Effect of low complexity regions within the PvMSP3\u03b1 block II on the tertiary structure of the protein and implications to immune escape mechanisms

Prevention of neosporosis is advantageous for cattle health and productivity. Previously, several vaccine candidates were nominated for vaccination against Neospora caninum. This study was premised on in silico evaluation of N. caninum IMP-1 in order to determine its physicochemical features and immunogenic epitopes. We employed a wide array of network-based tools for the prediction of antigenicity, allergenicity, solubility, posttranslational modification (PTM) sites, physicochemical properties, transmembrane domains and signal peptide, secondary and tertiary structures, and intrinsically disordered regions. Also, prediction and screening of potential continuous B cell peptides and those epitopes having stringent affinity to couple with mouse major histocompatibility complex (MHC) and cytotoxic T lymphocyte (CTL) receptors were accomplished. The protein had 393 residues with a molecular weight of 42.71 kDa, representing aliphatic index of 85.83 (thermotolerant) and GRAVY score of -0.447 (hydrophilic). There were 47 PTM sites without a signal peptide in the sequence. Secondary structure comprised mostly of extended strand and helices, followed by coils. The Ramachandran plot of the refined model showed 90.1%, 9.9%, 0.0%, and 0.0% residues in the favored, additional allowed, generously allowed, and disallowed regions, correspondingly. Additionally, various potential B cell (linear and conformational), CTL, and MHC binding epitopes were predicted for N. caninum IMP-1. The findings of the present study could be further directed for next-generation vaccine design against neosporosis.

Although glycoconjugate vaccines have provided enormous health benefits globally, they have been less successful in significant high-risk populations. Exploring novel approaches to the enhancement of glycoconjugate effectiveness, we investigated molecular and cellular mechanisms governing the immune response to a prototypical glycoconjugate vaccine. In antigen-presenting cells, a carbohydrate epitope is generated upon endolysosomal processing of group B streptococcal type III polysaccharide coupled to a carrier protein. In conjunction with a carrier protein-derived peptide, this carbohydrate epitope binds to major histocompatibility class II (MHCII) and stimulates carbohydrate-specific CD4+ T-cell clones to produce interleukins 2 and 4—cytokines essential for providing T-cell help to antibody-producing B cells. An archetypical glycoconjugate vaccine constructed to maximize the presentation of carbohydrate epitopes recognized by T cells is 50–100 times more potent and significantly more protective in an animal model of infection than is a currently used vaccine construct.

The Babesia bovis antigen 12D3 was analysed to identify potential T-cell epitopes. Two predictive algorithms identified 13 possible sites but there was minimal agreement between the different predictive methods. Experimental determination of the T-cell epitopes recognized by nine cattle was achieved using a panel of overlapping peptides which identified seven different epitopes, five of which were clustered together around residues 210–320 of the molecule. No T cell epitopes were located within the tightly disulphide bonded core of 12D3. Using a series of truncated peptides, the location of two of the epitopes was mapped to residues 35–43 and 266–275. The sequences of these two epitopes was compared with a database of previously described binding motifs for MHC II alleles and each epitope was found to contain three sequence motifs recognized by HLA-DR alleles. The BoLA-DRB3 alleles occurring in these cattle were determined by a sequence specific oligonucleotide hybridization assay. Within those cattle whose T cells proliferated in response to 12D3, there was a consistent pattern of epitope recognition and presence of particular DRB3 alleles. The implications for effective vaccine design are discussed.

The Babesia bovis antigen 12D3 was analysed to identify potential T-cell epitopes. Two predictive algorithms identified 13 possible sites but there was minimal agreement between the different predictive methods. Experimental determination of the T-cell epitopes recognized by nine cattle was achieved using a panel of overlapping peptides which identified seven different epitopes, five of which were clustered together around residues 210-320 of the molecule. No T cell epitopes were located within the tightly disulphide bonded core of 12D3. Using a series of truncated peptides, the location of two of the epitopes was mapped to residues 35-43 and 266-275. The sequences of these two epitopes was compared with a database of previously described binding motifs for MHC II alleles and each epitope was found to contain three sequence motifs recognized by HLA-DR alleles. The BoLA-DRB3 alleles occurring in these cattle were determined by a sequence specific oligonucleotide hybridization assay. Within those cattle whose T cells proliferated in response to 12D3, there was a consistent pattern of epitope recognition and presence of particular DRB3 alleles. The implications for effective vaccine design are discussed.

The highly conserved C-terminus of the M protein of group A streptococcus (GAS) is a promising vaccine candidate. An epitope within the conserved C-terminus of the M protein, peptide 145 (a 20-mer with the sequence: LRRDLDASREAKKQVEKALE), has been defined which is the target of opsonic antibodies in both humans and mice, and is recognized by the sera of most adults living in areas of high streptococcal exposure. However, due to potential cross-reactivity between T cells stimulated by this region of the M protein and host cardiac myosin, it is critical to define precisely the minimal protective epitopes within p145. Studies have shown that the immunodominant epitope expressed by p145 is conformational, occurring as an alpha-helical coiled-coil. To enable us to map the murine minimal B cell and T cell epitopes within p145, we have used a novel strategy that allowed us to present shorter sequences of p145 in a native-like conformation. The minimal B cell epitope was found to be contained within residues 7-20 of the p145 sequence, and we have shown that mice immunized with this region are able to generate antibodies that bind to and also opsonize the organism GAS. The T cell epitope is located at the N-terminal region of the p145 sequence, residues 3-14. We have managed, therefore, to define a vaccine candidate--a minimal opsonic B cell epitope within the p145 sequence--that does not incorporate a potentially deleterious T cell epitope.

BackgroundChronic obstructive pulmonary disease (COPD) is a lung disease characterised by airflow-limiting inflammation and mucus production. Acute exacerbations are a major cause of COPD-related morbidity and mortality and are mostly associated with bacterial or viral infections. A vaccine targeting non-typeable Haemophilus influenzae (NTHi) and Moraxella catarrhalis (Mcat), the main bacteria associated with exacerbations, was tested in a Phase 2 trial. We assessed “ex-vivo” expression of vaccine candidate and housekeeping genes pd, pe, pilA, gapA, ompP6 of NTHi, and uspA2, parE, polA of Mcat in sputum samples of COPD patients and determined whether expression of the vaccine candidate genes pd, pe, pilA (NTHi) and uspA2 (Mcat) differed between stable and exacerbation samples.MethodsA single-centre, prospective, observational cohort study was conducted where 123 COPD patients were seen on enrolment, followed monthly for 2 years, and reviewed after onset of acute exacerbations. We selected 69 patients with sputum samples positive for NTHi or Mcat by PCR during at least one stable and one exacerbation visit. mRNA was isolated from the sputum, and expression of NTHi and Mcat genes was analysed with RT-PCR. Statistical analyses compared mRNA concentrations between stable and exacerbation samples and in relationship to COPD severity and exacerbation frequency.ResultsThe vaccine candidate genes were variably expressed in sputum samples, suggesting they are expressed in the lung. Absolute and relative expression of all NTHi vaccine candidate genes and Mcat uspA2 were similar between exacerbation and stable samples. Expression of pd and pilA was slightly associated with the number of exacerbations in the year before enrolment, and uspA2 with the disease severity status at enrolment.ConclusionsThe NTHi-Mcat vaccine candidate genes were expressed in sputum samples, and each gene had a specific level of expression. No statistically significant differences in gene expression were detectable between stable and exacerbation samples. However, the history of COPD exacerbations was slightly associated with the expression of pd, pilA and uspA2.Trial registration NCT01360398 (https://www.clinicaltrials.gov)Graphical abstract

The emergence and re-emergence of arboviruses such as dengue, Chikungunya and Zika viruses causing morbidity and mortality around the globe are of serious concern. A safe and effective vaccine is essential to control viral transmission. The salivary proteins of the mosquito that aid in blood probing, feeding and development are immunogenic. We aimed to report a multi-epitope candidate vaccine chimera from Aedes aegyptii mosquito salivary proteins OBP 22 and OBP 10 that could confer protection against all pathogens transmitted by the vector. Linear and conformation B-cell epitopes and MHC class-I and class-II binding T- cell epitopes were predicted using bioinformatic tools. Selected B- and T-cell epitopes were chosen for designing a multiepitope vaccine construct. The chimeric construct was analyzed for its immunogenicity, TAP and proteasomal cleavage, allergenicity, and structural validation for its suitability to be used as a candidate vaccine. Molecular docking was carried out to analyze the binding interactions with TLRs molecules. A chimeric multiepitope vaccine was designed with the best-selected combination of immunogenic B-cell epitope, cytotoxic and helper T-cell and gamma interferon inducing epitopes with suitable adjuvant and linkers. The interacting residues between the candidate vaccine and the TLR molecules have been identified. The proposed multiepitope candidate vaccine was designed from the mosquito salivary protein OBP 22 and OBP 10. The candidate vaccine was found promising for the protection against arboviruses. Further clinical validation is warranted to prove its efficacy, safety and immunogenicity for its potential use.

Zika virus (ZIKV) has become a global concern in 2015-2016, which can infect adults and developing fetuses. ZIKV is a member of the Flaviviridae family, which can spread through Aedes mosquitoes, sexual intercourse, from mother to fetus, and blood transfusions. The genetic material is single-stranded RNA with positive polarity. Conventional vaccine development requires a long time and significant resources, so the bioinformatics approach is an efficient alternative for identifying B cell epitopes as vaccine candidates. This research uses bioinformatics or In silico methods to identify B cell epitopes with the immune epitope database (IEDB) web server. This research showed that the peptide sequence of "EWFHDIPLPWHAGADTGTPHWNNKEA" (peptide 6E) in the envelope protein E of ZIKV is a potential vaccine candidate. This peptide is predicted to have high antigenicity, non-allergenicity and non-toxicity. This study concluded that peptide 6E is a promising vaccine candidate. Further studies are needed in vitro and in vivo to reconfirm that it can be used as a potential ZIKV vaccine candidate and can be applied in the future.

<h3>Background</h3> There is an urgent need for a vaccine with efficacy against SARS-CoV-2. We hypothesize that peptide vaccines containing epitope regions optimized for concurrent B cell, CD4+ T cell, and...

ABSTRACTThe pre-erythrocytic stage of infection by malaria parasites represents a key target for vaccines that aim to eradicate malaria. Two important broad immune evasion strategies that can interfere with vaccine efficacy include the induction of dendritic cell (DC) dysfunction and regulatory T cells (Tregs) by blood-stage malaria parasites, leading to inefficient priming of T cells targeting liver-stage infections. The parasite also uses ‘surgical strike’ strategies, whereby polymorphism in pre-erythrocytic antigens can interfere with host immunity. Specifically, we review how even single amino acid changes in T cell epitopes can lead to loss of binding to major histocompatibility complex (MHC), lack of cross-reactivity, or antagonism and immune interference, where simultaneous or sequential stimulation with related variants of the same T cell epitope can cause T cell anergy or the conversion of effector to immunosuppressive T cell phenotypes.

BackgroundThe present pandemic COVID-19 is caused by SARS-CoV-2, a single-stranded positive-sense RNA virus from the Coronaviridae family. Due to a lack of antiviral drugs, vaccines against the virus are urgently required.MethodsIn this study, validated computational approaches were used to identify peptide-based epitopes from six structural proteins having antigenic properties. The Net-CTL 1.2 tool was used for the prediction of CD8+ T-cell epitopes, while the robust tools Bepi-Pred 2 and LBtope was employed for the identification of linear B-cell epitopes. Docking studies of the identified epitopes were performed using HADDOCK 2.4 and the structures were visualized by Discovery Studio and LigPlot+. Antigenicity, immunogenicity, conservancy, population coverage and allergenicity of the predicted epitopes were determined by the bioinformatics tools like VaxiJen v2.0 server, the Immune Epitope Database tools and AllerTOP v.2.0, AllergenFP 1.0 and ElliPro.ResultsThe predicted T cell and linear B-cell epitopes were considered as prime vaccine targets in case they passed the requisite parameters like antigenicity, immunogenicity, conservancy, non-allergenicity and broad range of population coverage. Among the predicted CD8+ T cell epitopes, potential vaccine targets from surface glycoprotein were; YQPYRVVVL, PYRVVVLSF, GVYFASTEK, QLTPTWRVY, and those from ORF3a protein were LKKRWQLAL, HVTFFIYNK. Similarly, RFLYIIKLI, LTWICLLQF from membrane protein and three epitopes viz; SPRWYFYYL, TWLTYTGAI, KTFPPTEPK from nucleocapsid phosphoprotein were the superior vaccine targets observed in our study. The negative values of HADDOCK and Z scores obtained for the best cluster indicated the potential of the epitopes as suitable vaccine candidates. Analysis of the 3D and 2D interaction diagrams of best cluster produced by HADDOCK 2.4 displayed the binding interaction of leading T cell epitopes within the MHC-1 peptide binding clefts. On the other hand, among linear B cell epitopes the majority of potential vaccine targets were from nucleocapsid protein, viz; 59−HGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMKDLS−105, 227−LNQLE SKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATK−266, 3−DNGPQNQRNAPRITFGGP−20, 29−GERSGARSKQRRPQGL−45. Two other prime vaccine targets, 370−NSASFSTFKCYGVSPTKLNDLCFTNV−395 and 260−AGAAAYYVGYLQPRT−274 were identified in the spike protein. The potential B-cell conformational epitopes were predicted on the basis of a higher protrusion index indicating greater solvent accessibility. These conformational epitopes were of various lengths and belonged to spike, ORF3a, membrane and nucleocapsid proteins.ConclusionsTaken together, eleven T cell epitopes, seven B cell linear epitopes and ten B cell conformational epitopes were identified from five structural proteins of SARS-CoV-2 using advanced computational tools. These potential vaccine candidates may provide important timely directives for an effective vaccine against SARS-CoV-2.

Evaluation of the protective efficacy of four novel identified membrane associated proteins of Streptococcus suis serotype 2

SARS-CoV-2 human T cell epitopes: Adaptive immune response against COVID-19

Immunoinformatics tools have multiple applications in human immunology research. One of their most prominent applications is the prediction of T cell epitopes to accelerate vaccine development. T cell epitopes are short peptides derived from pathogens that are recognized by the cells of the immune system (T cells) when presented on the surface of cells bound to a major histocompatibility complex (MHC) molecule, which results in a specific immune response. For their role as key drivers of the immune response, numerous algorithms have been developed to predict binding of peptides to MHC molecules; however, comparable tools are limited for other species. The goal of this thesis is to develop immunoinformatics tools for swine to aid in the design of vaccines for pathogens affecting the pork industry. One of the main reasons for the limited development of T cell epitope mapping tools for swine is the lack of data required to train and test the predictive algorithms. Through this research, we have developed PigMatrix, a tool for prediction of peptide binding to swine MHC molecules. In an initial analysis, PigMatrix predictive performance was favorable, in particular because its development did not require training data. Using PigMatrix, we have identified immunogenic peptides conserved in seven different strains of influenza A virus (IAV), a highly diverse virus that has a significant impact not only on swine, but also for humans. Protective potential of IAV vaccines is commonly predicted using genetic data and antibody cross-reactivity properties of the hemagglutinin (HA) surface protein, the most variable antigen and primary target of the antibody immune response. However, protection has been reported in the absence of cross-reactive antibodies to HA. To explore the role of T cell epitopes in vaccine protection, we have developed a method (EpiCC) to compare T cell epitope content between proteins. We found that the relationship of predicted T cell epitopes between HA sequences of a swine IAV inactivated vaccine and challenge strains was associated with protection, providing evidence that T cells contribute to vaccine efficacy. This approach may complement current methods for selection of influenza vaccines against novel viruses and influenza strains for vaccine development. Taken together, these findings demonstrate the potential of immunoinformatics tools for the development and evaluation of swine vaccines and will allow for further research to improve the tools and apply them to design novel vaccine candidates.

Multi-epitope vaccine (MEV) construction is a technique which combines multiple epitopes, both B cell epitopes and T cell epitopes which have the potential to elicit a much stronger immune response compared to a subunit vaccine. Therefore, recently, a lot of research has been focused on development and improvement of multiepitope vaccines. The strategy of designing a MEV in silico lies in a few basic steps, including procuring the amino acid sequence of the B cell and T cell epitopes from literature search, bioinformatics approach, to construct a potent immunogen capable of eliciting both humoral and cell-mediated response and finally joining these epitopes by linkers. However, a vaccine constructed by merely joining the epitopes may not always result in a stable globular structured protein. In this study, we have focused on developing a strategy where a potential vaccine candidate of Mycobacterium tuberculosis has been used as a scaffold and the low complexity regions of this scaffold have been replaced by the predicated epitopes. Essentially, instead of joining the epitopes by linkers, they have been carefully positioned on a scaffold of a protein that is itself a vaccine candidate to derive a MEV against Mycobacterium tuberculosis. In this study, a methodology has been detailed to tackle this great challenge using a simple approach of protein engineering. A scaffold-based MEV has been designed against Mtb by converting a vaccine candidate protein, Ag85A, into a scaffold by truncating its low complexity non-immunogenic regions, and the gaps were supplemented by the highly immunogenic epitopes. Replicated 500 ns molecular dynamics simulation at different temperatures (300 K and 310 K) and principal component analysis proved that MEV built on the scaffold is more stable than the conventional one.