A rationally designed multi-epitope vaccine candidate targeting conserved FiuA for broad Pseudomonas aeruginosa protection.

Allergic diseases are a global public health problem that affects up to 30% of the population in industrialized societies. More than 40% of allergic patients suffer from grass pollen allergy. Grass pollen allergens of group 1 and group 5 are the major allergens, since they induce allergic reactions in patients at high rates. In this study, we used immunoinformatic approaches to design an effective epitope-based vaccine against the grass group 1 allergens. After the alignment of all known pollen T-cell and B-cell epitopes from pollen allergens available in the public databases, the epitope GTKSEVEDVIPEGWKADTSY was identified as the most suitable for further analyses. The target sequence was subjected to immunoinformatics analyses to predict antigenic T-cell and B-cell epitopes. Population coverage analysis was performed for CD8+ and CD4+ T-cell epitopes. The selected T-cell epitopes (VEDVIPEGW and TKSEVEDVIPEGWKA) covered 78.87% and 98.20% of the global population and 84.57% and 99.86% of the population of Europe. Selected CD8+, CD4+ T-cell and B-cell epitopes have been validated by molecular docking analysis. CD8+ and CD4+ T-cell epitopes showed a very strong binding affinity to major histocompatibility complex (MHC) class I (MHC I) molecules and MHC class II (MHC II) molecules with global energy scores of -72.1 kcal/mol and -89.59 kcal/mol, respectively. The human IgE-Fc (PDB ID 4J4P) showed a lower affinity with B-cell epitope (ΔG = -34.4 kcal/mol), while the Phl p 2-specific human IgE Fab (PDB ID 2VXQ) had the lowest binding with the B-cell epitope (ΔG = -29.9 kcal/mol). Our immunoinformatics results demonstrated that the peptide GTKSEVEDVIPEGWKADTSY could stimulate the immune system and we performed ex vivo tests showed that the investigated epitope activates T cells isolated from patients with grass pollen allergy, but it is not recognized by IgE antibodies specific for grass pollen allergens. This confirms the importance of such studies to establish universal epitopes to serve as a basis for developing an effective vaccine against a particular group of allergens. Further in vivo studies are needed to validate the effectiveness of such a vaccine against grass pollen allergens.

HIV (human immunodeficiency virus) presents a global health crisis, causing significant AIDS-related deaths and over one million new infections annually. The curbing of HIV is an intricate and continuously evolving domain, marked by numerous challenges, including drug resistance and the absence of a significant cure or vaccine because of its mutating ability and diverse antigens in its envelope, prompting research for functional cures and long-term remission strategies. The endeavor to devise an HIV vaccine capable of eliciting robust and broadly cross-reactive humoral and cellular immune responses is a formidable undertaking, primarily due to the pronounced genetic heterogeneity of HIV-1, the variances observed in virus subtypes (clades) across distinct geographic regions, and the polymorphic nature of human leukocyte antigens (HLA). The viral envelope protein (gp120) selectively interacts with CD4 and chemokine receptors on the surface of target cells. It serves as the key initiator in the intricate viral entry into host cells, rendering it a compelling candidate for vaccine development. This study used bioinformatic tools to design a safe, hypoallergenic, and non-toxic mRNA HIV-1 vaccine by assembling immunogenic B- and T-cell epitopes from the gp120 protein. We identified antigenic, non-toxic, and non-allergic B-cell epitopes (IEPLGIAPTRAKRRVVER) and T-cell epitopes (QQKVHALFY, ITIGPGQVF, WQGVGQAMY, APTRAKRRV, KQQKVHALFYRLDIV, QQKVHALFYRLDIVQ, QKVHALFYRLDIVQI, SLAEEEIIIRSENLT, and IRSENLTNNVKTIIV). For designing the mRNA vaccine against HIV-1 gp120, we assembled the epitopes with 5' m7G cap, 5' UTR (untranslated region), Kozak sequence, signal peptide (tPA), RpfE (resuscitation-promoting factor E) adjuvant at N-terminal and MITD (MHC class I trafficking domain) adjuvant, stop codon, 3' UTR, and 120-nucleotide long poly(A) tail at the C-terminal with immunogenic robustness linkers. The mRNA vaccine is translated into a protein-based vaccine by the host body's ribosomes. Their comprehensive computational findings, including physicochemical, structural, and 3D refinement analyses, substantiated the stability and quality of the translated vaccine. Molecular docking and simulation revealed a strong and stable binding affinity of vaccine immunization with immune cells' pattern recognition receptors (TLR4). Immune simulations demonstrated a potent primary immune response characterized by a gradual increase in immunoglobulins and a corresponding decline in antigen concentration. This bioinformatics-driven study presents a promising HIV-1 mRNA vaccine candidate, underscoring the need for further experimental validation through preclinical and clinical trials. At the same time, its methodologies hold the potential for addressing other challenging infectious diseases, thereby impacting vaccinology broadly.

In silico epitope identification of unique multidrug resistance proteins from Salmonella Typhi for vaccine development

Coronaviruses (2019-nCoV) are large single-stranded RNA viruses that usually cause respiratory infections with a crude lethality ratio of 3.8% and high levels of transmissibility. There is yet no applicable clinical evaluation to assess the efficacy of various therapeutic agents that have been suggested as investigational drugs against the viruses despite their respective supposed hypothetical claims due to their antiviral potentials. Moreover, the development of a safe and effective vaccine has been suggested as an intervention to control the 2019-nCoV pandemic. However, a major concern in the development of a 2019-nCoV vaccine is the possibility of stimulating a corresponding immune response without enhancing the induction of the disease and associated side effects. The present investigation was carried out by predicting the antigenicity of the primary sequences of 2019-nCoV structural proteins and identification of B-cell and T-cell epitopes through the Bepipred and PEPVAC servers, respectively. The peptides of the vaccine construct include the selected epitopes based on the VaxiJen score with a threshold of 1.0 and β-defensinas an adjuvant. The putative binding of the vaccine constructs to intracellular toll-like receptors (TLRs) was assessed through molecular docking analysis and molecular dynamics simulations. The selected epitopes for the final vaccine construct are DPNFKD, SPLSLN, and LELQDHNE as B-cell epitopes and EPKLGSLVV, NFKDQVILL, and SSRSSSRSR as T-cell epitopes. The molecular docking analysis showed the vaccine construct could have favorable interactions with TLRs as indicated by the negative values of the computed binding energies. The constructed immunogen based on the immune informatics study could be employed in the strategy to develop potential vaccine candidates against 2019-nCoV.

Immunogenicity and immunodominant linear B-cell epitopes of a new DNA-based tetravalent vaccine against four major enteroviruses causing hand, foot, and mouth disease

To combat highly infectious Severe Acute Respiratory SyndromeICLE Coronavirus 2 (SARS-CoV-2), scientists and researchers are toiling hard globally to develop effective drugs and vaccines. By exploring the structural proteins of SARS-CoV-2 can be a feasible way to find an effective vaccine. In this study by using in-silico tools, we recommended B-cell and T-cell epitopes of spike protein from a Bangladeshi isolate which can be considered for incorporation into a vaccine against the SARS-CoV-2. Homology modelling, energy minimization process, and finally Ramachandran model was used for the prediction of a more stable conformation of the spike protein. The most important peptides were screened through the VaxiJen server followed by the IEDB server and CTLPred Score predicted and analysed the desired epitopes. In the final analysis, the peptide EVRQIAPGQTGKIADY (starting from 91) showed the highest antigenicity score (1.3837) as a B-cell epitope although GSTPCNGVEGFNCYFP, starting at 161, showed highest score (0.91) in an initial analysis. On the contrary, as a T-cell epitope, 71 KLNDLCFTNV-80 was found with the highest antigenicity score (2.6927) which was also found as an epitope in further analysis. A combination of B-cell and T-cell epitopes may evoke a humoral and cell-mediated immune response which will possibly lead to an effective vaccine. Further, the various computational analyses will provide valuable information that will pave the way for modelling a novel vaccine against SARS-CoV-2. © 2020, Bangladesh Society for Microbiology, Immunology and Advanced Biotechnology. All rights reserved.

Grafting of a hepatitis B S-preS(2) T-cell epitope on lysozyme enhances the immunogenicity of lysozyme in responder mice primed with the T-cell epitope.

BackgroundFoot-and-mouth disease virus (FMDV) causes an economically important and highly contagious disease of cloven-hoofed animals. FMD control in endemic regions is implemented using chemically inactivated whole-virus vaccines. Currently, efforts are directed to the development of safe and marked vaccines. We have previously reported solid protection against FMDV conferred by branched structures (dendrimeric peptides) harbouring virus-specific B and T-cell epitopes. In order to gain insights into the factors determining a protective immune response against FMDV, in this report we sought to dissect the immunogenicity conferred by different peptide-based immunogens. Thus, we have assessed the immune response and protection elicited in pigs by linear peptides harbouring the same FMDV B-cell or B and T-cell epitopes (B and TB peptides, respectively).ResultsPigs were twice immunized with either the B-cell epitope (site A) peptide or with TB, a peptide where the B-cell epitope was in tandem with the T-cell epitope [3A (21-35)]. Both, B and TB peptides were able to induce specific humoral (including neutralizing antibodies) and cellular immune responses against FMDV, but did not afford full protection in pigs. The data obtained showed that the T-cell epitope used is capable to induce efficient T-cell priming that contributes to improve the protection against FMDV. However, the IgA titres and IFNγ release elicited by these linear peptides were lower than those detected previously with the dendrimeric peptides.ConclusionsWe conclude that the incorporation of a FMDV specific T-cell epitope in the peptide formulation allows a significant reduction in virus excretion and clinical score after challenge. However, the linear TB peptide did not afford full protection in challenged pigs, as that previously reported using the dendrimeric construction indicating that, besides the inclusion of an adecuate T-cell epitope in the formulation, an efficient presentation of the B-cell epitope is crucial to elicit full protection by peptide vaccines.

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

Foot-and-mouth disease (FMD) is one of the most devastating animal diseases, affecting all cloven-hoofed domestic and wild animal species. Previous studies from our group using DNA vaccines encoding FMD virus (FMDV) B and T cell epitopes targeted to antigen presenting cells, allowed demonstrating total protection from FMDV homologous challenge in those animals efficiently primed for both humoral and cellular specific responses (Borrego et al. Antivir Res 92:359-363, 2011). In this study, a new DNA vaccine prototype expected to induce stronger and cross-reactive immune responses against FMDV which was designed by making two main modifications: i) adding a new B-cell epitope from the O-serotype to the B and T-cell epitopes from the C-serotype and ii) using a dual promoter plasmid that allowed inserting a new cistron encoding the anti-apoptotic Bcl-xL gene under the control of the internal ribosomal entry site (IRES) of encephalomyocarditis virus aiming to increase and optimize the antigen presentation of the encoded FMDV epitopes after in vivo immunization. In vitro studies showed that Bcl-xL significantly prolonged the survival of DNA transfected cells (p < 0.001). Accordingly, vaccination of Swiss out-bred mice with the dual promoter plasmid increased the total IgG responses induced against each of the FMDV epitopes however no significant differences observed between groups. The humoral immune response was polarized through IgG2a in all vaccination groups (p < 0.05); except peptide T3A; in correspondence with the Th1-like response observed, a clear bias towards the induction of specific IFN-γ secreting CD4⁺ and CD8⁺ T cell responses was also observed, being significantly higher (p < 0.05) in the group of mice immunized with the plasmid co-expressing Bcl-xL and the FMDV B and T cell epitopes.

Impact of the Underlying Mutation and the Route of Vector Administration on Immune Responses to Factor IX in Gene Therapy for Hemophilia B

Coronavirus disease 2019 vaccines: challenges of using global mass vaccination to achieve herd immunity.

Lassa virus (LASV) is responsible for an acute viral hemorrhagic fever known as Lassa fever. Sequence analyses of LASV proteome identified the most immunogenic protein that led to predict both T-cell and B-cell epitopes and further target and binding site depiction could allow novel drug findings for drug discovery field against this virus. To induce both humoral and cell-mediated immunity peptide sequence SSNLYKGVY, conserved region 41-49 amino acids were found as the most potential B-cell and T-cell epitopes, respectively. The peptide sequence might intermingle with 17 HLA-I and 16 HLA-II molecules, also cover 49.15-96.82% population coverage within the common people of different countries where Lassa virus is endemic. To ensure the binding affinity to both HLA-I and HLA-II molecules were employed in docking simulation with suggested epitope sequence. Further the predicted 3D structure of the most immunogenic protein was analyzed to reveal out the binding site for the drug design against Lassa Virus. Herein, sequence analyses of proteome identified the most immunogenic protein that led to predict both T-cell and B-cell epitopes and further target and binding site depiction could allow novel drug findings for drug discovery field against this virus.

T and B lymphocytes, the mediators of adaptive immune responses, express antigen‐specific receptors that allow them to discriminate between self and a virtually unlimited number of nonself molecules. Their receptors specifically recognise and bind subdomains of foreign macromolecules which are called epitopes. T‐cell epitopes (TCEs) and B‐cell epitopes (BCEs) differ fundamentally in the way they are recognised by the immune system. BCEs are recognised as three‐dimensional structures on the surface of native antigens. TCEs are parts of internalised and processed antigens that are presented to T lymphocytes in association with molecules of the major histocompatibility complex. As in a biological system T‐ and B‐cell receptors or antibody molecules face a virtual infinite number of structures, cognate interactions with epitopes are the basis of the primordial intelligence that drives the teleological choices of the immune system. Immunodominance directs the immune response towards selected epitopes. Key Concepts Surface immunoglobulins of B cells and antibodies recognise the B‐cell epitope (BCE) of an antigen in its native conformation, while T‐cell receptors (TCRs) recognise the T‐cell epitopes (TCEs) only after intracellular processing of the antigen, and in association with major histocompatibility complex (MHC) molecules. The main common feature of B‐cell epitopes is accessibility on the surface of the antigen. TCE peptides that bind to the same allele of MHC molecules share common ‘anchor’ residues (motifs) that contact the MHC molecule. TCEs presented by MHC class II molecules are longer and more variable in size and their anchor residues are less well defined than those of peptides presented by MHC class I molecules. Patterns of anchor residues facilitate the prediction of peptide binding to MHC molecules. The TCR–MHC–peptide tripartite cognate interaction in concert with coreceptors and other signalling modules mediate T‐cell activation. Immunodominance refers to the concept that only a small subset of the potential epitopes (TCEs or BCEs) present in a given antigen elicit an immune response. Mimotopes are small molecules that mimic the structure of complex conformational epitopes without any sequence homology. While TCEs can be predicted with some confidence, ill‐defined characteristic features of BCEs limit their predictability. Epitope‐based vaccines will allow to better manage desired and undesired cross‐reactivity.

Design and evaluation of a multi-epitope peptide against Japanese encephalitis virus infection in BALB/c mice