In silico design of a promiscuous chimeric multi-epitope vaccine against Mycobacterium tuberculosis

Goals and strategies in vaccine development against tuberculosis

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), continues to be a major health problem globally. The emergence of multi-drug-resistant TB and extensively drug-resistant TB has become a severe threat to TB control programs. Currently, the Bacille Calmette-Guerin (BCG) vaccine protects a child from disease dissemination efficiently, but its efficiency wanes in adults. Despite all the limitations of BCG and accelerated TB vaccine research, BCG remains the only approved vaccine available for TB. Anti-TB drug treatment has been successful in combating the disease, but it has various side effects and requires an extended drug treatment period. So, vaccination is the finest outlook that can surpass the above-mentioned limitations. Several vaccine candidates are in the pipeline, and the hope for a potential candidate to either boost the BCG vaccine or replace BCG is underway. This review discusses different approaches to TB vaccine development. It summarizes all the challenges and limitations in vaccine development, and its preclinical and clinical trials. Additionally, DNA vaccines and their vaccination techniques are also discussed. Furthermore, the immunoinformatics approach and nanomaterial-based vaccine delivery with practical and productive endpoints are also discussed. Lastly, the potential prospects are also suggested for further studies, which would help bring positive outcomes.

Integrated in-silico design and in vivo validation of multi-epitope vaccines for norovirus

BACKGROUND

Norovirus (NoVs) is a foodborne pathogen that causes acute gastroenteritis. The diversity of its principal antigenic protein poses a significant challenge to vaccine development and the prevention of large-scale outbreaks globally. Currently, no licensed vaccines against norovirus have been approved.

METHODS

We developed a novel pipeline that integrates multiple bioinformatics tools to design broad-spectrum vaccines against NoVs. Specifically, broad-spectrum T-cell epitope vaccines were designed based on consensus sequences and optimized epitope screening, while broad-spectrum B-cell spatial epitope vaccines were constructed using high-throughput antigenicity calculations and epitope mapping.

RESULTS

This pipeline underwent rigorous validation at three levels: firstly, In silico validation: Analysis of properties and structures demonstrated the appropriateness of amino acid composition and the structural integrity of the vaccine sequences. Secondly, theoretical assessment: Evaluation of human leukocyte antigen (HLA) subtype and antigenicity coverage indicated a broad theoretical protective spectrum for the designed vaccine immunogens. Furthermore, in silico simulation confirmed their ability to elicit an immune response. Finally, animal-level validation: Experiments in mice showed that both vaccine immunogens stimulated high levels of IgG and IgA. Notably, Vac-B induced a strong IgG response against GII.2 and a robust IgA response against GII.17, comparable to the immune response elicited by the wild-type NoV non-replicating virus-like particle (VLP) protein group.

CONCLUSIONS

Both in silico and in vivo experimental findings suggest that the proposed pipeline and vaccine immunogens could serve as valuable theoretical guidance for the development of multi-epitope vaccines against NoVs.

Synthesis of an Adjuvant-Free Single Polypeptide-Based Tuberculosis Subunit Vaccine that Elicits In Vivo Immunogenicity in Rats

A novel tuberculosis subunit vaccine specific for Mycobacterium tuberculosis dual antigens, culture filtrate protein-10 (CFP-10) and antigen 85B (Ag85B) conjugated with cholera toxin non-toxic B subunit (CTB), was expressed as a single polypeptide in high amounts and cost-effectively in Escherichia coli. The recovery and purification conditions for the recombinant fusion protein were established. This simple peptide vaccine required no exogenous adjuvant as it contained CTB, a potent immune modulator. The vaccine's physiochemical, structural, and immunological properties were determined using the in-silico tools. It was highly antigenic, non-allergenic, and non-toxic. Its BlastP search with human proteomes excluded the chances of autoimmune reactions. The tertiary structure model (3D) was validated by Ramachandran plot assessment. The 3D structure docking with Toll-like receptors, TLR-1, 2, 4, and 6, showed that the binding affinity between the vaccine peptide and TLRs was high, and their complex was stable, indicating a strong immune response. The in-silico immune simulation revealed the vaccine-induced both innate and adaptive immune responses. In-vivo validation of the immunogenicity of CTB.CFP10.Ag85B in Wistar rats revealed higher activation of IgG immune response compared to either antigen protein. Similar results were also obtained using the C-ImmSim simulation online server. A comparison of immunogenicity of CTB.CFP10.Ag85B with the only available TB vaccine, Bacillus Calmette-Guérin (BCG) or as a booster after vaccination of Wistar rats with BCG, indicated that the IgG levels were the highest in rats vaccinated with BCG, followed by a booster dose of CTB.CFP10.Ag85B fusion protein. The fusion protein would be a safe potential vaccine booster candidate in BCG-primed individuals against TB.

In silico screening and identification of CTL and HTL epitopes in the secreted virulence factors of Mycobacterium tuberculosis

Background

Mycobacterium tuberculosis (MTb) is a highly infectious pathogen and a global health threat due to its resilient cell wall and immune evasion strategies. Despite the availability of the antituberculosis Bacille Calmette-Guérin (BCG) vaccine, its efficacy varies (0%-80%) and gradually decreases over time. This study aimed to identify cytotoxic T-lymphocyte (CTL) and helper T-lymphocyte (HTL) epitopes in MTb secretory proteins using immunoinformatics tools.

Materials and methods

The Protein Variability Server was used to identify highly conserved sequences, and epitope population coverage was estimated for the Southeast Asian (SEA) region. Selected epitopes were also docked to their major histocompatibility complex alleles.

Results

Five secretory proteins critical to MTb pathogenesis and virulence were identified as antigenic (antigenicity score > 0.4). Predicted epitopes had IC50 values ≤ 500 nM, indicating strong binding affinity, with an estimated 94% population coverage in SEA. All candidate epitopes were highly conserved (Shannon index ≤ 0.1) and showed no significant sequence similarity to human proteins, allergens, or toxic peptides. Docking analysis confirmed favorable binding to their corresponding HLA alleles, as indicated by low Gibbs free energy change (ΔG) values and dissociation constants (K D nM).

Conclusions

Overall, this study identified immunoactive CTL and HTL epitopes that could serve as promising candidates for future antiTB vaccine development. Further in vitro and in vivo studies are required to validate these preliminary findings.

One Health Approach to the Computational Design of a Lipoprotein-Based Multi-Epitope Vaccine Against Human and Livestock Tuberculosis

Tuberculosis (TB) remains a major cause of ill health and one of the leading causes of death worldwide, with about 1.25 million deaths estimated in 2023. Control measures have focused principally on early diagnosis, the treatment of active TB, and vaccination. However, the widespread emergence of anti-tuberculosis drug resistance remains the major public health threat to progress made in global TB care and control. Moreover, the Bacillus Calmette-Guérin (BCG) vaccine, the only licensed vaccine against TB in children, has been in use for over a century, and there have been considerable debates concerning its effectiveness in TB control. A multi-epitope vaccine against TB would be an invaluable tool to attain the Global Plan to End TB 2023-2030 target. A rational approach that combines several B-cell and T-cell epitopes from key lipoproteins was adopted to design a novel multi-epitope vaccine candidate. In addition, interactions with TLR4 were implemented to assess its ability to elicit an innate immune response. The conservation of the selected proteins suggests the possibility of cross-protection in line with the One Health approach to disease control. The vaccine candidate was predicted to be both antigenic and immunogenic, and immune simulation analyses demonstrated its ability to elicit both humoral and cellular immune responses. Protein-protein docking and normal-mode analyses of the vaccine candidate with TLR4 predicted efficient binding and stable interaction. This study provides a promising One Health approach for the design of multi-epitope vaccines against human and livestock tuberculosis. Overall, the designed vaccine candidate demonstrated immunogenicity and safety features that warrant further experimental validation in vitro and in vivo.

In silico design of multi-epitope vaccine candidate based on structural proteins of porcine reproductive and respiratory syndrome virus

Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most common respiratory disease-causing viral agents. Swine infected with PRRSV exhibit severe respiratory symptoms and reproductive failure, leading to significant economic losses. To address this issue, inactivated and live-attenuated vaccines have been developed. However, the current commercially available PRRSV vaccines do not confer sufficient protection or have safety issues. The use of epitope-based subunit vaccines reduce safety risks by including only specific immunogenic portions of the antigens. To enhance immune protection, this study targeted multiple structural proteins of PRRSV, including GP2, GP3, GP4, GP5, membrane (M), envelope (E), GP5a, and nucleocapsid (N), to enable the discovery of novel epitopes. Thus, a reverse vaccinology approach was utilized to design a multi-epitope subunit vaccine construct against PRRSV. Using different tools, seven linear B cell, seven cytotoxic T cell, and three helper T cell epitopes were predicted to be safe, antigenic, and immunogenic. These epitopes were linked together, and a protein adjuvant, heparin-binding hemagglutinin, was added to increase the vaccine's immunogenicity. The construct was then docked to Toll-like receptor 4 (TLR4) to assess its ability to initiate the innate immune response. The final vaccine construct was determined to be antigenic, stable, non-allergenic, and soluble. Furthermore, the vaccine demonstrated stable binding to TLR4 based on coarse-grained and atomistic molecular dynamics simulations. Finally, the immune simulation of the vaccine construct showed a robust immune response against PRRSV. In this study, a candidate vaccine construct was successfully designed as a potential strategy against PRRSV.

In silicon desinging of RANKL-targeting vaccine for protection of osteoporosis based on the epitope of Denosumab

BACKGROUND

Life quality of osteoporosis patients is affected significantly due to the severely complications of fracture and pain. RANKL, indicated as the key mediator of osteoporosis, plays a pathogenic role of osteoclasts induction. To target this program, two medications, bisphosphonate and Denosumab, were developed and achieved remarkable advantages in clinics. Unfortunately, fracture-related side-effects always emerge unavoidably, after either long-term administration of bisphosphonates or Denosumab withdrawing. To address these challenges, vaccine-based approach has been adopted to achieve sustainable protection through induction and maintenance of effective antibodies in mild level over decades.

METHODS

A Denosumab binding peptide was firstly identified as the basic component of vaccine. This peptide was then fused with diphtheria toxin T domain, a widely used adjuvant protein. Its capabilities to penetrate the autologous tolerance and induce the immune responses was then demonstrated with in-silicon evaluation. Finally, the efficacy of the DR3 vaccine was assessed through immunization on the human RANKL transgenic mice model of osteoporosis.

RESULTS

The DTT-RANKL(220-245)3 vaccine, termed as DR3, were predicted as highly antigenic and non-allergenicity. This molecule was comprised of 46.5 % of helix, 8.5 % strand and 45.1 % coil, the optimized Z-value of the tertiary structure was 6.39, and the favored area in the Ramachandran plot was 96.1 % after refinement. Molecular docking showed a tight binding of DR3 vaccine to TLR2 (-9.2 kcal/mol) and TLR4 (-9.5 kcal/mol). In addition, the immune stimulation indicated robust responses post administration of DR3 vaccine, including high level production of of antibodies and cytokines, activated T and B lymphocytes, and the long-last immune memory. In agree with the simulation, vaccinated mice generated high titers anti-hRANKL antibodies and elevated levels of IL-4 and IL-10 at 7th week post immunization.

CONCLUSION

DR3 vaccine was aroused to benefit the prevention and treatment of osteoporosis, and other bone-resorptive diseases potentially.

Design of a Multiepitope Pan-Proteomic mRNA Vaccine Construct Against African Swine Fever Virus: A Reverse Vaccinology Approach

African swine fever (ASF), caused by African swine fever virus (ASFV), is a highly contagious disease with devastating effects on the global pig industry. This warrants the development of effective control strategies, such as vaccines. However, previously developed inactivated vaccines have proven ineffective, while live-attenuated vaccines carry inherent safety risks. The use of mRNA vaccines eliminates these risks offering a safe, cost-effective, and efficient vaccine strategy against ASFV. In this study, a reverse vaccinology approach was used to design a multiepitope pan-proteomic mRNA vaccine against ASFV. Various bioinformatics tools were employed to predict epitopes for cytotoxic T lymphocytes, helper T lymphocytes, and B lymphocytes. A 50S ribosomal L7/L12 protein adjuvant, 5' cap, poly(A) tail, signal peptide, and MHC-I-targeting domain were incorporated into the design using appropriate linkers to increase immunogenicity, stability, and recognition efficiency. The physicochemical properties of the final construct were evaluated, and docking analyses were done with Toll-like receptors (TLRs) 3, 4, and 7 to evaluate binding affinity. A molecular dynamics simulation was then performed to determine binding stability, while immune simulations evaluated host's immune response. Based on 100 ASFV proteomes, six epitopes that induce cytotoxic T-cell responses, five epitopes that induce helper T-cell responses, and four epitopes that induce antibody production were predicted. The designed vaccine construct was found to be nonallergenic, antigenic, and stable when bound to TLR4 while the binding pocket analyses of the vaccine construct to TLR3 and TLR7 indicate high translation efficiency. Immune simulations demonstrated successful induction of immune responses and generation of antigen-specific memory cells. In conclusion, this study introduces an mRNA vaccine construct as a potential disease control strategy against ASF for in vitro confirmation.

Design and evaluation of a multi-epitope DNA vaccine against HPV16

Cervical cancer, among the deadliest cancers affecting women globally, primarily arises from persistent infection with high-risk human papillomavirus (HPV). To effectively combat persistent infection and prevent the progression of precancerous lesions into malignancy, a therapeutic HPV vaccine is under development. This study utilized an immunoinformatics approach to predict epitopes of cytotoxic T lymphocytes (CTLs) and helper T lymphocytes (HTLs) using the E6 and E7 oncoproteins of the HPV16 strain as target antigens. Subsequently, through meticulous selection of T-cell epitopes and other necessary elements, a multi-epitope vaccine was constructed, exhibiting good immunogenic, physicochemical, and structural characteristics. Furthermore, in silico simulations showed that the vaccine not only interacted well with toll-like receptors (TLR2/TLR3/TLR4), but also induced a strong innate and adaptive immune response characterized by elevated Th1-type cytokines, such as interferon-gamma (IFN-γ) and interleukin-2 (IL2). Additionally, our study investigated the effects of different immunization intervals on immune responses, aiming to optimize a time-efficient immunization program. In animal model experiments, the vaccine exhibited robust immunogenic, therapeutic, and prophylactic effects. Administered thrice, it consistently induced the expansion of specific CD4 and CD8 T cells, resulting in substantial cytokines release and increased proliferation of memory T cell subsets in splenic cells. Overall, our findings support the potential of this multi-epitope vaccine in combating HPV16 infection and signify its candidacy for future HPV vaccine development.

A Universal Multi-Epitope Vaccine Design Against Porcine Reproductive and Respiratory Syndrome Virus via Bioinformatics and Immunoinformatics Approaches

Porcine reproductive and respiratory syndrome virus (PRRSV) causes reproductive disorders in sows and severe pneumonia in piglets, alongside immunosuppressive effects on the host. It poses a significant global threat to the swine industry, with no effective control measures currently available due to its complex pathogenesis and high variability. Conventional inactivated and attenuated vaccines provide inadequate protection and carry biosafety risks. In this study, we designed a universal multi-epitope peptide vaccine against PRRSV using bioinformatics and immunoinformatics approaches to address these limitations. By selecting sequences from seven representative PRRSV strains, we predicted highly conserved and immunogenic T cell (Th and CTL) epitopes across all encoded proteins. These were rationally concatenated with reported B cell neutralizing epitopes into a multi-epitope vaccine construct. We performed comprehensive assessments of the construct's physicochemical and biochemical properties, along with predictions and refinements of its secondary and tertiary structures. Molecular docking simulations with TLR2 and TLR4 revealed strong potential binding interactions. Immune simulations indicated that the multi-epitope vaccine could induce robust humoral and cellular immune responses. This study provides a scientific foundation for the development of safe and effective PRRSV subunit vaccines and offers new perspectives for designing vaccines against other viral diseases.

Advances of computational methods enhance the development of multi-epitope vaccines

Vaccine development is one of the most promising fields, and multi-epitope vaccine, which does not need laborious culture processes, is an attractive alternative to classical vaccines with the advantage of safety, and efficiency. The rapid development of algorithms and the accumulation of immune data have facilitated the advancement of computer-aided vaccine design. Here we systemically reviewed the in silico data and algorithms resource, for different steps of computational vaccine design, including immunogen selection, epitope prediction, vaccine construction, optimization, and evaluation. The performance of different available tools on epitope prediction and immunogenicity evaluation was tested and compared on benchmark datasets. Finally, we discuss the future research direction for the construction of a multiepitope vaccine.

T-Cell Epitope-Based Vaccines: A Promising Strategy for Prevention of Infectious Diseases

With the development of novel vaccine strategies, T-cell epitope-based vaccines have become promising prophylactic and therapeutic tools against infectious diseases that cannot be controlled via traditional vaccines. T-cell epitope-based vaccines leverage specific immunogenic peptides to elicit protective T-cell responses against infectious pathogens. Compared to traditional vaccines, they provide superior efficacy and safety, minimizing the risk of adverse side effects. In this review, we summarized and compared the prediction and identification methods of T-cell epitopes. By integrating bioinformatic prediction and experimental validation, efficient and precise screening of T-cell epitopes can be achieved. Importantly, we delved into the development approaches to diverse T-cell epitope-based vaccines, comparing their merits and demerits, as well as discussing the prevalent challenges and perspectives in their applications. This review offers fresh perspectives for the formulation of safe and efficacious epitope-based vaccines for the devastating diseases against which no vaccines are currently available.

DNA and RNA vaccines against tuberculosis: a scoping review of human and animal studies

Introduction

To comprehensively identify and provide an overview of in vivo or clinical studies of nucleic acids (NA)-based vaccines against TB we included human or animal studies of NA vaccines for the prevention or treatment of TB and excluded in vitro or in silico research, studies of microorganisms other than M. tuberculosis, reviews, letters, and low-yield reports.

Methods

We searched PubMed, Scopus, Embase, selected Web of Science and ProQuest databases, Google Scholar, eLIBRARY.RU, PROSPERO, OSF Registries, Cochrane CENTRAL, EU Clinical Trials Register, clinicaltrials.gov, and others through WHO International Clinical Trials Registry Platform Search Portal, AVMA and CABI databases, bioRxiv, medRxiv, and others through OSF Preprint Archive Search. We searched the same sources and Google for vaccine names (GX-70) and scanned reviews for references. Data on antigenic composition, delivery systems, adjuvants, and vaccine efficacy were charted and summarized descriptively.

Results

A total of 18,157 records were identified, of which 968 were assessed for eligibility. No clinical studies were identified. 365 reports of 345 animal studies were included in the review. 342 (99.1%) studies involved DNA vaccines, and the remaining three focused on mRNA vaccines. 285 (82.6%) studies used single-antigen vaccines, while 48 (13.9%) used multiple antigens or combinations with adjuvants. Only 12 (3.5%) studies involved multiepitope vaccines. The most frequently used antigens were immunodominant secretory antigens (Ag85A, Ag85B, ESAT6), heat shock proteins, and cell wall proteins. Most studies delivered naked plasmid DNA intramuscularly without additional adjuvants. Only 4 of 17 studies comparing NA vaccines to BCG after M. tuberculosis challenge demonstrated superior protection in terms of bacterial load reduction. Some vaccine variants showed better efficacy compared to BCG.

Systematic review registration

https://osf.io/, identifier F7P9G.

In silico design of Mycobacterium tuberculosis multi-epitope adhesin protein vaccines

Mycobacterium tuberculosis (Mtb) adhesin proteins are promising candidates for subunit vaccine design. Multi-epitope Mtb vaccine and diagnostic candidates were designed using immunoinformatic tools. The antigenic potential of 26 adhesin proteins were determined using VaxiJen 2.0. The truncated heat shock protein 70 (tnHSP70), 19 kDa antigen lipoprotein (lpqH), Mtb curli pili (MTP), and Phosphate transport protein S1 (PstS1) were selected based on the number of known epitopes on the Immune Epitope Database (IEDB). B- and T-cell epitopes were identified using BepiPred2.0, ABCpred, SVMTriP, and IEDB, respectively. Population coverage was analysed using prominent South African specific alleles on the IEDB. The allergenicity, physicochemical characteristics and tertiary structure of the tri-fusion proteins were determined. The in silico immune simulation was performed using C-ImmSim. Three truncated sequences, with predicted B and T cell epitopes, and without allergenicity or signal peptides were linked by three glycine-serine residues, resulting in the stable, hydrophilic molecules, tnlpqH-tnPstS1-tnHSP70 (64,86 kDa) and tnMTP-tnPstS1-tnHSP70 (63,96 kDa). Restriction endonuclease recognition sequences incorporated at the N- and C-terminal ends of each construct, facilitated virtual cloning using Snapgene, into pGEX6P-1, resulting in novel, highly immunogenic vaccine candidates (0,912-0,985). Future studies will involve the cloning, recombinant protein expression and purification of these constructs for downstream applications.

Molecular dynamics simulation and purification of chimeric L1/L2 protein from human papillomavirus type 52 expressed in Escherichia coli BL21 (DE3)

The available prophylactic vaccines for human papillomavirus (HPV) in the market are only effective against specific types of HPV, rendering them ineffective for other types of HPV infections. The objective of this research is to investigate the stability of the recombinant protein constructed, namely chimeric L1/L2 protein from HPV type 52, with improved cross-neutralization ability. The 3D model, predicted using Alphafold, Robetta, I-Tasser, and refined with Galaxy Refinement, is validated using Ramachandran plot analysis. The stability is verified through molecular dynamics simulations, considering parameters such as RMSD, RMSF, Rg, and SASA, where stable conditions are observed. The chimeric L1/L2 protein from HPV type 52 is purified using affinity chromatography, and the His-tag is cleaved using SUMO protease to obtain pure chimeric protein with the size of ~ 55 kDa. Western blot analysis confirms binding to anti-L1 HPV type 52 polyclonal antibody. The obtained vaccine candidate can be utilized as an effective prophylactic vaccine against HPV.

Discovering peptides and computational investigations of a multiepitope vaccine target Mycobacterium tuberculosis

Mycobacterium tuberculosis (MTB) is the causative agent of tuberculosis (TB), a prevalent airborne infectious disease. Despite the availability of the Bacille Calmette-Guerin vaccine, its global efficacy remains modest, and tuberculosis persists as a significant global public health threat. Addressing this challenge and advancing towards the End MTB Strategy, we developed a multiepitope vaccine (MEV) based on immunoinformatics and computational approaches. Immunoinformatics screening of MBT protein identified immune-dominant epitopes based on Major Histocompatibility Complex (MHC) allele binding, immunogenicity, antigenicity, allergenicity, toxicity, and cytokine inducibility. Selected epitopes were integrated into an MEV construct with adjuvant and linkers, forming a fully immunogenic vaccine candidate. Comprehensive analyses encompassed the evaluation of immunological and physicochemical properties, determination of tertiary structure, molecular docking with Toll-Like Receptors (TLR), molecular dynamics (MD) simulations for all atoms, and immune simulations. Our MEV comprises 534 amino acids, featuring 6 cytotoxic T lymphocyte, 8 helper T lymphocyte, and 7 linear B lymphocyte epitopes, demonstrating high antigenicity and stability. Notably, molecular docking studies and triplicate MD simulations revealed enhanced interactions and stability of MEV with the TLR4 complex compared to TLR2. In addition, the immune simulation indicated the capacity to effectively induce elevated levels of antibodies and cytokines, emphasizing the vaccine's robust immunogenic response. This study presents a promising MEV against TB, exhibiting favorable immunological and physicochemical attributes. The findings provide theoretical support for TB vaccine development. Our study aligns with the global initiative of the End MTB Strategy, emphasizing its potential impact on addressing persistent challenges in TB control.

Novel prophylactic and therapeutic multi-epitope vaccine based on Ag85A, Ag85B, ESAT-6, and CFP-10 of Mycobacterium tuberculosis using an immunoinformatics approach

BACKGROUND

Current tuberculosis (TB) control strategies face limitations, such as low antibiotic treatment compliance and a rise in multidrug resistance. Furthermore, the lack of a safe and effective vaccine compounds these challenges. The limited efficacy of existing vaccines against TB underscores the urgency for innovative strategies, such as immunoinformatics. Consequently, this study aimed to design a targeted multi-epitope vaccine against TB infection utilizing an immunoinformatics approach.

METHODS

The multi-epitope vaccine targeted Ag85A, Ag85B, ESAT-6, and CFP-10 proteins. The design adopted various immunoinformatics tools for cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), and linear B lymphocyte (LBL) epitope prediction, the assessment of vaccine characteristics, structure modeling, population coverage analysis, disulfide engineering, solubility prediction, molecular docking/dynamics with toll-like receptors (TLRs), codon optimization/cloning, and immune simulation.

RESULTS

The multi-epitope vaccine, which was assembled using 12 CTL, 25 HTL, and 21 LBL epitopes associated with CpG adjuvants, showed promising characteristics. The immunoinformatics analysis confirmed the antigenicity, immunogenicity, and lack of allergenicity. Physicochemical evaluations indicated that the proteins were stable, thermostable, hydrophilic, and highly soluble. Docking simulations suggested high-affinity binding to TLRs, including TLR2, TLR4, and TLR9. In silico immune simulation predicted strong T cell (cytokine release) and B cell (immunoglobulin release) responses.

CONCLUSION

This immunoinformatics-designed multi-epitope vaccine targeting Ag85A, Ag85B, ESAT-6, and CFP-10 proteins showed promising characteristics in terms of stability, immunogenicity, antigenicity, solubility, and predicted induction of humoral and adaptive immune responses. This suggests its potential as a prophylactic and therapeutic vaccine against TB.

Immunoinformatics and structural aided approach to develop multi-epitope based subunit vaccine against Mycobacterium tuberculosis

Tuberculosis is a highly contagious disease caused by Mycobacterium tuberculosis (Mtb), which is one of the prominent reasons for the death of millions worldwide. The bacterium has a substantially higher mortality rate than other bacterial diseases, and the rapid rise of drug-resistant strains only makes the situation more concerning. Currently, the only licensed vaccine BCG (Bacillus Calmette-Guérin) is ineffective in preventing adult pulmonary tuberculosis prophylaxis and latent tuberculosis re-activation. Therefore, there is a pressing need to find novel and safe vaccines that provide robust immune defense and have various applications. Vaccines that combine epitopes from multiple candidate proteins have been shown to boost immunity against Mtb infection. This study applies an immunoinformatic strategy to generate an adequate multi-epitope immunization against Mtb employing five antigenic proteins. Potential B-cell, cytotoxic T lymphocyte, and helper T lymphocyte epitopes were speculated from the intended proteins and coupled with 50 s ribosomal L7/L12 adjuvant, and the vaccine was constructed. The vaccine's physicochemical profile demonstrates antigenic, soluble, and non-allergic. In the meantime, docking, molecular dynamics simulations, and essential dynamics analysis revealed that the multi-epitope vaccine structure interacted strongly with Toll-like receptors (TLR2 and TLR3). MM-PBSA analysis was performed to ascertain the system's intermolecular binding free energies accurately. The immune simulation was applied to the vaccine to forecast its immunogenic profile. Finally, in silico cloning was used to validate the vaccine's efficacy. The immunoinformatics analysis suggests the multi-epitope vaccine could induce specific immune responses, making it a potential candidate against Mtb. However, validation through the in-vivo study of the developed vaccine is essential to assess its efficacy and immunogenicity profile, which will assure active protection against Mtb.

Analysis of the components of Mycobacterium tuberculosis heat-resistant antigen (Mtb-HAg) and its regulation of γδ T-cell function

BACKGROUND

Mycobacterium tuberculosis heat-resistant antigen (Mtb-HAg) is a peptide antigen released from the mycobacterial cytoplasm into the supernatant of Mycobacterium tuberculosis (Mtb) attenuated H37Ra strain after autoclaving at 121 °C for 20 min. Mtb-HAg can specifically induce γδ T-cell proliferation in vitro. However, the exact composition of Mtb-HAg and the protein antigens that are responsible for its function are currently unknown.

METHODS

Mtb-HAg extracted from the Mtb H37Ra strain was subjected to LC‒MS mass spectrometry. Twelve of the identified protein fractions were recombinantly expressed in Escherichia coli by genetic engineering technology using pET-28a as a plasmid and purified by Ni-NTA agarose resin to stimulate peripheral blood mononuclear cells (PBMCs) from different healthy individuals. The proliferation of γδ T cells and major γδ T-cell subset types as well as the production of TNF-α and IFN-γ were determined by flow cytometry. Their proliferating γδ T cells were isolated and purified using MACS separation columns, and Mtb H37Ra-infected THP-1 was co-cultured with isolated and purified γδ T cells to quantify Mycobacterium viability by counting CFUs.

RESULTS

In this study, Mtb-HAg from the attenuated Mtb H37Ra strain was analysed by LC‒MS mass spectrometry, and a total of 564 proteins were identified. Analysis of the identified protein fractions revealed that the major protein components included heat shock proteins and Mtb-specific antigenic proteins. Recombinant expression of 10 of these proteins in by Escherichia coli genetic engineering technology was used to successfully stimulate PBMCs from different healthy individuals, but 2 of the proteins, EsxJ and EsxA, were not expressed. Flow cytometry results showed that, compared with the IL-2 control, HspX, GroEL1, and GroES specifically induced γδ T-cell expansion, with Vγ2δ2 T cells as the main subset, and the secretion of the antimicrobial cytokines TNF-α and IFN-γ. In contrast, HtpG, DnaK, GroEL2, HbhA, Mpt63, EsxB, and EsxN were unable to promote γδ T-cell proliferation and the secretion of TNF-α and IFN-γ. None of the above recombinant proteins were able to induce the secretion of TNF-α and IFN-γ by αβ T cells. In addition, TNF-α, IFN-γ-producing γδ T cells inhibit the growth of intracellular Mtb.

CONCLUSION

Activated γδ T cells induced by Mtb-HAg components HspX, GroES, GroEL1 to produce TNF-α, IFN-γ modulate macrophages to inhibit intracellular Mtb growth. These data lay the foundation for subsequent studies on the mechanism by which Mtb-HAg induces γδ T-cell proliferation in vitro, as well as the development of preventive and therapeutic vaccines and rapid diagnostic reagents.

Enhancing tuberculosis vaccine development: a deconvolution neural network approach for multi-epitope prediction

Tuberculosis (TB) a disease caused by Mycobacterium tuberculosis (Mtb) poses a significant threat to human life, and current BCG vaccinations only provide sporadic protection, therefore there is a need for developing efficient vaccines. Numerous immunoinformatic methods have been utilized previously, here for the first time a deep learning framework based on Deconvolutional Neural Networks (DCNN) and Bidirectional Long Short-Term Memory (DCNN-BiLSTM) was used to predict Mtb Multiepitope vaccine (MtbMEV) subunits against six Mtb H37Rv proteins. The trained model was used to design MEV within a few minutes against TB better than other machine learning models with 99.5% accuracy. The MEV has good antigenicity, and physiochemical properties, and is thermostable, soluble, and hydrophilic. The vaccine's BLAST search ruled out the possibility of autoimmune reactions. The secondary structure analysis revealed 87% coil, 10% beta, and 2% alpha helix, while the tertiary structure was highly upgraded after refinement. Molecular docking with TLR3 and TLR4 receptors showed good binding, indicating high immune reactions. Immune response simulation confirmed the generation of innate and adaptive responses. In-silico cloning revealed the vaccine is highly expressed in E. coli. The results can be further experimentally verified using various analyses to establish a candidate vaccine for future clinical trials.

Construction of novel multi-epitope-based diagnostic biomarker HP16118P and its application in the differential diagnosis of Mycobacterium tuberculosis latent infection

Tuberculosis (TB) is an infectious disease that significantly threatens human health. However, the differential diagnosis of latent tuberculosis infection (LTBI) and active tuberculosis (ATB) remains a challenge for clinicians in early detection and preventive intervention. In this study, we developed a novel biomarker named HP16118P, utilizing 16 helper T lymphocyte (HTL) epitopes, 11 cytotoxic T lymphocyte (CTL) epitopes, and 8 B cell epitopes identified from 15 antigens associated with LTBI-RD using the IEDB database. We analyzed the physicochemical properties, spatial structure, and immunological characteristics of HP16118P using various tools, which indicated that it is a hydrophilic and relatively stable alkaline protein. Furthermore, HP16118P exhibited good antigenicity and immunogenicity, while being non-toxic and non-allergenic, with the potential to induce immune responses. We observed that HP16118P can stimulate the production of high levels of IFN-γ+ T lymphocytes in individuals with ATB, LTBI, and health controls. IL-5 induced by HP16118P demonstrated potential in distinguishing LTBI individuals and ATB patients (p=0.0372, AUC=0.8214, 95% CI [0.5843 to 1.000]) with a sensitivity of 100% and specificity of 71.43%. Furthermore, we incorporated the GM-CSF, IL-23, IL-5, and MCP-3 induced by HP16118P into 15 machine learning algorithms to construct a model. It was found that the Quadratic discriminant analysis model exhibited the best diagnostic performance for discriminating between LTBI and ATB, with a sensitivity of 1.00, specificity of 0.86, and accuracy of 0.93. In summary, HP16118P has demonstrated strong antigenicity and immunogenicity, with the induction of GM-CSF, IL-23, IL-5, and MCP-3, suggesting their potential for the differential diagnosis of LTBI and ATB.

Immunoinformatics, molecular docking and dynamics simulation approaches unveil a multi epitope-based potent peptide vaccine candidate against avian leukosis virus

Lymphoid leukosis is a poultry neoplastic disease caused by avian leukosis virus (ALV) and is characterized by high morbidity and variable mortality rates in chicks. Currently, no effective treatment and vaccination is the only means to control it. This study exploited the immunoinformatics approaches to construct multi-epitope vaccine against ALV. ABCpred and IEDB servers were used to predict B and T lymphocytes epitopes from the viral proteins, respectively. Antigenicity, allergenicity and toxicity of the epitopes were assessed and used to construct the vaccine with suitable adjuvant and linkers. Secondary and tertiary structures of the vaccine were predicted, refined and validated. Structural errors, solubility, stability, immune simulation, dynamic simulation, docking and in silico cloning were also evaluated.The constructed vaccine was hydrophilic, antigenic and non-allergenic. Ramchandran plot showed most of the residues in the favored and additional allowed regions. ProsA server showed no errors in the vaccine structure. Immune simulation showed significant immunoglobulins and cytokines levels. Stability was enhanced by disulfide engineering and molecular dynamic simulation. Docking of the vaccine with chicken's TLR7 revealed competent binding energies.The vaccine was cloned in pET-30a(+) vector and efficiently expressed in Escherichia coli. This study provided a potent peptide vaccine that could assist in tailoring a rapid and cost-effective vaccine that helps to combat ALV. However, experimental validation is required to assess the vaccine efficiency.

A comprehensive approach to developing a multi-epitope vaccine against Mycobacterium tuberculosis: from in silico design to in vitro immunization evaluation

Introduction

The Bacillus Calmette-Guérin (BCG) vaccine, currently used against tuberculosis (TB), exhibits inconsistent efficacy, highlighting the need for more potent TB vaccines.

Materials and methods

In this study, we employed reverse vaccinology techniques to develop a promising multi-epitope vaccine (MEV) candidate, called PP13138R, for TB prevention. PP13138R comprises 34 epitopes, including B-cell, cytotoxic T lymphocyte, and helper T lymphocyte epitopes. Using bioinformatics and immunoinformatics tools, we assessed the physicochemical properties, structural features, and immunological characteristics of PP13138R.

Results

The vaccine candidate demonstrated excellent antigenicity, immunogenicity, and solubility without any signs of toxicity or sensitization. In silico analyses revealed that PP13138R interacts strongly with Toll-like receptor 2 and 4, stimulating innate and adaptive immune cells to produce abundant antigen-specific antibodies and cytokines. In vitro experiments further supported the efficacy of PP13138R by significantly increasing the population of IFN-γ+ T lymphocytes and the production of IFN-γ, TNF-α, IL-6, and IL-10 cytokines in active tuberculosis patients, latent tuberculosis infection individuals, and healthy controls, revealing the immunological characteristics and compare the immune responses elicited by the PP13138R vaccine across different stages of Mycobacterium tuberculosis infection.

Conclusion

These findings highlight the potential of PP13138R as a promising MEV candidate, characterized by favorable antigenicity, immunogenicity, and solubility, without any toxicity or sensitization.

Next-Generation TB Vaccines: Progress, Challenges, and Prospects

Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), is a prevalent global infectious disease and a leading cause of mortality worldwide. Currently, the only available vaccine for TB prevention is Bacillus Calmette-Guérin (BCG). However, BCG demonstrates limited efficacy, particularly in adults. Efforts to develop effective TB vaccines have been ongoing for nearly a century. In this review, we have examined the current obstacles in TB vaccine research and emphasized the significance of understanding the interaction mechanism between MTB and hosts in order to provide new avenues for research and establish a solid foundation for the development of novel vaccines. We have also assessed various TB vaccine candidates, including inactivated vaccines, attenuated live vaccines, subunit vaccines, viral vector vaccines, DNA vaccines, and the emerging mRNA vaccines as well as virus-like particle (VLP)-based vaccines, which are currently in preclinical stages or clinical trials. Furthermore, we have discussed the challenges and opportunities associated with developing different types of TB vaccines and outlined future directions for TB vaccine research, aiming to expedite the development of effective vaccines. This comprehensive review offers a summary of the progress made in the field of novel TB vaccines.

A multi-epitope based vaccine against the surface proteins expressed in cyst and trophozoite stages of parasite Entamoeba histolytica

Entamoeba histolytica, an anaerobic parasite, infects humans and other primates and causes fatal diseases, such as amebiasis, amebic liver abscesses, and many others. Thousands of people are infected and dying due to the need for a proper protective cure, especially in poor sanitizing regions, such as Latin America, Asia, and Africa. Around 10% of the world population is infected by E. histolytica every year. Consequently, novel preventive approaches are required to eliminate the threats of the parasite. A designed vaccine targeting the exposed proteins that are common between cyst and trophozoite stages of the parasite's life cycle would be an effective way to repress the impact of the parasite. Therefore, an in silico bioinformatics approach was performed to design an effective vaccine targeting surface proteins common between both stages of the parasite's life cycle using B-cell and T-cell epitopes. The epitopes derived from the conserved portions of the proteins and their corresponding isomers specific to the parasite suggested that the vaccine could benefit cross-protection. Furthermore, the three-dimensional structure of the designed vaccine was modelled, refined, and validated using multiple bioinformatics tools. The physiological properties and solubility were also predicted using different algorithmic tools and found to be highly soluble in nature. The vaccine was found interactcted with TLR immune receptors, and the stability was observed via dynamics simulation. Codon optimization and cloning were performed for expression analysis. Immune simulation prediction anticipated significant immune responses with a high IgG and IgM antibodies expression, Th and Tc cells population, B-cell population, memory cells, INF-γ, and IL-2 cytokines. Therefore, the constructed multi-epitope putative vaccine can effectively neutralize the parasite's harmful effects.