Cell Epitope Peptides Research Articles

Exploring the allergenic potential of sesame oleosins: Isolation and bioinformatics analysis

This study examined two oleosins of 17 kDa and 15 kDa isolated from Yuzhi white sesame seeds through oil body extraction. The allergens were identified as oleosin H1 (Ses i 4) and oleosin L (Ses i 5) using SDS-PAGE, dot blot analysis, and LC-MS/MS. PCR analysis revealed high sequence homology for the oleosin proteins in the sesame seeds. Utilizing AlphaFold2, bioinformatics tools, and protein-protein docking, the structure and function of these oleosins were analyzed. Ten potential B cell epitope peptides were predicted and mapped onto the α-helix and random coil-dominated oleosome membrane conformation. IgE binding simulations identified key epitopes, B3 (FLTSGAFGL) and B4 (KRGVQEGTLY) for oleosin H1, and B8 (GGFGVAALSV) and B9 (DQLESAKTKL) for oleosin L. Mutational analysis highlighted Glu135, Phe102, Tyr128, Tyr139, Gly136, and Gly132 in oleosin H1, and Leu120, Lys119, and Leu113 in oleosin L as critical residues for binding stability, providing insights into the sensitization mechanism of these epitopes. The integration of bioinformatics and immunoinformatics in this study has contributed to a deeper understanding of the allergy properties of sesame oleosins.

Crohn’s patients and healthy infants share immunodominant B cell response to commensal flagellin peptide epitopes

Inflammatory bowel disease (IBD) is a chronic manifestation of dysregulated immune response to the gut microbiota in genetically predisposed hosts. Nearly half of patients with Crohn's disease (CD) develop selective serum immunoglobulin (Ig)G response to flagellin proteins expressed by bacteria in the Lachnospiraceae family. This study aimed to identify the binding epitopes of these IgG antibodies and assess their relevance in CD and in homeostasis. Sera from an adult CD cohort, a treatment-naïve pediatric CD cohort, and 3 independent non-IBD infant cohorts were analyzed using novel techniques including a flagellin peptide microarray and a flagellin peptide cytometric bead array. A dominant B cell peptide epitope in patients with CD was identified, located in the highly conserved "hinge region" between the D0 and D1 domains at the amino-terminus of Lachnospiraceae flagellins. Elevated serum IgG reactivity to the hinge peptide was strongly associated with incidence of CD and the development of disease complications in children with CD up to 5 years in advance. Notably, high levels of serum IgG to the hinge epitope were also found in most infants from 3 different geographic regions (Uganda, Sweden, and the United States) at 1 year of age, which decrements rapidly afterward. These findings identified a distinct subset of patients with CD, united by a shared reactivity to a dominant commensal bacterial flagellin epitope, that may represent failure of a homeostatic response to the gut microbiota beginning in infancy.

Abstract 6746: A B-cell targeted TLR9 agonist antibody conjugate potentiates cancer vaccine efficacy and rejuvenates vaccine responses in the elderly

Abstract TLR9 agonists (unmethylated CpG oligodeoxynucleotides) are clinically validated as vaccine adjuvants and cancer therapeutics1,2. We developed a Toll-like Receptor Agonist Antibody Conjugate (TRAAC) comprised of a potent TLR9 agonist (T-CpG) conjugated to an antibody against CD22, a receptor restricted to B cells (TAC-001). Systemically administered TAC-001 delivers T-CpG to B cells, resulting in TLR9 activation, and innate and adaptive anti-tumor immunity3. TAC-001 is being evaluated as an immunotherapy in a Phase 1 clinical trial in patients with advanced solid tumors (NCT05399654)4. In this study, we investigated whether TAC-001 mouse surrogate, mCD22 TRAAC, can potentiate cancer vaccine efficacy using preclinical vaccination models. Human Nectin-4 ectodomain protein (N4, 94% homology to its mouse ortholog) was used as a neoantigen-like vaccine, alone and in combination with mCD22 TRAAC, MPLA (a TLR4 agonist), or unconjugated T-CpG. Mice were immunized, then challenged 2 months later with syngeneic CT26 tumors expressing N4. Mice in treatment combination cohorts that resisted tumor development were split into two groups and rechallenged 3.5 months later with a more aggressive tumor, syngeneic 4T1 or 4T1 expressing N4. The combination of vaccine with mCD22 TRAAC was the only treatment able to inhibit growth of the 4T1-N4 tumor. No efficacy was observed in mice inoculated with parental 4T1, thereby demonstrating neoantigen vaccine specific anti-tumor immunity. An MHCI restricted peptide of HER2/neu, GP2, fused to a B cell epitope peptide, P4, and conjugated to KLH, was used as another vaccine model5. GP2-P4-KLH was administered to mice alone or in combination with mCD22 TRAAC or unconjugated T-CpG. Ex vivo GP2/GP2-P4 stimulation of lymphoid organ immune cells from mice treated with vaccine plus mCD22 TRAAC resulted in elevated Granzyme B, IFNγ and IL17A levels, indicating that mCD22 TRAAC enhances T cell activation and cytotoxic activity. Lastly, to investigate the effect of mCD22 TRAAC in elderly mice, SARS-CoV-2 spike protein was used as a vaccine. Spike was administered alone or in combination with mCD22 TRAAC, MPLA or T-CpG. Combining mCD22 TRAAC with vaccine resulted in high levels of spike neutralizing IgG in both youth and elderly cohorts, showing that mCD22 TRAAC rejuvenates vaccine responses in elderly. In all studies, mCD22 TRAAC led to the most potent vaccine recall response, with high antigen specific IgG titers skewing towards a Th1 phenotype, as shown by elevated levels of effector function antibodies of IgG2a subclass and increased IFNγ production. These findings provide a strong rationale for combining TAC-001 with cancer vaccines. References1Hyer et al., Vaccine 2018; 36(19) 2Long et al., Annals of Oncology 2018; 29(8) 3Kuo et al., Cancer Research 2021; 81(13)4Perez et al., JITC 2023; 11(1) 5Nordin et al., Cancers 2021; 13(19) Citation Format: Maja Z. Bonacorsi, Amy Chen, Ons Harrabi, Min Li, Emma R. Sangalang, Danielle Fontaine, Janet Sim, Pavel Strop, Hong I. Wan, Maria Jose Costa. A B-cell targeted TLR9 agonist antibody conjugate potentiates cancer vaccine efficacy and rejuvenates vaccine responses in the elderly [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6746.

Impact of antiretroviral therapy during acute or early HIV infection on virologic and immunologic outcomes: results from a multinational clinical trial.

To assess how antiretroviral therapy (ART) initiation during acute or early HIV infection (AEHI) affects the viral reservoir and host immune responses. Single-arm trial of ART initiation during AEHI at 30 sites in the Americas, Africa, and Asia. HIV DNA was measured at week 48 of ART in 5 million CD4 + T cells by sensitive qPCR assays targeting HIV gag and pol . Peripheral blood mononuclear cells were stimulated with potential HIV T cell epitope peptide pools consisting of env , gag , nef, and pol peptides and stained for expression of CD3, CD4, CD8, and intracellular cytokines/chemokines. From 2017 to 2019, 188 participants initiated ART during Fiebig stages I ( n = 6), II ( n = 43), III ( n = 56), IV ( n = 23), and V ( n = 60). Median age was 27 years (interquartile range 23-38), 27 (14%) participants were female, and 180 (97%) cisgender. Among 154 virally suppressed participants at week 48, 100% had detectable HIV gag or pol DNA. Participants treated during Fiebig I had the lowest HIV DNA levels ( P < 0.001). Week 48 HIV DNA mostly did not correlate with concurrent CD4 + or CD8 + T cell HIV-specific immune responses (rho range -0.11 to +0.19, all P > 0.025). At week 48, the magnitude, but not polyfunctionality, of HIV-specific T cell responses was moderately reduced among participants who initiated ART earliest. Earlier ART initiation during AEHI reduced but did not eliminate the persistence of HIV-infected cells in blood. These findings explain the rapid viral rebound observed after ART cessation in early-treated individuals with undetectable HIV DNA by less sensitive methods.

Omicron BA.2 breakthrough infection elicits CD8+ T cell responses recognizing the spike of later Omicron subvariants.

Here, we examine peripheral blood memory T cell responses against the SARS-CoV-2 BA.4/BA.5 variant spike among vaccinated individuals with or without Omicron breakthrough infections. We provide evidence supporting a lack of original antigenic sin in CD8+ T cell responses targeting the spike. We show that BNT162b2-induced memory T cells respond to the BA.4/BA.5 spike. Among individuals with BA.1/BA.2 breakthrough infections, IFN-γ-producing CD8+ T cell responses against the BA.4/BA.5 spike increased. In a subgroup with BA.2 breakthrough infections, IFN-γ-producing CD8+ T cell responses against the BA.2-mutated spike region increased and correlated directly with responses against the BA.4/BA.5 spike, indicating that BA.2 spike-specific CD8+ T cells elicited by BA.2 breakthrough infection cross-react with the BA.4/BA.5 spike. We identified CD8+ T cell epitope peptides that are present in the spike of BA.2 and BA.4/BA.5 but not the original spike. These peptides are fully conserved in the spike of now-dominant XBB lineages. Our study shows that breakthrough infection by early Omicron subvariants elicits CD8+ T cell responses that recognize epitopes within the spike of newly emerging subvariants.

Activity Relationship of Poly(ethylenimine)-Based Liposomes as Group A Streptococcus Vaccine Delivery Systems.

Untreated group A Streptococcus (GAS) can lead to a range of life-threatening diseases, including rheumatic heart disease. To date, no therapeutic or prophylactic vaccines are commercially available to treat or prevent GAS infection. Development of a peptide-based subunit vaccine offers a promising solution, negating the safety issues of live-attenuated or inactive vaccines. Subunit vaccines administer small peptide fragments (antigens), which are typically poorly immunogenic. Therefore, these peptide antigens require formulation with an immune stimulant and/or vaccine delivery platform to improve their immunogenicity. We investigated polyelectrolyte complexes (PECs) and polymer-coated liposomes as self-adjuvanting delivery vehicles for a GAS B cell peptide epitope conjugated to a universal T-helper epitope and a synthetic toll-like receptor 2-targeting moiety lipid core peptide-1 (LCP-1). A structure-activity relationship of cationic PEC vaccines containing different external PEI-coatings (poly(ethylenimine); 10 kDa PEI, 25 kDa PEI, and a synthetic mannose-functionalized 25 kDa PEI) formed vaccines PEC-1, PEC-2, and PEC-3, respectively. All three PEC vaccines induced J8-specific systemic immunoglobulin G (IgG) antibodies when administered intranasally to female BALB/c mice without the use of additional adjuvants. Interestingly, PEC-3 induced the highest antibody titers among all tested vaccines, with the ability to effectively opsonize two clinically isolated GAS strains. A comparative study of PEC-2 and PEC-3 with liposome-based delivery systems was performed subcutaneously. LCP-1 was incorporated into a liposome formulation (DPPC, DPPG and cholesterol), and the liposomes were externally coated with PEI (25 kDa; Lip-2) or mannosylated PEI (25 kDa; Lip-3). All liposome vaccines induced stronger humoral immune responses compared to their PEC counterparts. Notably, sera of mice immunized with Lip-2 and Lip-3 produced significantly higher opsonic activity against clinically isolated GAS strains compared to the positive control, P25-J8 emulsified with the commercial adjuvant, complete Freund's adjuvant (CFA). This study highlights the capability of a PEI-liposome system to act as a self-adjuvanting vehicle for the delivery of GAS peptide antigens and protection against GAS infection.

Peptide immunotherapy for aeroallergens.

Background: Allergen specific immunotherapy (SIT) has been used for more than a century. Researchers have been working to improve efficacy and reduce the side effects. Objective: We have reviewed the literature about peptides immunotherapy for inhaled allergens. The mechanism of SIT is to induce regulatory T (Treg) cells and to reduce T helper (Th)2 cells to induce class switching from IgE to IgG and induce blocking antibodies to inhibit allergen binding of IgE. Methods: The relevant published literatures on the peptide SIT for aeroallergens have been searched on the medline. Results: Modification of allergens and routes of treatment has been performed. Among them, many researchers were interested in peptide immunotherapy. T-cell epitope peptide has no IgE epitope, that is able to bind IgE, but rather induces Treg and reduces Th2 cells, which was considered an ideal therapy. Results from cellular and animal model studies have been successful. However, in clinical studies, T-cell peptide immunotherapy has failed to show efficacy and caused side effects, because of the high effective rate of placebo and the development of IgE against T-cell epitope peptides. Currently, the modifications of IgE-allergen binding by blocking antibodies are considered for successful allergen immunotherapy. Conclusion: Newly developed hypoallergenic B cell epitope peptides and computational identification methods hold great potential to develop new peptide immunotherapies.

Preparation, Identification and Application of β-Lactoglobulin Hydrolysates with Oral Immune Tolerance.

To reveal, for the first time, the mechanism of T cell epitope release from β-lactoglobulin that induces oral immune tolerance, a strategy for the prediction, preparation, identification and application of β-lactoglobulin hydrolysate with oral immune tolerance was established using the bioinformatics method, hydrolysis, mass spectrometry, T cell proliferation assays and animal experiments. Some T cell epitope peptides of β-lactoglobulin were identified for the first time. The hydrolysates of trypsin, protamex and papain showed oral tolerance, among which the hydrolysates of protamex and papain have been reported for the first time. Although the neutral protease hydrolysate contained T cell epitopes, it still had allergenicity. The mechanism behind oral immune tolerance induction by T cell epitopes needs to be further revealed. In addition, the trypsin hydrolysate with abundant T cell epitopes was added to whey protein to prepare the product for oral immune tolerance. Overall, this study provides insights into the development of new anti-allergic milk-based products and their application in the clinical treatment of milk allergies.

Development of the B cell cancer vaccine HER-vaxx for the treatment of her-2 expressing cancers.

Her-2/neu is a tumor-associated protein that is overexpressed in a number of malignancies, including advanced cancer of the stomach, and has been proposed as a human cancer vaccine target. Overexpression of Her-2/neu in human breast and gastric carcinomas correlates with a more aggressive course of disease that results in poorer overall survival rates and shorter times to disease progression than in patients with tumors without overexpression of Her-2/neu. Cancer vaccines have the ability to stimulate the native immune system and in particular engineered B cell epitopes can elicit high affinity polyclonal antibodies with similar efficacy to Her-2 monoclonal antibodies such as trastuzumab (Roche). HER-Vaxx is under development as a therapeutic B cell vaccine for the treatment of gastric cancer in patients with Her-2/neu overexpressing metastatic or advanced adenocarcinoma of the stomach or gastroesophageal junction, referred to as advanced cancer of the stomach. P467-CRM197, the vaccine's immunogenic component, contains a single peptide antigen composed of 3 individual linear B cell epitope peptide sequences selected from the oncoprotein Her-2/neu that induce the patient's own B cells to produce endogenous anti-Her-2/neu antibodies. This review provides results from comprehensive preclinical studies encompassing primary and secondary pharmacodynamics, biodistribution and safety studies. These studies were performed to support clinical development of HER-Vaxx. Results from the GLP toxicology study in rodents showed that the vaccine did not produce any observable adverse effects suggesting that the doses proposed for the clinical trial should be well tolerated in patients.

Preparation, Characteristics, Toxicity, and Efficacy Evaluation of the Nasal Self-assembled Nanoemulsion Tumor Vaccine In Vitro and In Vivo.

Epitope peptides have attracted widespread attention in the field of tumor vaccines because of their safety, high specificity, and convenient production; in particular, some MHC I-restricted epitopes can induce effective cytotoxic T lymphocyte activity to clear tumor cells. Additionally, nasal administration is an effective and safe delivery technique for tumor vaccines due to its convenience and improved patient compliance. However, epitope peptides are unsuitable for nasal delivery because of their poor immunogenicity and lack of delivery efficiency. Nanoemulsions (NEs) are thermodynamically stable systems that can be loaded with antigens and delivered directly to the nasal mucosal surface. Ile-Lys-Val-Ala-Val (IKVAV) is the core pentapeptide of laminin, an integrin-binding peptide expressed by human respiratory epithelial cells. In this study, an intranasal self-assembled epitope peptide NE tumor vaccine containing the synthetic peptide IKVAV-OVA257-264 (I-OVA) was prepared by a low-energy emulsification method. The combination of IKVAV and OVA257-264 can enhance antigen uptake by nasal mucosal epithelial cells. Here, we establish a protocol to study the physicochemical characteristics by transmission electron microscopy (TEM), atomic force microscopy (AFM), and dynamic light scattering (DLS); stability in the presence of mucin protein; toxicity by examining the cell viability of BEAS-2B cells and the nasal and lung tissues of C57BL/6 mice; cellular uptake by confocal laser scanning microscopy (CLSM); release profiles by imaging small animals in vivo; and the protective and therapeutic effect of the vaccine by using an E.G7 tumor-bearing model. We anticipate that the protocol will provide technical and theoretical clues for the future development of novel T cell epitope peptide mucosal vaccines.

A high-throughput screening RT-qPCR assay for quantifying surrogate markers of immunity from PBMCs.

Immunoassays that quantitate cytokines and other surrogate markers of immunity from peripheral blood mononuclear cells (PBMCs), such as flow cytometry or Enzyme-Linked Immunosorbent Spot (ELIspot), allow highly sensitive measurements of immune effector function. However, those assays consume relatively high numbers of cells and expensive reagents, precluding comprehensive analyses and high-throughput screening (HTS). To address this issue, we developed a sensitive and specific reverse transcription-quantitative PCR (RT-qPCR)-based HTS assay, specifically designed to quantify surrogate markers of immunity from very low numbers of PBMCs. We systematically evaluated the volumes and concentrations of critical reagents within the RT-qPCR protocol, miniaturizing the assay and ultimately reducing the cost by almost 90% compared to current standard practice. We assessed the suitability of this cost-optimized RT-qPCR protocol as an HTS tool and determined the assay exceeds HTS uniformity and signal variance testing standards. Furthermore, we demonstrate this technique can effectively delineate a hierarchy of responses from as little as 50,000 PBMCs stimulated with CD4+ or CD8+ T cell peptide epitopes. Finally, we establish that this HTS-optimized protocol has single-cell analytical sensitivity and a diagnostic sensitivity equivalent to detecting 1:10,000 responding cells (i.e., 100 Spot Forming Cells/106 PBMCs by ELIspot) with over 90% accuracy. We anticipate this assay will have widespread applicability in preclinical and clinical studies, especially when samples are limited, and cost is an important consideration.

A third vaccination with a single T cell epitope confers protection in a murine model of SARS-CoV-2 infection

Understanding the mechanisms and impact of booster vaccinations are essential in the design and delivery of vaccination programs. Here we show that a three dose regimen of a synthetic peptide vaccine elicits an accruing CD8+ T cell response against one SARS-CoV-2 Spike epitope. We see protection against lethal SARS-CoV-2 infection in the K18-hACE2 transgenic mouse model in the absence of neutralizing antibodies, but two dose approaches are insufficient to confer protection. The third vaccine dose of the single T cell epitope peptide results in superior generation of effector-memory T cells and tissue-resident memory T cells, and these tertiary vaccine-specific CD8+ T cells are characterized by enhanced polyfunctional cytokine production. Moreover, fate mapping shows that a substantial fraction of the tertiary CD8+ effector-memory T cells develop from re-migrated tissue-resident memory T cells. Thus, repeated booster vaccinations quantitatively and qualitatively improve the CD8+ T cell response leading to protection against otherwise lethal SARS-CoV-2 infection.

Exosomal Vaccine Loading T Cell Epitope Peptides of SARS-CoV-2 Induces Robust CD8+ T Cell Response in HLA-A Transgenic Mice.

PurposeCurrent vaccines for the SARS-CoV-2 virus mainly induce neutralizing antibodies but overlook the T cell responses. This study aims to generate an exosomal vaccine carrying T cell epitope peptides of SARS-CoV-2 for the induction of CD8+ T cell response.MethodsThirty-one peptides presented by HLA-A0201 molecule were conjugated to the DMPE-PEG-NHS molecules, and mixed with DSPE-PEG to form the peptide-PEG-lipid micelles, then fused with exosomes to generate the exosomal vaccine, followed by purification using size-exclusion chromatography and validation by Western blotting, liquid nuclear magnetic resonance (NMR) test and transmission electron microscopy. Furthermore, the exosomal vaccine was mixed with Poly (I:C) adjuvant and subcutaneously administered for three times into the hybrid mice of HLA-A0201/DR1 transgenic mice with wild-type mice. Then, the epitope-specific T cell responses were detected by ex vivo ELISPOT assay and intracellular cytokine staining.ResultsThe exosomal vaccine was purified from the Peak 2 fraction of FPLC and injected into the hybrid mice for three times. The IFN-γ spot forming units and the frequencies of IFN-γ+/CD8+ T cells were 10–82-fold and 13–65-fold, respectively, higher in the exosomal vaccine group compared to the Poly (I:C) control group, without visible organ toxicity. In comparison with the peptides cocktail vaccine generated in our recent work, the exosomal vaccine induced significantly stronger T cell response.ConclusionExosomal vaccine loading T cell epitope peptides of SARS-CoV-2 virus was initially generated without pre-modification for both peptides and exosomes, and elicited robust CD8+ T cell response in HLA-A transgenic mice.

Harnessing anti-cytomegalovirus immunity for local immunotherapy against solid tumors

Tumor infiltration by T cells profoundly affects cancer progression and responses to immunotherapy. However, the tumor immunosuppressive microenvironment can impair the induction, trafficking, and local activity of antitumor T cells. Here, we investigated whether intratumoral injection of virus-derived peptide epitopes could activate preexisting antiviral T cell responses locally and promote antitumor responses or antigen spreading. We focused on a mouse model of cytomegalovirus (CMV), a highly prevalent human infection that induces vigorous and durable T cell responses. Mice persistently infected with murine CMV (MCMV) were challenged with lung (TC-1), colon (MC-38), or melanoma (B16-F10) tumor cells. Intratumoral injection of MCMV-derived T cell epitopes triggered in situ and systemic expansion of their cognate, MCMV-specific CD4 + or CD8 + T cells. The MCMV CD8 + T cell epitopes injected alone provoked arrest of tumor growth and some durable remissions. Intratumoral injection of MCMV CD4 + T cell epitopes with polyinosinic acid:polycytidylic acid (pI:C) preferentially elicited tumor antigen–specific CD8 + T cells, promoted tumor clearance, and conferred long-term protection against tumor rechallenge. Notably, secondary proliferation of MCMV-specific CD8 + T cells correlated with better tumor control. Importantly, intratumoral injection of MCMV-derived CD8 + T cell–peptide epitopes alone or CD4 + T cell–peptide epitopes with pI:C induced potent adaptive and innate immune activation of the tumor microenvironment. Thus, CMV-derived peptide epitopes, delivered intratumorally, act as cytotoxic and immunotherapeutic agents to promote immediate tumor control and long-term antitumor immunity that could be used as a stand-alone therapy. The tumor antigen–agnostic nature of this approach makes it applicable across a broad range of solid tumors regardless of their origin.

New modular platform based on multi-adjuvanted amphiphilic chitosan nanoparticles for efficient lipopeptide vaccine delivery against group A streptococcus

An effective vaccine against group A streptococcus (GAS) is highly desirable for definitive control of GAS infections. In the present study, two variants of amphiphilic chitosan nanoparticles-based GAS vaccines were developed. The vaccines were primarily composed of encapsulated KLH protein (a source of T helper cell epitopes) and lipidated M-protein derived B cell peptide epitope (lipoJ14) within the amphiphilic structure of nanoparticles. The only difference between them was one of the nanoparticles vaccines received additional surface coating with poly (I:C). The formulated vaccines exhibited nanosized particles within the range of 220–240 nm. Cellular uptake study showed that nanoparticles vaccine without additional poly (I:C) coating has greater uptake by dendritic cells and macrophages compared to nanoparticles vaccine that was functionalized with poly (I:C). Both vaccines were found to be safe in mice and showed negligible cytotoxicity against HEK293 cells. Upon immunization in mice, both nanoparticle vaccines produced high antigen-specific antibodies titres that were regulated by a balanced Th1 and Th2 response compared to physical mixture. These antibodies elicited high opsonic activity against the tested GAS strains. Overall, our data demonstrated that amphiphilic chitosan nanoparticles platform induced a potent immune response even without additional inclusion of poly (I:C).

The Use of Molecular Dynamics Simulation Method to Quantitatively Evaluate the Affinity between HBV Antigen T Cell Epitope Peptides and HLA-A Molecules.

Chronic hepatitis B virus (HBV), a potentially life-threatening liver disease, makes people vulnerable to serious diseases such as cancer. T lymphocytes play a crucial role in clearing HBV virus, while the pathway depends on the strong binding of T cell epitope peptide and HLA. However, the experimental identification of HLA-restricted HBV antigenic peptides is extremely time-consuming. In this study, we provide a novel prediction strategy based on structure to assess the affinity between the HBV antigenic peptide and HLA molecule. We used residue scanning, peptide docking and molecular dynamics methods to obtain the molecular docking model of HBV peptide and HLA, and then adopted the MM-GBSA method to calculate the binding affinity of the HBV peptide–HLA complex. Overall, we collected 59 structures of HLA-A from Protein Data Bank, and finally obtained 352 numerical affinity results to figure out the optimal bind choice between the HLA-A molecules and 45 HBV T cell epitope peptides. The results were highly consistent with the qualitative affinity level determined by the competitive peptide binding assay, which confirmed that our affinity prediction process based on an HLA structure is accurate and also proved that the homologous modeling strategy for HLA-A molecules in this study was reliable. Hence, our work highlights an effective way by which to predict and screen for HLA-peptide binding that would improve the treatment of HBV infection.

Structure-activity relationship of lipid, cyclic peptide and antigen rearrangement of physically mixed vaccines

Currently there is no approved vaccine to prevent and/or treat group A Streptococcus (GAS) infection. With increasing reports of GAS antibiotic resistance, vaccine adjuvants and targeted delivery systems which induce a strong immune response are a widely acknowledged unmet need. Through extensive structure-activity studies, we investigated a cyclic decapeptide physically mixed with a GAS B cell peptide epitope (J8), a universal T helper epitope (PADRE), and different synthetic lipidic moieties as a conceivable self-adjuvanting GAS vaccine. We explored the structure (orientation)-relationship of the chemically-conjugated B cell epitope and T helper epitope peptide as part of this physically-mixed vaccine. Following in vivo assessment in mice, these cyclic lipopeptide vaccines showed successful induction of J8-specific systemic IgG antibodies when administered subcutaneously without additional adjuvant. Interestingly, an exposed C-terminus of the GAS B cell epitope and a 16-carbon alpha-amino fatty acid lipid was required for strong immunoreactivity, capable of effectively opsonising multiple strains of clinically-isolated GAS bacteria. Physicochemical assessment proved the alpha helix structure of the GAS B cell epitope was retained, impacting particle self-assembly and vaccine immunoreactivity. This study showed the capability for a self-adjuvanting cyclic delivery system to act as a vehicle for the delivery of GAS peptide antigens to treat GAS infection.

Proteomics for Development of Food Allergy Vaccines.

Food allergy is a hypersensitivity reaction to food products initiated by immunologic mechanisms, which represents one of the major concerns in food safety. New therapies for food allergies including oral and epicutaneous allergen-specific immunotherapy are required, and B cell epitope-based allergy vaccines are a good promise to improve this field. In this chapter, we describe a workflow for the design of food allergy vaccines using proteomic tools. The strategy is defined based on the characterization of B cell epitopes for a particular food allergen. For that, the workflow comprises five consecutive steps: (1) shotgun proteomics analysis of different protein isoforms for a particular food allergen, (2) downloading all protein sequences for the specific allergen included in UniProtKB database, (3) analysis by protein-based bioinformatics of B cell epitopes, (4) synthesizing of the selected B cell peptide epitopes, and (5) performing of immunoassays using sera from healthy and allergic patients. The results from this method provide a rationale repository of B cell epitopes for the design of new specific immunotherapies for a particular food allergen. The strategy was optimized for all the beta-parvalbumins (β-PRVBs), which are considered as the main fish allergens. Using this workflow, a total of 35 peptides were identified as B cell epitopes, among them the top 4 B cell peptide epitopes that may induce protective immune response were selected as potential peptide vaccine candidates for fish allergy.

In Silico Design of Recombinant Chimera T Cell Peptide Epitope Vaccines for Visceral Leishmaniasis.

Visceral leishmaniasis (VL) is a neglected tropical disease caused by protozoan parasites of the genus Leishmania. Systemic VL is fatal if untreated and there are no prophylactic human vaccines available. Several studies suggest that Th1 cell-mediated immunity plays a major role in protecting against VL. In this chapter we describe a method for designing recombinant chimera vaccines in silico based on the prediction of T cell epitopes within protein antigens identified as potential protective immunogens. Development of a recombinant chimera protein (RCP) vaccine using T cell epitope peptides identified from four Leishmania proteins is used as an exemplar of this method.

New highly antigenic linear B cell epitope peptides from PvAMA-1 as potential vaccine candidates.

Peptide-based vaccines have demonstrated to be an important way to induce long-lived immune responses and, therefore, a promising strategy in the rational of vaccine development. As to malaria, among the classic vaccine targets, the Apical membrane antigen (AMA-1) was proven to have important B cell epitopes that can induce specific immune response and, hence, became key players for a vaccine approach. The peptides selection was carried out using a bioinformatic approach based on Hidden Markov Models profiles of known antigens and propensity scale methods based on hydrophilicity and secondary structure prediction. The antigenicity of the selected B-cell peptides was assessed by multiple serological assays using sera from acute P.vivax infected subjects. The synthetic peptides were recognized by 45.5%, 48.7% and 32.2% of infected subjects for peptides I, II and III respectively. Moreover, when synthetized together (tripeptide), the reactivity increases up to 62%, which is comparable to the reactivity found against the whole protein PvAMA-1 (57%). Furthermore, IgG reactivity against the tripeptide after depletion was reduced by 42%, indicating that these epitopes may be responsible for a considerable part of the protein immunogenicity. These results represent an excellent perspective regarding future chimeric vaccine constructions that may come to contemplate several targets with the potential to generate the robust and protective immune response that a vivax malaria vaccine needs to succeed.