cell and T-cell epitopes from the hypothetical proteins (HPs) retrieved from the genome of the MG_G37T strain, a previously uncharacterized yet promising vaccine target. Using multiple softwares, a systematic pipeline was utilized to assess the sub-cellular localization, antigenicity, and allergenicity of the selected proteins. Results: Sub-cellular localization analysis identified the presence of several outer membrane and extracellular proteins in the genome of MG_G37T, indicating their surface association and accessibility to immune surveillance. Antigenicity and allergenicity prediction tools led to the identification of two top-scoring hypothetical proteins (fig|2097.71.peg.1 (UniProt ID: P22747) and fig|2097.70.peg.33 (UniProt ID: Q57081)) that demonstrated strong antigenic potential, non-allergenic properties, and suitability as vaccine candidates. Epitope mapping and structural modeling analyses further validated the immunogenic potential of these epitopes, highlighting their ability to interact with host immune components effectively. Comparative analyses with mouse allelic regions indicated the potential translational relevance of these predicted epitopes for preclinical studies. Conclusions: In particular, this study highlights the potential of these two hypothetical proteins as a promising vaccine candidate and provides a strong reason for experimental validation towards the design and development of effective vaccines to combat M. genitalium infections in the era of antimicrobial resistance. Full article
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24 pages, 1890 KB  
Review
Identification of T-Cell Epitopes and Vaccine Development for African Swine Fever Virus
by Wanyi Ni, Hanchun Yang and Nianzhi Zhang
Vaccines 2025, 13(9), 955; https://doi.org/10.3390/vaccines13090955 - 7 Sep 2025
Viewed by 1730
Abstract
African swine fever virus (ASFV) has inflicted severe devastation on the global pig industry, yet a globally approved vaccine remains unavailable. Given that cellular immunity is critical for ASFV prevention, the development of vaccines based on T-cell epitopes emerges as a promising strategy [...] Read more.
African swine fever virus (ASFV) has inflicted severe devastation on the global pig industry, yet a globally approved vaccine remains unavailable. Given that cellular immunity is critical for ASFV prevention, the development of vaccines based on T-cell epitopes emerges as a promising strategy to control this virus. This review synthesizes the recent advancements and challenges in the research on ASFV T-cell epitopes, while offering insights into the potential impact of novel T-cell epitope-based vaccines. Notably, only a limited number of ASFV T-cell epitopes have been experimentally identified to date, covering fewer than 20 ASFV proteins. This bottleneck is attributed to challenges such as high swine leukocyte antigen (SLA) polymorphism, suboptimal accuracy of predicting tools, and complex experimental validation procedures. Although current studies on ASFV-specific T-cell immune responses and epitope identification are insufficient to meet vaccine development needs, continuous progress in T-cell immunology research in recent years has brought this goal closer to reality. Full article
(This article belongs to the Special Issue African Swine Fever Virus Vaccine Development)
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28 pages, 8441 KB  
Review
Recombinant Chimeric Virus-like Particles of Human Papillomavirus Produced by Distinct Cell Lineages: Potential as Prophylactic Nanovaccine and Therapeutic Drug Nanocarriers
by Cyntia Silva Oliveira, Dirce Sakauchi, Érica Akemi Kavati Sasaki and Aurora Marques Cianciarullo
Viruses 2025, 17(9), 1209; https://doi.org/10.3390/v17091209 - 4 Sep 2025
Viewed by 2335
Abstract
Antigenicity and immunogenicity define a potent immunogen in vaccinology. Nowadays, there are simplified platforms to produce nanocarriers for small-peptide antigen delivery, derived from various infectious agents for the treatment of a variety of diseases, based on virus-like particles (VLPs). They have good cell-penetrating [...] Read more.
Antigenicity and immunogenicity define a potent immunogen in vaccinology. Nowadays, there are simplified platforms to produce nanocarriers for small-peptide antigen delivery, derived from various infectious agents for the treatment of a variety of diseases, based on virus-like particles (VLPs). They have good cell-penetrating properties and protective action for target molecules from degradation. Human papillomavirus (HPV) causes anogenital warts and six types of cancer in infected women, men, or children, posing a challenge to global public health. The HPV capsid is composed of viral type-specific L1 and evolutionarily conserved L2 proteins. Produced in heterologous systems, the L1 protein can self-assemble into VLPs, nanoparticles sized around 50–60 nm, used as prophylactic vaccines. Devoid of the viral genome, they are safe for users, offering no risk of infection because VLPs do not replicate. The immune response induced by HPV VLPs is promoted by conformational viral epitopes, generating effective T- and B-cell responses. Produced in different cell systems, HPV16 L1 VLPs can be obtained on a large scale for use in mass immunization programs, which are well established nowadays. The expression of heterologous proteins was evaluated at various transfection times by transfecting cells with vectors encoding codon-optimized HPV16L1 and HPV16L2 genes. Immunological response induced by chimeric HPV16 L1/L2 VLP was evaluated through preclinical assays by antibody production, suggesting the potential of broad-spectrum protection against HPV as a prophylactic nanovaccine. These platforms can also offer promising therapeutic strategies, covering the various possibilities for complementary studies to develop potential preventive and therapeutic vaccines with broad-spectrum protection, using in silico new epitope selection and innovative nanotechnologies to obtain more effective immunobiologicals in combating HPV-associated cancers, influenza, hepatitis B and C, tuberculosis, human immunodeficiency virus (HIV), and many other illnesses. Full article
(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)
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