Designing multiepitope-based vaccine against Eimeria from immune mapped protein 1 (IMP-1) antigen using immunoinformatic approach

Exploring the nuclear proteins, viral capsid protein, and early antigen protein using immunoinformatic and molecular modeling approaches to design a vaccine candidate against Epstein Barr virus

The available Epstein Barr virus vaccine has tirelessly harnessed the gp350 glycoprotein as its target epitope, but the result has not been preventive. Right here, we designed a global multi-epitope vaccine for EBV; with special attention to making sure all strains and preventive antigens are covered. Using a robust computational vaccine design approach, our proposed vaccine is armed with 6-16 mers linear B-cell epitopes, 4-9 mer CTL epitopes, and 8-15 mer HTL epitopes which are verified to induce interleukin 4, 10 & IFN-gamma. We employed deep computational mining coupled with expert intelligence in designing the vaccine, using human Beta defensin-3-which has been reported to induce the same TLRs as EBV-as the adjuvant. The tendency of the vaccine to cause autoimmune disorder is quenched by the assurance that the construct contains no EBNA-1 homolog. The protein vaccine construct exhibited excellent physicochemical attributes such as Aliphatic index 59.55 and GRAVY - 0.710; and a ProsaWeb Z score of - 3.04. Further computational analysis revealed the vaccine docked favorably with EBV indicted TLR 1, 2, 4 & 9 with satisfactory interaction patterns. With global coverage of 85.75% and the stable molecular dynamics result obtained for the best two interactions, we are optimistic that our nontoxic, non-allergenic multi-epitope vaccine will help to ameliorate the EBV-associated diseases-which include various malignancies, tumors, and cancers-preventively.

A preliminary study of the immunogenic response of plant-derived multi-epitopic peptide vaccine candidate of Mycoplasma gallisepticum in chickens

Mycoplasma gallisepticum (MG) is responsible for chronic respiratory disease in avian species, characterized by symptoms like respiratory rales and coughing. Existing vaccines for MG have limited efficacy and require multiple doses. Certain MG cytoadherence proteins (GapA, CrmA, PlpA, and Hlp3) play a crucial role in the pathogen's respiratory tract colonization and infection. Plant-based proteins and therapeutics have gained attention due to their safety and efficiency. In this study, we designed a 21.4-kDa multi-epitope peptide vaccine (MEPV) using immunogenic segments from cytoadherence proteins. The MEPV's effectiveness was verified through computational simulations. We then cloned the MEPV, introduced it into the plant expression vector pSiM24-eGFP, and expressed it in Nicotiana benthamiana leaves. The plant-produced MEPV proved to be immunogenic when administered intramuscularly to chickens. It significantly boosted the production of immunoglobulin Y (IgY)-neutralizing antibodies against cytoadherence protein epitopes in immunized chickens compared to that in the control group. This preliminary investigation demonstrates that the plant-derived MEPV is effective in triggering an immune response in chickens. To establish an efficient poultry health management system and ensure the sustainability of the poultry industry, further research is needed to develop avian vaccines using plant biotechnology.

Designing of a new multi-epitope vaccine against Leishmania major using Leish-F1 epitopes: An In-silico study

Cutaneous leishmaniasis (CL) is the most common form of the disease which can cause malignant lesions on the skin. Vaccination for the prevention and treatment of leishmaniasis can be the most effective way to combat this disease. In this study, we designed a novel multi-epitope vaccine against Leishmania major (L. major) using immunoinformatics tools to assess its efficacy in silico. Sequences of Leish-F1 protein (TSA, Leif, and LMSTI1) of L. major were taken from GenBank. The helper T (Th) and cytotoxic T (Tc) epitopes of the protein were predicted. The final multi-epitope consisted of 18 CTL epitopes joined by AAY linker. There were also nine HTL epitopes in the structure of the vaccine construct, joined by GPGPG linker. The profilin adjuvant (the toll-like receptor 11 agonist) was also added into the construct by AAY Linker. There were 613 residues in the structure of the vaccine construct. The multi-epitope vaccine candidate was stable and non-allergic. The data obtained from the binding of final multi-epitope vaccine-TLR11 residues (band lengths and weighted scores) unveiled the ligand and the receptor high score of binding affinity. Moreover, in silico assessment of the vaccine construct cloning achieved its suitable expression in E. coli host. Based on these results, the current multi-epitope vaccine prevents L. major infection in silico, while further confirmatory assessments are required.

Proteome based analysis of circulating SARS-CoV-2 variants: approach to a universal vaccine candidate

The discovery of the first infectious variant in Wuhan, China, in December 2019, has posed concerns over global health due to the spread of COVID-19 and subsequent variants. While the majority of patients experience flu-like symptoms such as cold and fever, a small percentage, particularly those with compromised immune systems, progress from mild illness to fatality. COVID-19 is caused by a RNA virus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Our approach involved utilizing immunoinformatic to identify vaccine candidates with multiple epitopes and ligand-binding regions in reported SARS-CoV-2 variants. Through analysis of the spike glycoprotein, we identified dominant epitopes for T-cells and B-cells, resulting in a vaccine construct containing two helper T-cell epitopes, six cytotoxic T-cell epitopes, and four linear B-cell epitopes. Prior to conjugation with adjuvants and linkers, all epitopes were evaluated for antigenicity, toxicity, and allergenicity. Additionally, we assessed the vaccine Toll-Like Receptors complex (2, 3, and 4). The vaccine construct demonstrated antigenicity, non-toxicity, and non-allergenicity, thereby enabling the host to generate antibodies with favorable physicochemical characteristics. Furthermore, the 3D structure of the B-cell construct exhibited a ProSA-web z-score plot with a value of -1.71, indicating the reliability of the designed structure. The Ramachandran plot analysis revealed that 99.6% of the amino acid residues in the vaccine subunit were located in the high favored observation region, further establishing its strong candidacy as a vaccination option.

Multi-epitope vaccine candidates based on mycobacterial membrane protein large (MmpL) proteins against Mycobacterium ulcerans

Buruli ulcer (BU) is a neglected tropical disease. It is caused by the bacterium Mycobacterium ulcerans and is characterized by skin lesions. Several studies were performed testing the Bacillus Calmette-Guérin (BCG) vaccine in human and animal models and M. ulcerans-specific vaccines in animal models. However, there are currently no clinically accepted vaccines to prevent M. ulcerans infection. The aim of this study was to identify T-cell and B-cell epitopes from the mycobacterial membrane protein large (MmpL) proteins of M. ulcerans. These epitopes were analysed for properties including antigenicity, immunogenicity, non-allergenicity, non-toxicity, population coverage and the potential to induce cytokines. The final 8 CD8+, 12 CD4+ T-cell and 5 B-cell epitopes were antigenic, non-allergenic and non-toxic. The estimated global population coverage of the CD8+ and CD4+ epitopes was 97.71%. These epitopes were used to construct five multi-epitope vaccine constructs with different adjuvants and linker combinations. The constructs underwent further structural analyses and refinement. The constructs were then docked with Toll-like receptors. Three of the successfully docked complexes were structurally analysed. Two of the docked complexes successfully underwent molecular dynamics simulations (MDS) and post-MDS analysis. The complexes generated were found to be stable. However, experimental validation of the complexes is required.

Coevolution based immunoinformatics approach considering variability of epitopes to combat different strains: A case study using spike protein of SARS-CoV-2

In the recent past several vaccines were developed to combat the COVID-19 disease. Unfortunately, the protective efficacy of the current vaccines has been reduced due to the high mutation rate in SARS-CoV-2. Here, we successfully implemented a coevolution based immunoinformatics approach to design an epitope-based peptide vaccine considering variability in spike protein of SARS-CoV-2. The spike glycoprotein was investigated for B- and T-cell epitope prediction. Identified T-cell epitopes were mapped on previously reported coevolving amino acids in the spike protein to introduce mutation. The non-mutated and mutated vaccine components were constructed by selecting epitopes showing overlapping with the predicted B-cell epitopes and highest antigenicity. Selected epitopes were linked with the help of a linker to construct a single vaccine component. Non-mutated and mutated vaccine component sequences were modelled and validated. The in-silico expression level of the vaccine constructs (non-mutated and mutated) in E. coli K12 shows promising results. The molecular docking analysis of vaccine components with toll-like receptor 5 (TLR5) demonstrated strong binding affinity. The time series calculations including root mean square deviation (RMSD), radius of gyration (RGYR), and energy of the system over 100 ns trajectory obtained from all atom molecular dynamics simulation showed stability of the system. The combined coevolutionary and immunoinformatics approach used in this study will certainly help to design an effective peptide vaccine that may work against different strains of SARS-CoV-2. Moreover, the strategy used in this study can be implemented on other pathogens.

Infection, Transmission, Pathogenesis and Vaccine Development against Mycoplasma gallisepticum

Mycoplasma sp. comprises cell wall-less bacteria with reduced genome size and can infect mammals, reptiles, birds, and plants. Avian mycoplasmosis, particularly in chickens, is primarily caused by Mycoplasma gallisepticum (MG) and Mycoplasma synoviae. It causes infection and pathology mainly in the respiratory, reproductive, and musculoskeletal systems. MG is the most widely distributed pathogenic avian mycoplasma with a wide range of host susceptibility and virulence. MG is transmitted both by horizontal and vertical routes. MG infection induces innate, cellular, mucosal, and adaptive immune responses in the host. Macrophages aid in phagocytosis and clearance, and B and T cells play critical roles in the clearance and prevention of MG. The virulent factors of MG are adhesion proteins, lipoproteins, heat shock proteins, and antigenic variation proteins, all of which play pivotal roles in host cell entry and pathogenesis. Prevention of MG relies on farm and flock biosecurity, management strategies, early diagnosis, use of antimicrobials, and vaccination. This review summarizes the vital pathogenic mechanisms underlying MG infection and recapitulates the virulence factors of MG-host cell adhesion, antigenic variation, nutrient transport, and immune evasion. The review also highlights the limitations of current vaccines and the development of innovative future vaccines against MG.

Identification of potential candidate vaccines against Mycobacterium ulcerans based on the major facilitator superfamily transporter protein

Buruli ulcer is a neglected tropical disease that is characterized by non-fatal lesion development. The causative agent is Mycobacterium ulcerans (M. ulcerans). There are no known vectors or transmission methods, preventing the development of control methods. There are effective diagnostic techniques and treatment routines; however, several socioeconomic factors may limit patients' abilities to receive these treatments. The Bacillus Calmette-Guérin vaccine developed against tuberculosis has shown limited efficacy, and no conventionally designed vaccines have passed clinical trials. This study aimed to generate a multi-epitope vaccine against M. ulcerans from the major facilitator superfamily transporter protein using an immunoinformatics approach. Twelve M. ulcerans genome assemblies were analyzed, resulting in the identification of 11 CD8+ and 7 CD4+ T-cell epitopes and 2 B-cell epitopes. These conserved epitopes were computationally predicted to be antigenic, immunogenic, non-allergenic, and non-toxic. The CD4+ T-cell epitopes were capable of inducing interferon-gamma and interleukin-4. They successfully bound to their respective human leukocyte antigens alleles in in silico docking studies. The expected global population coverage of the T-cell epitopes and their restricted human leukocyte antigens alleles was 99.90%. The population coverage of endemic regions ranged from 99.99% (Papua New Guinea) to 21.81% (Liberia). Two vaccine constructs were generated using the Toll-like receptors 2 and 4 agonists, LprG and RpfE, respectively. Both constructs were antigenic, non-allergenic, non-toxic, thermostable, basic, and hydrophilic. The DNA sequences of the vaccine constructs underwent optimization and were successfully in-silico cloned with the pET-28a(+) plasmid. The vaccine constructs were successfully docked to their respective toll-like receptors. Molecular dynamics simulations were carried out to analyze the binding interactions within the complex. The generated binding energies indicate the stability of both complexes. The constructs generated in this study display severable favorable properties, with construct one displaying a greater range of favorable properties. However, further analysis and laboratory validation are required.

Vaccines against chicken coccidiosis with particular reference to previous decade: progress, challenges, and opportunities

Chicken coccidiosis is an economically significant disease of commercial chicken industry accounting for losses of more than £10.4 billion (according to 2016 prices). Additionally, the costs incurred in prophylaxis and therapeutics against chicken coccidiosis in developing countries (for instance Pakistan according to 2018 prices) reached US $45,000.00 while production losses for various categories of chicken ranges 104.74 to US $2,750,779.00. The infection has been reported from all types of commercial chickens (broiler, layer, breeder) having a range of reported prevalence of 7-90%. The concern of resistance towards major anticoccidials has provided a way forward to vaccine research and development. For prophylaxis of chicken coccidiosis, live virulent, attenuated, ionophore tolerant strains and recombinant vaccines have been extensively trialed and commercialized. Eimeria antigens and novel vaccine adjuvants have elicited the protective efficacy against coccidial challenge. The cost of production and achieving robust immune responses in birds are major challenges for commercial vaccine production. In the future, research should be focused on the development of multivalent anticoccidial vaccines for commercial poultry. Efforts should also be made on the discovery of novel antigens for incorporation into vaccine designs which might be more effective against multiple Eimeria species. This review presents a recap to the overall progress against chicken Eimeria with particular reference to previous decade. The article presents critical analysis of potential areas for future research in chicken Eimeria vaccine development.

Deciphering the immunogenic T-cell epitopes from spike protein of SARS-CoV-2 concerning the diverse population of India

Scientists are rigorously looking for an efficient vaccine against the current pandemic due to the SARS-CoV-2 virus. The reverse vaccinology approach may provide us with significant therapeutic leads in this direction and further determination of T-cell/B-cell response to antigen. In the present study, we conducted a population coverage analysis referring to the diverse Indian population. From the Immune epitope database (IEDB), HLA- distribution analysis was performed to find the most promiscuous T-cell epitope out of In silico determined epitope of Spike protein from SARS-CoV-2. Epitopes were selected based on their binding affinity with the maximum number of HLA alleles belonging to the highest population coverage rate values for the chosen geographical area in India. 404 cleavage sites within the 1288 amino acids sequence of spike glycoprotein were determined by NetChop proteasomal cleavage prediction suggesting the presence of adequate sites in the protein sequence for cleaving into appropriate epitopes. For population coverage analysis, 179 selected epitopes present the projected population coverage up to 97.45% with 56.16 average hit and 15.07 pc90. 54 epitopes are found with the highest coverage among the Indian population and highly conserved within the given spike RBD domain sequence. Among all the predicted epitopes, 9-mer TRFASVYAW and RFDNPVLPF along with 12-mer LLAGTITSGWTF and VSQPFLMDLEGK epitopes are observed as the best due to their decent docking score and best binding affinity to corresponding HLA alleles during MD simulations. Outcomes from this study could be critical to design a vaccine against SARS-CoV-2 for a different set of populations within the country.Communicated by Ramaswamy H. Sarma.