Lipids as Activators of Innate Immunity in Peptide Vaccine Delivery

BACKGROUND

Innate immune system plays an important role in pathogen detection and the recognition of vaccines, mainly through pattern recognition receptors (PRRs) that identify pathogen components (danger signals). One of the typically recognised bacterial components are lipids in conjugation with peptides, proteins and saccharides. Lipidic compounds are readily recognised by the immune system, and thus are ideal candidates for peptide- based vaccine delivery. Thus, bacterial or synthetic lipids mixed with, or conjugated to, antigens have shown adjuvant properties. These systems have many advantages over traditional adjuvants, including low toxicity and good efficacy for stimulating mucosal and systemic immune responses.

METHODS

The most recent literature on the role of lipids in stimulation of immune responses was selected for this review. The vast majority of reviewed papers were published in the last decade. Older but significant findings are also cited.

RESULTS

This review focuses on the development of lipopeptide vaccine systems including application of palmitic acid, bacterial lipopeptides, glycolipids and the lipid core peptide and their routes of administration. The use of liposomes as a delivery system that incorporates lipopeptides is discussed. The review also includes a brief description of immune system in relation to vaccinology and discussion on vaccine delivery routes.

CONCLUSION

Lipids and their conjugates are an ideal frontrunner in the development of safe and efficient vaccines for different immunisation routes.

Opportunities for an atherosclerosis vaccine: From mice to humans

Atherosclerosis, the major underlying cause of cardiovascular diseases (CVD), is the number one killer globally. The disease pathogenesis involves a complex interplay between metabolic and immune components. Although lipid-lowering drugs such as statins curb the risks associated with CVD, significant residual inflammatory risk remains. Substantial evidence from experimental models and clinical studies has established the role of inflammation and immune effector mechanisms in the pathogenesis of atherosclerosis. Several stages of the disease are affected by host-mediated antigen-specific adaptive immune responses that play either protective or proatherogenic roles. Therefore, strategies to boost an anti-atherogenic humoral and T regulatory cell response are emerging as preventative or therapeutic strategies to lowering inflammatory residual risks. Vaccination holds promise as an efficient, durable and relatively inexpensive approach to induce protective adaptive immunity in atherosclerotic patients. In this review, we discuss the status and opportunities for a human atherosclerosis vaccine. We describe (1) some of the immunomodulatory therapeutic interventions tested in atherosclerosis (2) the immune targets identified in pre-clinical and clinical investigations (3) immunization strategies evaluated in animal models (4) past and ongoing clinical trials to examine the safety and efficacy of human atherosclerosis vaccines and (5) strategies to improve and optimize vaccination in humans (antigen selection, formulation, dose and delivery).

Designing, characterization, and immune stimulation of a novel multi-epitopic peptide-based potential vaccine candidate against monkeypox virus through screening its whole genome encoded proteins: An immunoinformatics approach

BACKGROUND

The current monkeypox virus (MPXV) spread in the non-epidemic regions raises global concern. Presently, the smallpox vaccine is used against monkeypox with several difficulties. Conversely, no next-generation vaccine is available against MPXV. Here, we proposed a novel multi-epitopic peptide-based in-silico potential vaccine candidate against the monkeypox virus.

METHODS

The multi-epitopic potential vaccine construct was developed from antigen screening through whole genome-encoded 176 proteins of MPXV. Afterward, ten common B and T cell epitopes (9-mer) having the highest antigenicity and high population coverage were chosen, and a vaccine construct was developed using peptide linkers. The vaccine was characterized through bioinformatics to understand antigenicity, non-allergenicity, physicochemical properties, and binding affinity to immune receptors (TLR4/MD2-complex). Finally, the immune system simulation of the vaccine was performed through immunoinformatics and machine learning approaches.

RESULTS

The highest antigenic epitopes were used to design the vaccine. The docked complex of the vaccine and TLR4/MD2 had shown significant free binding energy (-98.37 kcal/mol) with a definite binding affinity. Likewise, the eigenvalue (2.428517e-05) from NMA analysis of this docked complex reflects greater flexibility, adequate molecular motion, and reduced protein deformability, and it can provoke a robust immune response.

CONCLUSIONS

The designed vaccine has shown the required effectiveness against MPXV without any side effects, a significant milestone against the neglected disease.

Optimization of peptide-based cancer vaccine compositions, by sequential screening, using versatile liposomal platform

Therapeutic cancer vaccines need thoughtful design to efficiently deliver appropriate antigens and adjuvants to the immune system. In the current study, we took advantage of the versatility of a liposomal platform to conceive and customize vaccines containing three elements needed for the induction of efficient antitumor immunity: i) a CD4 epitope peptide able to activate CD4⁺ T helper cells, ii) a CD8 tumor-specific epitope peptide recognized by CD8⁺ T cytotoxic cells and iii) Pattern Recognition Receptor (PRR) agonists which stand as adjuvants. Each type of component, conjugated to liposomes, was evaluated individually by comparing their vaccine efficacy after immunization of naïve mice. These screening steps resulted in the optimization of three liposomal constructs bearing a peptide from HA influenza virus protein as CD4 epitope, a peptide from HPV16 E7 oncoprotein as CD8 epitope and TLR4, TLR2/6 or NOD1 agonists as adjuvant, which displayed antitumor efficiency against a mouse model of disseminated tumors transformed by HPV16. Our results validated the interest of our customizable liposomal platform as delivery system for cancer vaccination. We also demonstrated its interest as tool for vaccine design allowing the strategical selection of components, and the evaluation of epitope-adjuvant association.

The Use of Microwave-Assisted Solid-Phase Peptide Synthesis and Click Chemistry for the Synthesis of Vaccine Candidates Against Hookworm Infection

A protein-based vaccine approach against hookworm infection has failed to deliver the expected outcome, due to a problem with an allergic response in the patient or difficulties in the proteins' production. This implication could be overcome by using a chemically synthesized peptide-based vaccine approach. This approach utilizes minimal pathogenic components that are necessary for the stimulation of the immune response without triggering adverse side effects. To boost the peptide's immunogenicity, a lipid core peptide (LCP) system can be utilized as a carrier molecule/immunostimulant. This chapter describes in detail the synthesizing of protected lipoamino acid, the self-adjuvanting moiety (LCP core), the peptide epitope, and the final vaccine candidate. The subunit peptide and the LCP core were synthesized using microwave-assisted solid-phase peptide synthesis (SPPS). Then the final hookworm vaccine construct was assembled using the copper-catalyzed azide-alkyne cycloaddition, or "click," reaction.

Peptides-based vaccine against SARS-nCoV-2 antigenic fragmented synthetic epitopes recognized by T cell and β-cell initiation of specific antibodies to fight the infection

The World Health Organization has declared the rapidly spreading coronavirus to be a global pandemic. The FDA is yet to approve a vaccine for human novel coronavirus. Here, we developed a peptide-based vaccine and used high-throughput screening by molecular dynamics simulation to identify T-cell- and β-cell-recognized epitopes for producing specific antibodies against SARS-nCoV-2. We construct ~ 12 P' antigenic epitope peptides to develop a more effective vaccine and identify specific antibodies. These epitope peptides selectively presented the best antigen presentation scores for both human pMHC class I and II alleles to develop a strong binding affinity. All antigens identified of SARS-nCoV-2 different proteins by each attached specific ~ 1-7 L linker adaptor were used to construct a broad single peripheral peptide vaccine. It is expected to be highly antigenic with a minimum allergic effect. As a result of these exciting outcomes, expressing a vaccine using the intimated peptide was highly promising and positive to be highly proposed as epitope-based peptide vaccine of specific antibody against SARS-nCoV-2 by initiating T cells and β-cells. An in vitro study for the proposed peptide-based vaccine is mostly recommended. Further clinical trials are required to check the efficacy of this vaccine.

Immunoinformatics prediction of potential B-cell and T-cell epitopes as effective vaccine candidates for eliciting immunogenic responses against Epstein-Barr virus

BACKGROUND

The ongoing search for viable treatment options to curtail Epstein Barr Virus (EBV) pathogenicity has necessitated a paradigmatic shift towards the design of peptide-based vaccines. Potential B-cell and T-cell epitopes were predicted for nine antigenic EBV proteins that mediate epithelial cell-attachment and spread, capsid self-assembly, DNA replication and processivity.

METHODS

Predictive algorithms incorporated in the Immune Epitope Database (IEDB) resources were used to determine potential B-cell epitopes based on their physicochemical attributes. These were combined with a string-kernel method and an antigenicity predictive AlgPred tool to enhance accuracy in the end-point selection of highly potential antigenic EBV B-cell epitopes. NetCTL 1.2 algorithms enabled the prediction of probable T-cell epitopes which were structurally modeled and subjected to blind peptide-protein docking with HLA-A*02:01. All-atom molecular dynamics (MD) simulation and Molecular Mechanics Generalized-Born Surface Area methods were used to investigate interaction dynamics and affinities of predicted T-cell peptide-protein complexes.

RESULTS

Computational predictions and sequence overlapping analysis yielded 18 linear (continuous) and discontinuous (conformational) subunit epitopes from the antigenic proteins with characteristic surface accessibility, flexibility and antigenicity, and predictive scores above the threshold value (1) set. A novel site was identified on HLA-A*02:01 with preferential affinity binding for modeled BMRF2, BXLF1 and BGLF4 T-cell epitopes. Interaction dynamics and energies were also computed in addition to crucial residues that mediated complex formation and stability.

CONCLUSION

This study implemented an integrative meta-analytical approach to model highly probable B-cell and T-cell epitopes as potential peptide-vaccine candidates for the treatment of EBV-related diseases.

Screening and identification of T helper 1 and linear immunodominant antibody-binding epitopes in spike 1 domain and membrane protein of feline infectious peritonitis virus

Feline infectious peritonitis virus (FIP virus: FIPV) causes a fatal disease in wild and domestic cats. The development of an FIP-preventive vaccine requires an antigen that does not induce antibody-dependent enhancement, and T helper (Th)1 activity plays an important role in protect against FIPV infection. In the present study, we identified synthetic peptides including Th1 and a linear immunodominant antibody-binding epitope in the S1 domain and M protein of FIPV. We also identified peptides that strongly induce Th1 activity from those derived from the structural proteins (S, M, and N proteins) of FIPV based on this and previous studies (Satoh et al. [19]). No Th1 epitope-containing peptide was identified in the peptides derived from the S1 domain of type I FIPV. In contrast, 7 Th1 epitope-containing peptides were identified in the S1 domain of type II FIPV, and no linear immunodominant antibody-binding epitope was contained in any of these peptides. Eleven Th1 epitope-containing peptides common to each serotype were identified in the M protein-derived peptides, and 2 peptides (M-11 and M-12) contained the linear immunodominant antibody-binding epitope. Of the peptides derived from the S, M, and N proteins of FIPV, those that induced significantly stronger Th1 activity than that of the FIPV antigen were rescreened, and 4 peptides were identified. When 3 of these peptides (M-9, I-S2-15, and II-S1-24) were selected and administered with CpG-ODNs to SPF cats, M-9 and II-S1-24 induced Th1 activity. Our results may provide important information for the development of a peptide-based vaccine against FIPV infection.

Cancer vaccines as a targeted immunotherapy approach for breast cancer: an update of clinical evidence

INTRODUCTION

Breast cancer (BC) is the first common neoplastic malignancy and the second leading cause of death in women worldwide. Conventional treatments for BC are often associated with severe side effects and may even lead to late recurrence. For this reason, in recent years, cancer immunotherapy (e.g., cancer vaccines), a novel approach based on the specificity and amplification of acquired immune responses, has been considered as a potential candidate in particular to treat metastatic BC.

AREAS COVERED

In this review, we summarize and discuss the recent development of therapeutic vaccines for BC, use of specific BC cellular antigens, antigen selection, and probable causes for their insufficient effectiveness.

EXPERT OPINION

Despite development of several different BC vaccines strategies including protein/peptide, dendritic cell, and genetic vaccines, until now, no BC vaccine has been approved for clinical use. Most of the current BC vaccines themselves fail to bring clinical benefit to BC patients and are applied in combination with radiotherapy, chemotherapy, or targeted therapy. It is hoped that with advances in our knowledge about tumor microenvironment and the development of novel combination strategies, the tumor immunosuppressive mechanisms can be overcome and prolonged immunologic and effective anti-tumor response can be developed in patients.

In silico design of a broad-spectrum multiepitope vaccine against influenza virus

Influenza remains a global health concern due to its potential to cause pandemics as a result of rapidly mutating influenza virus strains. Existing vaccines often struggle to keep up with these rapidly mutating flu viruses. Therefore, the development of a broad-spectrum peptide vaccine that can stimulate an optimal antibody response has emerged as an innovative approach to addressing the influenza threat. In this study, an immunoinformatic approach was employed to rapidly predict immunodominant epitopes from different antigens, aiming to develop an effective multiepitope influenza vaccine (MEV). The immunodominant B-cell linear epitopes of seasonal influenza strains hemagglutinin (HA) and neuraminidase (NA) were predicted using an antibody-peptide microarray, involving a human cohort including vaccinees and infected patients. On the other hand, bioinformatics tools were used to predict immunodominant cytotoxic T-cell (CTL) and helper T-cell (HTL) epitopes. Subsequently, these epitopes were evaluated by various immunoinformatic tools. Epitopes with high antigenicity, high immunogenicity, non-allergenicity, non-toxicity, as well as exemplary conservation were then connected in series with appropriate linkers and adjuvants to construct a broad-spectrum MEV. Moreover, the structural analysis revealed that the MEV candidates exhibited good stability, and the docking results demonstrated their strong affinity to Toll-like receptors 4 (TLR4). In addition, molecular dynamics simulation confirmed the stable interaction between TLR4 and MEVs. Three injections with MEVs showed a high level of B-cell and T-cell immune responses according to the immunological simulations in silico. Furthermore, in-silico cloning was performed, and the results indicated that the MEVs could be produced in considerable quantities in Escherichia coli (E. coli). Based on these findings, it is reasonable to create a broad-spectrum MEV against different subtypes of influenza A and B viruses in silico.

Immunogenicity of late stage specific peptide antigens of Mycobacterium tuberculosis

Global burden of latent TB infection comprises one-third of the world population. Identifying potential Mycobacterium tuberculosis (Mtb) latency associated antigens that can generate protective immunity against the pathogen is crucial for designing an effective TB vaccine. Usually the immune system responds to a small number of amino acids as MHC Class I or Class II peptides. The precision to trigger epitope specific protective T-cell immune response could therefore be achieved with synthetic peptide-based subunit vaccine. In the present study we have considered an immunoinformatic approach using available softwares (ProPred, IEDB, NETMHC, BIMAS, Vaxijen2.0) and docking and visualizing softwares (CABSDOCK, HEX, Pymol, Discovery Studio) to select 10 peptides as latency antigens from 4 proteins (Rv2626, Rv2627, Rv2628, and Rv2032) of DosR regulon of Mtb. As Intracellular IFN-γ secreted by T cells is the most essential cytokine in Th1 mediated protective immunity, these peptides were verified as potential immunogenic epitopes in Peripheral Blood Mononuclear Cells (PBMCs) of 10 healthy contacts of TB patients (HTB) and 10 Category I Pulmonary TB patients (PTB).The antigen-specific CD4 and CD8 T cells expressing intracellular IFN-γ were analyzed using monoclonal antibodies in all subjects by multi-parameter flow cytometry. Both, PTB and HTB individuals responded to DosR peptides by showing increased frequency of IFN-γ⁺CD4 and IFN-γ⁺CD8 T cells. The T-cell responses were significantly higher in PTB patients in comparision to the HTB individuals. Additionally, our synthetic peptides and pools showed higher frequencies of IFN-γ⁺CD4 and IFN-γ⁺CD8 T cells than the peptides of Ag85B. This pilot study can be taken up further in larger sample size which may support the untapped opportunity of designing Mtb DosR inclusive peptide based post-exposure subunit vaccine.

Airway administration of a highly versatile peptide-based liposomal construct for local and distant antitumoral vaccination

With the discovery of tumor-associated antigens such as ErbB2, vaccination is considered as a promising strategy to prevent the development of cancer or treat the existing disease. Among routes of immunization, the respiratory route provides the opportunity to develop non-invasive approach for vaccine delivery. In the current study, this administration route was used in order to investigate the potency of a highly versatile di-epitopic liposomal construct to exhibit local or distant antitumoral efficiency after prophylactic or therapeutic vaccination in mice. Well-characterized liposomes, containing the ErbB2 (p63-71) TCD8(+) and HA (p307-319) TCD4(+) peptide epitopes and the Pam2CAG adjuvant, were formulated and administered into the airway of naïve BALB/c mice. The nanoparticle vaccine candidate induced local and specific systemic immune response, as measured by immune cell infiltration and chemokine and cytokine production in BALF or lung tissue, and by spleen T-cell activation ex vivo, respectively. This potent immune response resulted in an efficient antitumor activity against both lung and solid s.c. tumors. Interestingly, the antitumor efficacy was observed after both prophylactic and therapeutic vaccinations, which are the most judicious ones to fight cancer. Our data showed an undeniable interest of liposomal peptide-based vaccines in antitumor vaccination by the respiratory route, opening new perspectives for cancer treatment.

Application of Fmoc-SPPS, Thiol-Maleimide Conjugation, and Copper(I)-Catalyzed Alkyne-Azide Cycloaddition "Click" Reaction in the Synthesis of a Complex Peptide-Based Vaccine Candidate Against Group A Streptococcus

Fmoc solid-phase peptide synthesis (SPPS) is the most common approach used to synthesize natural and unnatural peptides. However, the synthesis of sequences longer than 30-60 amino acids is associated with a drastic reduction in peptide quality. Thus, large and complex peptides are normally synthesized as fragments, which are then conjugated together. Here, we describe the synthesis of a large, branched peptide, a multi-epitope vaccine candidate against Group A Streptococcus, with the help of microwave-assisted Fmoc-SPPS, thiol-maleimide conjugation, and copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC) "click" reaction.

Malaria: Paving the way to developing peptide-based vaccines against invasion in infectious diseases

Malaria remains a large-scale public health problem, killing more than 400,000 people and infecting up to 230 million worldwide, every year. Unfortunately, despite numerous efforts and research concerning vaccine development, results to date have been low and/or strain-specific. This work describes a strategy involving Plasmodium falciparum Duffy binding-like (DBL) and reticulocyte-binding protein homologue (RH) family-derived minimum functional peptides, netMHCIIpan3.2 parental and modified peptides' in silico binding prediction and modeling some Aotus major histocompatibility class II (MHCII) molecules based on known human molecules' structure to understand their differences. These are used to explain peptides' immunological behaviour when used as vaccine components in the Aotus model. Despite the great similarity between human and Aotus immune system molecules, around 50% of Aotus allele molecules lack a counterpart in the human immune system which could lead to an Aotus-specific vaccine. It was also confirmed that functional Plasmodium falciparum' conserved proteins are immunologically silent (in both the animal model and in-silico prediction); they must therefore be modified to elicit an appropriate immune response. Some peptides studied here had the desired behaviour and can thus be considered components of a fully-protective antimalarial vaccine.

Designing peptide-based vaccine candidates for Plasmodium falciparum erythrocyte binding antigen 175

Plasmodium falciparum leads to a virulent form of malaria. Progress has been achieved in understanding the mechanisms involved in the malarial infection, still there is no effective vaccine to prevent severe infection. An effective vaccine against malaria should be one which can induce immune responses against multiple epitopes in the context of predominantly occurring HLA alleles. In this study, an integrated approach was employed to identify promiscuous peptides of a well-defined sequence of erythrocyte binding antigen-175 and promiscuous peptides for HLA alleles were designed using bioinformatics tools. A peptide with 15 amino acids (ILAIAIYESRILKRK) was selected based on its high binding affinity score and synthesized. This promiscuous peptide was used as stimulating antigen in lymphoproliferative responses to evaluate the cellular immune response. It was observed this peptide evokes lymphoproliferative and cytokine responses in individuals naturally exposed to the malaria parasite. The intensity of PBMCs proliferation was observed to be higher in sera obtained from P. falciparum exposed as compared to unexposed healthy individuals, suggesting earlier recognition of peptide of this region by T cells. Furthermore, the binding mode of HLA-peptide complex and their interaction may lead to a rational and selective peptide-based vaccine candidate design approach which can be used as a malaria prophylaxis.

Experimental cystic echinococcosis as a proof of concept for the development of peptide-based vaccines following a novel rational workflow

Vaccines are among the most important advances in medicine throughout the human history. However, conventional vaccines exhibit several drawbacks in terms of design and production costs. Peptide-based vaccines are attractive alternatives, since they can be designed mainly in silico, can be produced cheaply and safely, and are able to induce immune responses exclusively towards protective epitopes. Yet, a proper peptide design is needed, not only to generate peptide-specific immune responses, but also for them to recognize the native protein in the occurrence of a natural infection. Herein, we propose a rational workflow for developing peptide-based vaccines including novel steps that assure the cross-recognition of native proteins. In this regard, we increased the probability of generating efficient antibodies through the selection of linear B-cell epitopes free of post-translational modifications followed by analyzing the 3D-structure similarity between the peptide in-solution vs. within its parental native protein. As a proof of concept, this workflow was applied to a set of seven previously suggested potential protective antigens against the infection by Echinococcus granulosus sensu lato. Finally, two peptides were obtained showing the capacity to induce specific antibodies able to exert anti-parasite activities in different in vitro settings, as well as to provide significant protection in the murine model of secondary echinococcosis.

An Immunoinformatics Approach in Design of Synthetic Peptide Vaccine Against Influenza Virus

Peptide-based vaccines are an appealing strategy which involves usage of short synthetic peptides to engineer a highly targeted immune response. These short synthetic peptides contain potential T- and B-cell epitopes. Experimental approaches in identifying these epitopes are time-consuming and expensive; hence immunoinformatics approach came into picture. Immuninformatics approach involves epitope prediction tools, molecular docking, and population coverage analysis in design of desired immunogenic peptides. In order to overcome the antigenic variation of viruses, conserved regions are targeted to find the potential epitopes. The present chapter demonstrates the use of immunoinformatics approach to select potential peptide containing multiple T- (CD8+ and CD4+) and B-cell epitopes from Avian H3N2 M1 Protein. Further, molecular docking (to analyse HLA-peptide interaction) and population coverage analysis have been used to verify the potential of peptide to be presented by polymorphic HLA molecules. In silico approach of epitope prediction has proven to be successful methodology in screening the putative epitopes among numerous possible vaccine targets in a given protein.

Immunogenic evaluation of multi-epitope peptide-loaded PCPP microparticles as a vaccine candidate against Toxoplasma Gondii

Toxoplasmosis is a major health problem and socioeconomic burden, affecting around 30-50% of the global population. Poly(dicarboxylatophenoxy)phosphazene (PCPP) polymer was chosen as adjuvant for the immunogenic peptide antigen. Peptide-loaded PCPP microparticles were synthesized via the coacervation method and the characterization studies of microparticles were conducted to determine their size, charge, morphology, encapsulation efficacy, and loading capacity. To evaluate in vivo efficacy of the vaccine candidate, Balb/c mice were immunized with the formulations. Brain and spleen tissues were isolated from animals to investigate cytokine levels, lymphocyte proliferation, and brain cyst formation. As a result, antibody and cytokine responses in groups immunized with peptide-loaded PCPP microparticles were found to be significantly higher when compared to the control group. In conclusion, our novel multi-epitope peptide-loaded PCPP microparticle-based vaccine formulation demonstrated considerable humoral and cellular immune responses against T. gondii and protected mice against T. gondii infection during Toxoplasmosis.

Design of an Epitope-Based Peptide Vaccine Against the Major Allergen Amb a 11 Using Immunoinformatic Approaches

Allergic diseases are a socially significant problem of global importance. The number of people suffering from pollen allergies has increased dramatically in recent decades. Pollen allergies affect up to 30% of the world population. Pollen of the common ragweed (Ambrosia artemisiifolia L.) is one of the most aggressive allergens in the world. We have used a series of immunoinformatics approaches to design an effective epitope-based vaccine, which might induce a competent immunity against a major allergen Amb a 11. CD8+ and CD4+ T-cell epitopes and their corresponding MHC restricted alleles were identified by prediction tools provided by immune epitope database (IEDB). Among T-cell epitopes, MHC class I peptide (GLMEPAFTYV) and MHC class II peptide (LVCFSFSLVLILGLV) were identified as most suitable. From all predicted B-cell epitopes, only one epitope (GKLVKFSEQQLVDC) containing sequence from the conserved region was chosen for next processing. Selected epitopes have been validated by molecular docking analysis. These epitopes showed a very strong binding affinity to MHC I molecule and MHC II molecule with binding energy scores − 729.3 and − 725.0 kcal/mole respectively. Performed experimental validation showed that only the MHC class II peptide (LVCFSFSLVLILGLV) can stimulate T cells from ragweed allergic patients and IgE antibodies specific to the ragweed pollen do not recognize this epitope. Therefore, this peptide could be potentially used as a vaccine against the major allergen Amb a 11. The B-cell epitope GKLVKFSEQQLVDC forms a stable complex with the IgE molecule (energy weighted score − 695,0 kcal/mole). Tested sera from patients with ragweed allergy showed that the ragweed specific IgE antibodies can bind to the identified B-cell epitope. Population coverage analysis was performed for CD8+ and CD4+ T-cell epitopes. It was predicted that CD4+ T-cell epitope (LVCFSFSLVLILGLV) covers 90.56% of the population of Europe and 99.36% of the world population. CD8+ T-cell epitope (GLMEPAFTYV) has a population coverage of 77.37% for Europe and 71.35% for all the world.

Detection of SARS-CoV-2 peptide-specific antibodies in Syrian hamster serum by ELISA

Golden Syrian hamsters are increasingly used as a permissive animal model for SARS-CoV-2 virus studies, but the lack of immunological assays and other immunological reagents for hamsters limits its full potential. Herein, we developed an ELISA method to detect antibodies specific to peptides and proteins derived from SARS-CoV-2 virus in immunized golden Syrian hamsters. Under optimized conditions, this assay quantitates antibodies specific for individual viral peptides, peptide pools, and proteins. Hence, this ELISA method allows investigators to quantitatively assess humoral immune responses at the peptide and protein levels and has potential application in the development of peptide-based vaccines to be tested in hamsters.

In silico discovery of epitopes of gag and env proteins for the development of a multi-epitope vaccine candidate against Maedi Visna Virus using reverse vaccinology approach

Maedi Visna Virus (MVV) causes a chronic viral disease in sheep. Since there is no specific therapeutic drug that targets MVV, development of a vaccine against the MVV is inevitable. This study aimed to analyze the gag and env proteins as vaccine candidate proteins and to identify epitopes in these proteins. In addition, it was aimed to construct a multi-epitope vaccine candidate. According to the obtained results, the gag protein was detected to be more conserved and had a higher antigenicity value. Also, the number of alpha helix in the secondary structure was higher and transmembrane helices were not detected. Although many B cell and MHC-I/II epitopes were predicted, only 19 of them were detected to have the properties of antigenic, non-allergenic, non-toxic, soluble, and non-hemolytic. Of these epitopes, five were remarkable due to having the highest antigenicity value. However, the final multi-epitope vaccine was constructed with 19 epitopes. A strong affinity was shown between the final multi-epitope vaccine and TLR-2/4. In conclusion, the gag protein was a better antigen. However, both proteins had epitopes with high antigenicity value. Also, the final multi-epitope vaccine construct had a potential to be used as a peptide vaccine due to its immuno-informatics results.

Identification of highly conserved surface-exposed peptides of spike protein for multiepitope vaccine design against emerging omicron variants: An immunoinformatic approach

The COVID-19 pandemic, originating in Wuhan in 2019, was caused by SARS-CoV-2, leading to significant global fatalities. Despite the development of vaccines, the virus mutates, creating variants that evade vaccine-induced immunity. To address SARS-CoV-2's evolving nature, a multiepitope vaccine was developed using immunoinformatics approach, specifically targeting the Omicron variant's spike protein. This vaccine includes six CD8 + and eleven CD4 + epitopes selected for their immunogenicity, non-toxicity, and significant conservation among former Variants of Concern (VOCs) and Variants of Interest (VOIs), such as Alpha, Beta, Gamma, Delta, Lambda, Mu, R1, and Zeta, as well as current Variants Under Monitoring (VUMs) like XBB.1.5, XBB.1.16, EG.5, BA.2.86, and JN.1. Notably, certain epitopes like ELLHAPATV and PYRVVVLSFELLHAP were fully conserved across all tested variants in the spike protein's receptor binding domain (RBD). Others, such as NATRFASVYAWNRKR, were fully conserved in all former VOCs and VOIs and 93.33 % in current VUMs, while ERDISTEIYQAGNKP was entirely conserved in current VUMs within the RBD region. The study went on to model, refine, and validate the vaccine prototype's tertiary structure. Docking experiments and molecular dynamic simulations revealed robust and stable interactions with Toll-like receptor 4. Cloning and codon optimization confirmed successful expression in E. coli. Subsequently, the immunological reaction of the multiepitope vaccine demonstrated that the three-time administration of the prototype significantly enhanced the antibody response while decreasing the number of antigens. The designed vaccine's epitopes showed significant combined global population coverage of 100 % with 89.75 % for CD8 + and 99.98 % for CD4 + epitopes and conservation across SARS-CoV-2 variants especially in current monitoring omicron subvariants, supporting its broader applicability and potential efficacy. Although, this promising vaccine candidate needs to undergo clinical trials to determine its effectiveness in neutralising SARS-CoV-2.

Examining homology between MPXV and immunogenic VACV-derived peptides

The mpox virus (MPXV) came to global attention with the 2022 global outbreak. Current vaccination and post-exposure prophylaxis against MPXV consists of live vaccinia whole virus-based vaccines including ACAM2000®, JYNNEOS™, and LC16m8 originally developed against smallpox. Here, we analyzed 152 vaccinia-derived peptides we identified by mass spectrometry for homology with MPXV-1 and MPXV-2 sequences to evaluate their potential relevance to MPXV-specific immunity. We found that 93 (61.2 %) of these sequences were 100 % homologous to both clades. This supports the long-standing hypothesis that immunologic cross-reactivity is due to sequence homology between poxviruses. Our results also suggest the utility of VACV-derived peptides for an mpox peptide-based vaccine candidate. The development of peptide-based vaccines against MPXV could offer significant advantages over currently available vaccines, such as no cold chain requirement, stability, and reduced manufacturing costs.

Designing a Novel di-epitope Diphtheria Vaccine: A Rational Structural Immunoinformatics Approach

BACKGROUND

The design of an epitope-based vaccine against diphtheria toxin (DT) originated from the idea that many strong binder epitopes may be structurally located in the depth of DT. Subsequently, many ineffective antibodies may be produced by the presentation of those epitopes to T and B lymphocytes. The other critical issue is the population coverage of a vaccine that has been neglected in traditional vaccines.

Objective: Given the issues above, our study aimed to design a peptide-based diphtheria vaccine, considering the issues of unwanted epitopes and population coverage.

Methods: The frequencies of pre-determined HLA alleles were listed. A country in which almost all HLA alleles had been determined in almost all geographical distribution was selected. The epitopes within the sequence of diphtheria toxin were predicted by the NetMHCIIPan server based on the selected HLA alleles. Strong binder epitopes on the surface of diphtheria toxin were selected by structural epitope mapping. The epitopes, which cover almost all the human population for each of the HLA alleles in the candidate country, were then selected as epitopebased vaccines.

Results: At first, 793 strong binder epitopes were predicted, of which 82 were surface epitopes. Nine surface epitopes whose amino acids had extruding side chains were selected. Finally, 2 epitopes had the most population coverage and were suggested as a di-epitope diphtheria vaccine. The population coverage of the di-epitope vaccine in France and the world was 100 and 99.24 %, respectively. HLA-DP had the most roles in epitope presentation.

Conclusion: Our results indicated that 97.75 % of unwanted antibodies (791 epitopes) have been reduced. Achieving two immunodominant surface epitopes confirmed our rational filtration strategy for sequential reduction of unwanted epitopes. Our novel insight may pave a new way to designing novel peptide-based vaccines to avoid producing non-specific antibodies.

Immunogenicity of a peptide-based vaccine for measles: a pilot evaluation in a mouse model

Although neutralizing antibody is an established correlate of protection for measles, T cell-mediated responses play at least two critical roles in immunity to measles: first, through provision of 'help' enabling robust humoral immune responses; and second, through clearance of measles virus-infected cells. Previously, we identified 13 measles-derived peptides that bound to human leukocyte antigen (HLA) molecules in Priess cells infected with measles virus. In this study, we evaluated the immunogenicity of these peptides in a transgenic mouse model. Our results demonstrated that these peptides induced Th1-biased immune responses at varying levels. Of the 13 peptides, the top four immunogenic peptides were further selected for a viral challenge study in mice. A vaccine based on a combination of these four peptides reduced morbidity and weight loss after viral challenge compared to placebo. Our results emphasize the potential of T cell-mediated, peptide-based vaccines against measles.