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Background: Multi-valent based vaccines have advantage over conventional vaccines because of its multi-faceted action targeted at antigen; thereby raising hope of a more sustained actions against allergens. Escherichia coli (E. coli) is a bacterium that is commonly found in the gut of humans and warm-blooded animals. An increasing number of outbreaks are associated with the consumption of fruits and vegetables (including sprouts, spinach, lettuce, coleslaw, and salad) thereby contamination may be due to contact with faeces from domestic or wild animals at some stages during cultivation or handling. Due to the reported increase in resistance to antibiotics used for Escherichia coli control; an effective vaccine is a would-be alternative of proven interest. Hence, a need for a rational, strategic, and efficient vaccine candidate against E.coli is of paramount necessity by the use of the most current bioinformatics tools to achieve this task. Method: In this study, immunoinformatics tools mined from diverse molecular databases were used for a novel putative epitope based oral vaccine against E.coli. The prospective vaccine proteins were carefully screened and validated to achieve a high thorough-put three-dimensional protein structure. The eventual propsective vaccine candidate proteins was evaluated for its non-allergenicity, antigenicity, solubility, appropriate molecular weight testing and isoelectric point evaluation. Conclusion: The resultant vaccine candidate could serve as a promising anti-E.coli vaccine candidate. Immunoinformatics is a new field over pharmaco-therapeutics; this newest technology should continue to be a rescue from age-long traditional approach in vaccine developments.

Abstract Background Among the most common causes of invasive aspergillosis and acute bronchopulmonary aspergillosis is Aspergillus fumigatus. Transmission with A. fumigatus produces aggressive aspergillosis in allogeneic haematopoietic stem cell transplant recipients, HIV patients, and cancer patients. Asthmatics and cystic fibrosis patients are allergic to A. fumigatus. MHC class-II binding epitopes can initiate immunogenic responses in patients. In this study, we deployed immunoinformatic study to reveal epitopes from fungal proteins. Results In modern research, we found multiple epitopes ITLKLLHRYSYKLAG, KLVLRAFPNHFRGDS, RYSYKLAGVNQVDVV, GKSFELNQAARAVTQ, and LHRYSYKLAGVNQVD from crucial proteins of A. fumigatus 5,8-linoleate diol synthase (ACO55067.2) and ChainB-chitinase A1 (2XVN_B). RYSYKLAGVNQVDVV, GKSFELNQAARAVTQ, and LHRYSYKLAGVNQVD epitopes interact with HLA-DRB01_0101, while ITLKLLHRYSYKLAG and KLVLRAFPNHFRGDS epitopes interact with HLA-DRB01_1501. Molecular docking analysis reveals atomic contact energy (ACE) value for these five epitopes shown below −5 Kcal/mol in docked state. Conclusions The invasive aspergillosis and acute bronchopulmonary aspergillosis are caused by harmful fungal pathogen Aspergillus fumigatus. Our modern immunoinformatic research shows ITLKLLHRYSYKLAG, KLVLRAFPNHFRGDS, RYSYKLAGVNQVDVV, GKSFELNQAARAVTQ, and LHRYSYKLAGVNQVD epitopes could bind to MHC-II HLA allelic determinants and can initiate immunogenic response in patients affected by Aspergillus fumigatus.

Abstract Background The novel coronavirus (SARS-CoV-2) caused lethal infections worldwide during an unprecedented pandemic. Identification of the candidate viral epitopes is the first step in the design of vaccines against the viral infection. Several immunoinformatic approaches were employed to identify the SARS-CoV-2 epitopes that bind specifically with the major histocompatibility molecules class I (MHC-I). We utilized immunoinformatic tools to analyze the whole viral protein sequences, to identify the SARS-CoV-2 epitopes responsible for binding to the most frequent human leukocyte antigen (HLA) alleles in the Egyptian population. These alleles were also found with high frequency in other populations worldwide. Results Molecular docking approach showed that using the co-crystallized MHC-I and T cell receptor (TCR) instead of using MHC-I structure only, significantly enhanced docking scores and stabilized the conformation, as well as the binding affinity of the identified SARS-CoV-2 epitopes. Our approach directly predicts 7 potential vaccine subunits from the available SARS-CoV-2 spike and ORF1ab protein sequence. This prediction has been confirmed by published experimentally validated and in silico predicted spike epitope. On the other hand, we predicted novel epitopes (RDLPQGFSA and FCLEASFNY) showing high docking scores and antigenicity response with both MHC-I and TCR. Moreover, antigenicity, allergenicity, toxicity, and physicochemical properties of the predicted SARS-CoV-2 epitopes were evaluated via state-of-the-art bioinformatic approaches, showing high efficacy of the proposed epitopes as a vaccine candidate. Conclusion Our predicted SARS-CoV-2 epitopes can facilitate vaccine development to enhance the immunogenicity against SARS-CoV-2 and provide supportive data for further experimental validation. Our proposed molecular docking approach of exploiting both MHC and TCR structures can be used to identify potential epitopes for most microbial pathogens, provided the crystal structure of MHC co-crystallized with TCR.

Background & Objective: The most common cause of milk production loss in cattle and water buffalo is bovine ephemeral fever (BEF). Previous cases have been reported in Iran's south regions, with a low mortality rate. As a result, studying BEFV and identifying ideal epitopes for further developing diagnostic paths is important. Materials & Methods: To investigate BEFV N protein epitopes, we collected samples, extracted and sequenced DNA, and then used the ExPaSy translate method to deduce the amino acid sequence. Various immunoinformatics techniques were used to analyze physical/chemical properties, secondary structure of protein sequences, membrane topology, antigenic property, and 3D structure. BCPRED and the DiscoTope server, respectively, predicted linear and discontinuous epitopes of BEFV N protein. Finally, the PatchDock server was used to dock peptides and antibodies. Result: Three linear epitopes and sixteen discontinuous epitopic positions were discovered. Furthermore, molecular docking between epitopes and low-binding-energy antibodies revealed that they have easy access to the immune system. Conclusion: In this study, bioinformatics techniques were used to predict epitopes of the BEFV N protein for further developing BEFV diagnostic paths. Furthermore, experimental validation is needed for these epitopes.

Background: The arboviruses Zika virus (ZIKV) is a pathogen that threatens human health. Scientists have warned that a single mutation in the mosquito-borne ZIKV could spark another major outbreak of the disease in humans. Therefore, designing a suitable vaccine for this virus seems necessary. This study aimed to predict the protective epitopes of envelope protein from the Zika virus with bioinformatics methods for multi-epitope vaccine development. Materials and Methods: Computational studies including the identification of potential B-cell and T-cell epitopes were used. For generating a multi-epitopic vaccine construct (MEVC), selected epitopes are connected by suitable linkers. To enhance protein immunogenicity, Maltosebound protein was added to the MEVC after the prediction and refinement of the 3D structure of the designed vaccine. The binding mode of the MEVC with toll-like receptor was investigated by molecular docking technique. Finally, molecular dynamics and in silico cloning were performed for the designed vaccine. Results: This study showed that this recombinant vaccine is nontoxic, nonallergenic, and thermostable and elicits immune responses against the Zika virus. Conclusion: The computational data suggest that the MEVC has appropriate characteristics and a high-quality structure.

Monkeypox virus (MPXV) belonging to poxviridae family causes chronic viral disease in various mammals including human and monkeys. Conventional vaccines developed against smallpox of poxviridae, are not specific against Mpox. Also, they can cause various side effects after vaccination. In this study, we aimed to analyze the A17L, A28L, A37R, A43R, E8L, H3L, B6R, and M1R structural proteins of MPXV and identify epitopes in them which can be used to generate vaccine antigens. Among the proteins analyzed, the M1R protein was predicted to be more appropriate for use in vaccine research due to its high antigenicity value and other physicochemical features. Also, A17L, B6R and E8L had high antigenicity values. E8L protein was more conserved while the A37R, A43R, and B6R proteins had signal peptides. Although a total of eight B cell epitopes were predicted in all proteins analyzed, CNGETK epitope belonging to B6R protein had the highest antigenicity value (1.7083), as well as was non-allergenic, non-toxic, and soluble. Based on T cell epitope analyses performed on all proteins, fourteen MHC-I/II epitopes were predicted that are antigenic, non-allergenic and non-toxic, as well as soluble. Among them, MHC-I related-HEIYDRNVGF epitope in A28L protein had the highest antigenicity value (1.6650) and MHC-II related-IGNIKIVQIDIRDIK epitope in A37R protein had the highest antigenicity value (2.0280). In conclusion, eight structural proteins of MPXV were successfully analyzed and 22 important epitopes were identified that could serve as vaccine antigens or in serological studies to develop diagnostic tools. [ABSTRACT FROM AUTHOR]

Brucellosis is a zoonotic disease caused by Brucella , which is difficult to eliminate by conventional drugs. Therefore, a novel multi-epitope vaccine (MEV) was designed to prevent human Brucella infection. Based on the method of "reverse vaccinology", cytotoxic T lymphocyte epitopes (CTLEs), helper T lymphocyte epitopes (HTLEs), linear B-cell epitopes (LBEs) and conformational B-cell epitopes (CBEs) of four Brucella proteins (VirB9, VirB10, Omp 19 and Omp 25) were obtained. In order to keep the correct protein folding, the multiple epitopes was constructed by connecting epitopes through linkers. In view of the significant connection between human leukocyte antigen CTLA-4 and B7 molecules found on antigen presenting cells (APCs), a new vaccine (V_C4MEV) for preventing brucellosis was created by combining CTLA-4 immunoglobulin variable region (IgV_CTLA-4) with MEV protein. Immunoinformatics analysis showed that V_C4MEV has a good secondary and tertiary structure. Additionally, molecular docking and molecular dynamics simulation (MD) revealed a robust binding affinity between IgV_ CTLA-4 and the B7 molecule. Notably, the vaccine V_C4MEV was demonstrated favorable immunogenicity and antigenicity in both in vitro and in vivo experiments. V_C4MEV had the potential to activate defensive cells and immune responses, offering a hopeful approach for developing vaccines against Brucella in the upcoming years. • Human brucellosis is a neglected public health issue in China. • There has no safe and effective licensed vaccine for human brucellosis. • Vaccine constructs based on T cell and B cell epitopes of different proteins. • The IgV_CTLA-4 can be used as adjuvant and guide to enhance immune response. • The new preventive vaccine (V_4MEV) against brucellosis exerts good immune effect. [ABSTRACT FROM AUTHOR]

Klebsiella pneumoniae is a primary cause of clinical mastitis in dairy cows, with prevention being crucial, as treatments often fail due to antimicrobial resistance. Recent studies identified type I fimbrial antigens of K. pneumoniae as promising vaccine candidates, but there are limited research data. In this study, 3 fimbriae genes (fimA , fimC and fimG) were cloned and recombinantly expressed in Escherichia coli and their protective efficacy against K. pneumoniae evaluated in a mouse model. All 3 recombinant fimbriae proteins elicited strong humoral immune responses in mice, significantly increasing IgG, IgG1 and IgG2a. Notably, using a model of mice challenged with an intraperitoneal injection of bacteria, FimG significantly reduced bacterial loads in the spleen and lung, whereas FimA and FimC had limited protection for these organs. Either active or passive immunization with FimG produced substantial protective effects in mice challenged with K. pneumoniae LD 100 ; in contrast, the mortality rate in the FimA-immunized group was similar to that of the control group, whereas FimC had weak protection. We concluded that the FimG recombinant protein vaccine had a favorable protective effect, with potential for immunization against K. pneumoniae mastitis. • Three Klebsiella pneumoniae recombinant type I fimbrial protein subunits were purified for vaccine trials. • Immunization of mice with fimbrial protein subunits elicited a strong humoral antibody response. • Immunization with FimG protected against Klebsiella pneumoniae infection. [ABSTRACT FROM AUTHOR]

One of the most important breakthroughs in healthcare is the development of vaccines. The life cycle and its gene expression in the numerous virus-associated disorders must be considered when choosing the target vaccine antigen for Epstein–Barr virus (EBV). The vaccine candidate used in the current study will also be effective against all other herpesvirus strains, based on the conservancy study, which verified that the protein is present in all herpesviruses. From the screening, two B-cell epitopes, four MHC-I, and five MHC-II restricted epitopes were chosen for further study. The refined epitopes indicated 70.59% coverage of the population in Malaysia and 93.98% worldwide. After removing the one toxin (PADRE) from the original vaccine design, it was projected that the new vaccine would not be similar to the human host and would instead be antigenic, immunogenic, non-allergenic, and non-toxic. The vaccine construct was stable, thermostable, soluble, and hydrophilic. The immunological simulation projected that the vaccine candidate would be subject to a long-lasting active adaptive response and a short-lived active innate response. With IgM concentrations of up to 450 cells per mm3 and active B-cell concentrations of up to 400 cells per mm3, the B-cells remain active for a considerable time. The construct also discovered other conformational epitopes, improving its ability to stimulate an immune response. This suggests that, upon injection, the epitope will target the B-cell surface receptors and elicit a potent immune response. Furthermore, the discotope analysis confirmed that our conformational B-cell epitope was not displaced during the design. Lastly, the docking complex was stable and exhibited little deformability under heat pressure. These computational results are very encouraging for future testing of our proposed vaccine, which may potentially help in the management and prevention of EBV infections worldwide.

Mycoplasma hyorhinis (M. hyorhinis) is responsible for infections in the swine population. Such infections are usually cured by using antimicrobials and lead to develop resistance. Until now, there has been no effective vaccine to eradicate the disease. This study used conserved domains found in seven members of the variable lipoprotein (VlpA-G) family in order to design a multi-epitope candidate vaccine (MEV) against M. hyorhinis. The immunoinformatics approach was followed to predict epitopes, and a vaccine construct consisting of an adjuvant, two B cell epitopes, two HTL epitopes, and one CTL epitope was designed. The suitability of the vaccine construct was identified by its non-allergen, non-toxic, and antigenic nature. A molecular dynamic simulation was executed to assess the stability of the TLR2 docked structure. An immune simulation showed a high immune response toward the antigen. The protein sequence was reverse-translated, and codons were optimized to gain a high expression level in E. coli. The proposed vaccine construct may be a candidate for a multi-epitope vaccine. Experimental validation is required in future to test the safety and efficacy of the hypothetical candidate vaccine.

Streptococcus iniae infection is recognized as a disease with substantial economic losses, infecting a wide range of fish species. The limitations of current vaccines and strategies have led to the identification of new methods to control this disease. Multi-epitope vaccines which employ various immunogenic proteins can be promising. The current research project aimed to design an efficient multi-epitope vaccine against Streptococcus iniae infection in fish. To this end, six immunogenic proteins of Streptococcus iniae, including FBA, ENO, Sip11, GAPDH, MtsB, and SCPI proteins, were applied for epitope prediction. The best B cell, T cell, and IFNγ epitopes of the immunogenic proteins, as well as interleukin-8, were used to construct a multi-epitope vaccine. Thereafter, different parameters of the designed vaccine, including physicochemical features, antigenicity, secondary structure, and tertiary structure, were evaluated. Moreover, the interaction of the interleukin-8 domain of the designed vaccine and its receptor was investigated by molecular docking strategy. Finally, nucleotide sequence of the vaccine was adapted to express in Escherichia coli. The results of the present study pointed out that the designed vaccine was a stable vaccine with molecular weight and antigenicity score of 45 kDa and 0.936, respectively. Furthermore, the structure analysis results revealed that the designed vaccine contained 23.49% alpha helix, with 90.5% residues in favored region. Finally, it was demonstrated that the interleukin-8 domain of the designed vaccine could be successfully docked to its receptor with the lowest energy of -1020.9. Based on the obtained results, it seems that the designed vaccine can be an efficient candidate to prevent Streptococcus iniae infection in fish.

Abstract Background As the new pandemic created by COVID-19 virus created the need of rapid acquisition of a suitable vaccine against SARS-CoV-2 to develop Immunity and to reduce the mortality, the aim of this study was to identify SARS-CoV-2 S protein and N antigenic epitopes by using immunoinformatic methods to design a vaccine against SARS-CoV-2, for which S and N protein-dependent epitopes are predicted. B cell, CTL and HTL were determined based on antigenicity, allergenicity and toxicity that were non-allergenic, non-toxic, and antigenic and were selected for the design of a multi-epitope vaccine structure. Then, in order to increase the safety of Hbd-3 and Hbd-2 as adjuvants, they were connected to the N and C terminals of the vaccine construct, respectively, with a linker. The three-dimensional structure of the structure was predicted and optimized, and its quality was evaluated. The vaccine construct was ligated to MHCI. Finally, after optimizing the codon to increase expression in E. coli K12, the vaccine construct was cloned into pET28a (+) vector. Results Epitopes which were used in our survey were based on non-allergenic, non-toxic and antigenic. Therefore, 543-amino-acid-long multi-epitope vaccine formation was invented through linking 9 cytotoxic CTL, 5 HTL and 14 B cell epitopes with appropriate adjuvants and connectors that can control the SARS coronavirus 2 infection and could be more assessed in medical scientific researches. Conclusion We believe that the proposed multi-epitope vaccine can effectively evoke an immune response toward SARS-CoV-2.

Human African trypanosomiasis (HAT) is a neglected tropical disease that is caused by flagellated parasites of the genus Trypanosoma. HAT imposes a significant socio-economic burden on many countries in sub-Saharan Africa and its control is hampered by several drawbacks ranging from the ineffectiveness of drugs, complex dosing regimens, drug resistance, and lack of a vaccine. Despite more than a century of research and investigations, the development of a vaccine to tackle HAT is still challenging due to the complex biology of the pathogens. Advancements in computational modeling coupled with the availability of an unprecedented amount of omics data from different organisms have allowed the design of new generation vaccines that offer better antigenicity and safety profile. One of such new generation approaches is a multi-epitope vaccine (MEV) designed from a collection of antigenic peptides. A MEV can stimulate both cellular and humoral immune responses as well as avoiding possible allergenic reactions. Herein, we take advantage of this approach to design a MEV from conserved hypothetical plasma membrane proteins of Trypanosoma brucei gambiense, the trypanosome subspecies that is responsible for the west and central African forms of HAT. The designed MEV is 402 amino acids long (41.5 kDa). It is predicted to be antigenic, non-toxic, to assume a stable 3D conformation, and to interact with a key immune receptor. In addition, immune simulation foresaw adequate immune stimulation by the putative antigen and a lasting memory. Therefore, the designed chimeric vaccine represents a potential candidate that could be used to target HAT.

Background: High mortality rate of pigs peaked in 2020 due to the re-emergence of a deadly African swine fever virus (ASFV) which has led to transcontinental outbreaks in Europe, reportedly from 2014 to 2019, and in Asia and the Pacific from 2018–2020. Given the huge socioeconomic consequences of the disease, vaccines that will prime the immunity of swine against this pathogen is a dire necessity. Methods: In silico identification and characterization of highly conserved cytotoxic T-cell (CD8+) epitopes derived from one of its structural proteins, pp220, were analyzed. Protein sequences of pp220 were retrieved and clustered to obtain highly conserved sequences. Cross-reactive epitopes were filtered out, and the remaining epitopes were docked with swine leukocyte antigen-1*0401 (SLA-1*0401). Furthermore, the epitope stability was determined by comparing binding energy, dissociation constant, and eigenvalues of the epitopes with the values of positive control, influenza-epitope complex. Results: This study showed that 20 highly conserved epitopes promiscuously bind to two or more SLAs and 9 of which epitopes (ALDLSLIGF, QIYKTLLEY, FLNKSTQAY, IADAINQEF, IINPSITEY, AINTFMYYY, SLYPTQFDY, RSNPGSFYW, and RLDRKHILM) that were validated exhibit potential immunogenicity based on the acceptable binding energy, dissociation constant, and eigenvalues. Conclusion: This study has identified epitopes that show high conservancy, reducing the chance of epitope immune evasion. It is anticipated that the identified epitopes must be further evaluated as a potential immunotherapeutic agent in developing an epitope-based vaccine against ASFV.

Background: L-glutaminase (L-glutaminase or glutamine amidohydrolase: EC 3.5.1.2) is an antileukemic agent which catalyzes the deamidation of glutamine to glutamic acid and ammonia. It is a highly potent antitumor drug solely or in combination with L-asparaginase. In the market, various microbial glutaminases are available, which are used in treatment. The high immunogenicity was reported with microbial glutaminase when they are introduced in the body during the treatment of acute lymphoblastic leukemia (ALL). Methods: This study was aimed to determine the immunogenicity of the less studied enzyme L-glutaminase from Escherichia coli, Pseudomonas sp., and Bacillus sp. to reduce the allergenicity caused by this enzyme. In the present study, we determined the immunogenicity and allergenicity of microbial glutaminase using an immunoinformatics approach to predict immunogenic and allergenic epitopes with their structural analysis also. Results: We found high immunogenicity of glutaminase from these three microbial sources but did not find a significant difference in their immunogenicity, while E. coli glutaminase showed a high relative frequency of allergenic epitopes. Conclusions: In our knowledge, this is the first research report that presented the immunogenic epitopes and structural allergenic determinants that warrant further work to minimize the immune response of glutaminase and could contribute to reducing the side effect and hypersensitivity response of glutaminase during the treatment.

Abstract The emergence of antibiotic resistance (AR) in bacteria is becoming an alarming health concern because it allows them to adapt themselves to changing environments. It is possible to prevent the spread of AR in many ways, such as reducing antibiotic misuse in human and veterinary medicine. Streptococcus pseudopneumoniae is one of these AR bacterial species that can cause pneumonia in humans and is responsible for high mortality and morbidity rates. It is oval shaped gram-positive bacterium that shows resistance to several antibiotics like penicillin, tetracycline, ciprofloxacin, erythromycin, and co-trimoxazale and no approved vaccine is available to overcome diseases of the pathogen. Thus, substantial efforts are necessary to select protective antigens from a whole genome of pathogens that are easily tested experimentally. The in silico designed vaccine was safe and potent in immunizing individuals against the aforementioned pathogens. Herein, we utilized a subtractive genomic approach to identify potential epitope-based vaccine candidates against S. pseudopneumoniae. In total, 50850 proteins were retrieved from the NCBI, representing the complete genome of S. pseudopneumoniae. Out of the total, CD-HIT analysis identified 1022 proteins as non-redundant and 49828 proteins as redundant and further subjected for subcellular localization in which bulk of proteins was located in the cytoplasm, with seven extracellular proteins (penicillin-binding protein, alpha-amylase, solute-binding protein, hypothetical protein, CHAP domain-containing protein, polysaccharide deacetylase family protein, hypothetical protein). Six immune cells epitopes (SNLQSENDRL, RNDSLQKQAR, NPTTTSEGF, KVKKKNNKK, AYSQGSQKEH, and SVVDQVSGDF) were predicted with the help of the IEDB server. To design a multi-epitopes vaccine these immune cell epitopes were together by GPGPG and adjuvant linker to enhance immune response efficacy. The 3D structure of the designed vaccine was modeled and conducted molecular docking and dynamic simulation studies were to check the binding efficacy with immune cells receptor and dynamic behavior of the docked complex. Finally, we concluded that the designed vaccine construct can provoke a proper and protective immune response against S. pseudopneumoniae.

Introduction:Klebsiella pneumoniae (K. pneumoniae) and Pseudomonas aeruginosa (P. aeruginosa) are the most common Gram-negative bacteria associated with pneumonia and coinfecting the same patient. Despite their high virulence, there is no effective vaccine against them.Methods: In the current study, the screening of several proteins from both pathogens highlighted FepA and OmpK35 for K. pneumonia in addition to HasR and OprF from P. aeruginosa as promising candidates for epitope mapping. Those four proteins were linked to form a multitope vaccine, that was formulated with a suitable adjuvant, and PADRE peptides to finalize the multitope vaccine construct. The final vaccine’s physicochemical features, antigenicity, toxicity, allergenicity, and solubility were evaluated for use in humans.Results: The output of the computational analysis revealed that the designed multitope construct has passed these assessments with satisfactory scores where, as the last stage, we performed a molecular docking study between the potential vaccine construct and K. pneumonia associated immune receptors, TLR4 and TLR2, showing affinitive to both targets with preferentiality for the TLR4 receptor protein. Validation of the docking studies has proceeded through molecular dynamics simulation, which estimated a strong binding and supported the nomination of the designed vaccine as a putative solution for K. pneumoniae and P. aeruginosa coinfection. Here, we describe the approach for the design and assessment of our potential vaccine.

BackgroundNocardia genus, a complex group of species classified to be aerobic actinomycete, can lead to severe concurrent infection as well as disseminated infection, typically in immunocompromised patients. With the expansion of the susceptible population, the incidence of Nocardia has been gradually growing, accompanied by increased resistance of the pathogen to existing therapeutics. However, there is no effective vaccine against this pathogen yet. In this study, a multi-epitope vaccine was designed against the Nocardia infection using reverse vaccinology combined with immunoinformatics approaches.MethodsFirst, the proteomes of 6 Nocardia subspecies Nocardia subspecies (Nocardia farcinica, Nocardia cyriacigeorgica, Nocardia abscessus, Nocardia otitidiscaviarum, Nocardia brasiliensis and Nocardia nova) were download NCBI (National Center for Biotechnology Information) database on May 1st, 2022 for the target proteins selection. The essential, virulent-associated or resistant-associated, surface-exposed, antigenic, non-toxic, and non-homologous with the human proteome proteins were selected for epitope identification. The shortlisted T-cell and B-cell epitopes were fused with appropriate adjuvants and linkers to construct vaccines. The physicochemical properties of the designed vaccine were predicted using multiple online servers. The Molecular docking and molecular dynamics (MD) simulation were performed to understand the binding pattern and binding stability between the vaccine candidate and Toll-like receptors (TLRs). The immunogenicity of the designed vaccines was evaluated via immune simulation.Results3 proteins that are essential, virulent-associated or resistant-associated, surface-exposed, antigenic, non-toxic, and non-homologous with the human proteome were selected from 218 complete proteome sequences of the 6 Nocardia subspecies epitope identification. After screening, only 4 cytotoxic T lymphocyte (CTL) epitopes, 6 helper T lymphocyte (HTL) epitopes, and 8 B cell epitopes that were antigenic, non-allergenic, and non-toxic were included in the final vaccine construct. The results of molecular docking and MD simulation showed that the vaccine candidate has a strong affinity for TLR2 and TLR4 of the host and the vaccine-TLR complexes were dynamically stable in the natural environment. The results of the immune simulation indicated that the designed vaccine had the potential to induce strong protective immune responses in the host. The codon optimization and cloned analysis showed that the vaccine was available for mass production.ConclusionThe designed vaccine has the potential to stimulate long-lasting immunity in the host, but further studies are required to validate its safety and efficacy.

Rickettsioses, caused by intracellular bacteria of the rickettsia genus, pose a global health threat, particularly affecting underserved communities. Delays in diagnosis and treatment due to limited healthcare access result in severe cases and fatalities. To address this, a multi-epitope vaccine targeting OmpB and GroEL proteins in epidemic and endemic typhus rickettsia was developed using immunoinformatics techniques. T-cell and B-cell epitopes were predicted from OmpB and GroEL proteins, resulting in 5 CTL, 4 HTL, and 4 B-cell epitopes. These epitopes were linked appropriately and combined with suitable adjuvants to construct the vaccine. The vaccine's physicochemical properties and tertiary structure were validated within acceptable ranges. Molecular docking analysis demonstrated favorable binding with TLR4 receptors and MHC molecules, further confirmed by molecular dynamics simulation. Immune simulation analysis predicted T-cell, IFN, and IL-2 responses upon vaccine administration. The vaccine sequence was then optimized and cloned into a plasmid vector pET-23a(+) at the Hind and AlwNI restriction sites. In this in silico experiment, a multi-epitope vaccine derived from OmpB and GroEL proteins is presented, the first validation steps of which have been completed. Subject to successful in vivo studies, this vaccine could prove to be a promising therapeutic strategy against rickettsiosis and address a critical public health challenge.

Whooping cough is a highly contagious respiratory disease caused by the gram-negative bacterium Bordetella pertussis, which was first reported more than a century ago. Recent data indicate that the reoccurrence of this disease is linked to bacterial resistance against the immune system's defense mechanisms and reduced effectiveness of vaccines. Therefore, the development of new and efficient vaccines and medications is urgently required. This study employed an immunoinformatics approach to identify potential vaccine targets from the proteome of B. pertussis strain NC_018518.1, aiming to create a multi-epitope subunit vaccine against B. pertussis. Following immunization steps, suitable extracellular and outer-membrane proteins with a peptide signal were carefully selected. To construct a multi-epitope vaccine, proteins involved in pathogenicity but not found in human hosts were chosen. T and B cell epitopes were extracted from these selected proteins and screened using various immunoinformatics tools. The epitopes commonly predicted by multiple servers were added to the candidate list based on their immunogenicity, antigenicity, and toxicity analysis. The candidate vaccine was then designed by incorporating an appropriate linker, adjuvant, and graft with the selected epitopes. Various bioinformatics tools were employed to evaluate the antigenicity, allergenicity, solubility, and physicochemical properties of the candidate vaccine. The prediction of its secondary and tertiary structures and subsequent validation steps were conducted. Our findings demonstrate that the candidate vaccine elicits both humoral and cell-mediated immune responses, suggesting its potential as a pertussis vaccine. However, further experimental validation is necessary to fully assess the proposed vaccine's potential.

BackgroundWith the increasing incidence of tuberculosis (TB) and the shortcomings of existing TB vaccines to prevent TB in adults, new TB vaccines need to be developed to address the complex TB epidemic.MethodThe dominant epitopes were screened from antigens to construct a novel epitope vaccine termed HP13138PB. The immune properties, structure, and function of HP13138PB were predicted and analyzed with bioinformatics and immunoinformatics. Then, the immune responses induced by the HP13138PB were confirmed by enzyme-linked immunospot assay (ELISPOT) and Th1/Th2/Th17 multi-cytokine detection kit.ResultThe HP13138PB vaccine consisted of 13 helper T lymphocytes (HTL) epitopes, 13 cytotoxic T lymphocytes (CTL) epitopes, and 8 B-cell epitopes. It was found that the antigenicity, immunogenicity, and solubility index of the HP13138PB vaccine were 0.87, 2.79, and 0.55, respectively. The secondary structure prediction indicated that the HP13138PB vaccine had 31% of α-helix, 11% of β-strand, and 56% of coil. The tertiary structure analysis suggested that the Z-score and the Favored region of the HP13138PB vaccine were -4.47 88.22%, respectively. Furthermore, the binding energies of the HP13138PB to toll-like receptor 2 (TLR2) was -1224.7 kcal/mol. The immunoinformatics and real-world experiments showed that the HP13138PB vaccine could induce an innate and adaptive immune response characterized by significantly higher levels of cytokines such as interferon-gamma (IFN-γ), tumor necrosis factor-α (TNF-α), interleukin-4 (IL-4), and IL-10.ConclusionThe HP13138PB is a potential vaccine candidate to prevent TB, and this study preliminarily evaluated the ability of the HP13138PB to generate an immune response, providing a precursor target for developing TB vaccines.

IntroductionThe current monkeypox (MPX) outbreak, caused by the monkeypox virus (MPXV), has turned into a global concern, with over 59,000 infection cases and 23 deaths worldwide.ObjectivesHerein, we aimed to exploit robust immunoinformatics approach, targeting membrane-bound, enveloped, and extracellular proteins of MPXV to formulate a chimeric antigen. Such a strategy could similarly be applied for identifying immunodominant epitopes and designing multi-epitope vaccine ensembles in other pathogens responsible for chronic pathologies that are difficult to intervene against.MethodsA reverse vaccinology pipeline was used to select 11 potential vaccine candidates, which were screened and mapped to predict immunodominant B-cell and T-cell epitopes. The finalized epitopes were merged with the aid of suitable linkers, an adjuvant (Resuscitation-promoting factor), a PADRE sequence (13 aa), and an HIV TAT sequence (11 aa) to formulate a multivalent epitope vaccine. Bioinformatics tools were employed to carry out codon adaptation and computational cloning. The tertiary structure of the chimeric vaccine construct was modeled via I-TASSER, and its interaction with Toll-like receptor 4 (TLR4) was evaluated using molecular docking and molecular dynamics simulation. C-ImmSim server was implemented to examine the immune response against the designed multi-epitope antigen.Results and discussionThe designed chimeric vaccine construct included 21 immunodominant epitopes (six B-cell, eight cytotoxic T lymphocyte, and seven helper T-lymphocyte) and is predicted non-allergen, antigenic, soluble, with suitable physicochemical features, that can promote cross-protection among the MPXV strains. The selected epitopes indicated a wide global population coverage (93.62%). Most finalized epitopes have 70%–100% sequence similarity with the experimentally validated immune epitopes of the vaccinia virus, which can be helpful in the speedy progression of vaccine design. Lastly, molecular docking and molecular dynamics simulation computed stable and energetically favourable interaction between the putative antigen and TLR4.ConclusionOur results show that the multi-epitope vaccine might elicit cellular and humoral immune responses and could be a potential vaccine candidate against the MPXV infection. Further experimental testing of the proposed vaccine is warranted to validate its safety and efficacy profile.

Infectious bursal disease virus is the causative agent of infectious bursal disease (Gumboro disease), a highly contagious immunosuppressive disease of chicken with a substantial economic impact on small- and large-scale poultry industries worldwide. Currently, live attenuated vaccines are widely used to control the disease in chickens despite their issues with safety (immunosuppression and bursal atrophy) and efficiency (breaking through the maternally-derived antibody titer). To overcome the drawbacks, the current study has, for the first time, attempted to construct a computational model of a multiepitope based vaccine candidate against infectious bursal disease virus, which has the potential to overcome the safety and protection issues found in the existing live-attenuated vaccines. The current study used a reverse vaccinology based immunoinformatics approach to construct the vaccine candidate using major and minor capsid proteins of the virus, VP2 and VP3, respectively. The vaccine construct was composed of four CD8+ epitopes, seven CD4+ T-cell epitopes, 11 B-cell epitopes and a Cholera Toxin B adjuvant, connected using appropriate flexible peptide linkers. The vaccine construct was evaluated as antigenic with VaxiJen Score of 0.6781, immunogenic with IEDB score of 2.89887 and non-allergenic. The 55.64 kDa construct was further evaluated for its physicochemical characteristics, which revealed that it was stable with an instability index of 16.24, basic with theoretical pI of 9.24, thermostable with aliphatic index of 86.72 and hydrophilic with GRAVY score of −0.256. The docking and molecular dynamics simulation studies of the vaccine construct with Toll-like receptor-3 revealed fair structural interaction (binding affinity of −295.94 kcal/mol) and complex stability. Further, the predicted induction of antibodies and cytokines by the vaccine construct indicated the possible elicitation of the host's immune response against the virus. The work is a significant attempt to develop next-generation vaccines against the infectious bursal disease virus though further experimental studies are required to assess the efficacy and protectivity of the proposed vaccine candidate in vivo.

BackgroundGlässer's disease, caused by Haemophilus parasuis (HPS), is responsible for economic losses in the pig industry worldwide. However, the existing commercial vaccines offer poor protection and there are significant barriers to the development of effective vaccines.MethodsIn the current study, we aimed to identify potential vaccine candidates and design a multi-epitope vaccine against HPS by performing pan-genomic analysis of 121 strains and using a reverse vaccinology approach.ResultsThe designed vaccine constructs consist of predicted epitopes of B and T cells derived from the outer membrane proteins of the HPS core genome. The vaccine was found to be highly immunogenic, non-toxic, and non-allergenic as well as have stable physicochemical properties. It has a high binding affinity to Toll-like receptor 2. In addition, in silico immune simulation results showed that the vaccine elicited an effective immune response. Moreover, the mouse polyclonal antibody obtained by immunizing the vaccine protein can be combined with different serotypes and non-typable Haemophilus parasuis in vitro.ConclusionThe overall results of the study suggest that the designed multi-epitope vaccine is a promising candidate for pan-prophylaxis against different strains of HPS.

Introduction: The present work sought to identify MHC-I-restricted peptide signatures for arbovirus using in silico and in vitro peptide microarray tools. Methods: First, an in-silico analysis of immunogenic epitopes restricted to four of the most prevalent human MHC class-I was performed by identification of MHC affinity score. For that, more than 10,000 peptide sequences from 5 Arbovirus and 8 different viral serotypes, namely Zika (ZIKV), Dengue (DENV serotypes 1-4), Chikungunya (CHIKV), Mayaro (MAYV) and Oropouche (OROV) viruses, in addition to YFV were analyzed. Haplotype HLA-A*02.01 was the dominant human MHC for all arboviruses. Over one thousand HLA-A2 immunogenic peptides were employed to build a comprehensive identity matrix. Intending to assess HLAA*02:01 reactivity of peptides in vitro, a peptide microarray was designed and generated using a dimeric protein containing HLA-A*02:01. Results: The comprehensive identity matrix allowed the identification of only three overlapping peptides between two or more flavivirus sequences, suggesting poor overlapping of virus-specific immunogenic peptides amongst arborviruses. Global analysis of the fluorescence intensity for peptide-HLA-A*02:01 binding indicated a dose-dependent effect in the array. Considering all assessed arboviruses, the number of DENV-derived peptides with HLA-A*02:01 reactivity was the highest. Furthermore, a lower number of YFV-17DD overlapping peptides presented reactivity when compared to non-overlapping peptides. In addition, the assessment of HLA-A*02:01-reactive peptides across virus polyproteins highlighted non-structural proteins as "hot-spots". Data analysis supported these findings showing the presence of major hydrophobic sites in the final segment of non-structural protein 1 throughout 2a (Ns2a) and in nonstructural proteins 2b (Ns2b), 4a (Ns4a) and 4b (Ns4b). Discussion: To our knowledge, these results provide the most comprehensive and detailed snapshot of the immunodominant peptide signature for arbovirus with MHC-class I restriction, which may bring insight into the design of future virus-specific vaccines to arboviruses and for vaccination protocols in highly endemic areas. [ABSTRACT FROM AUTHOR]

Coxsackievirus B (CVB) is one of the major viral pathogens of human myocarditis and cardiomyopathy without any effective preventive measures; therefore, it is necessary to develop a safe and efficacious vaccine against CVB. Immunoinformatics methods are both economical and convenient as in-silico simulations can shorten the development time. Herein, we design a novel multi-epitope vaccine for the prevention of CVB by using immunoinformatics methods. With the help of advanced immunoinformatics approaches, we predicted different B-cell, cytotoxic T lymphocyte (CTL), and helper T lymphocyte (HTL) epitopes, respectively. Subsequently, we constructed the multi-epitope vaccine by fusing all conserved epitopes with appropriate linkers and adjuvants. The final vaccine was found to be antigenic, non-allergenic, and stable. The 3D structure of the vaccine was then predicted, refined, and evaluated. Molecular docking and dynamics simulation were performed to reveal the interactions between the vaccine with the immune receptors MHC-I, MHC-II, TLR3, and TLR4. Finally, to ensure the complete expression of the vaccine protein, the sequence of the designed vaccine was optimized and further performed in-silico cloning. In conclusion, the molecule designed in this study could be considered a potential vaccine against CVB infection and needed further experiments to evaluate its safety and efficacy. [ABSTRACT FROM AUTHOR]

Background: Our previous study developed a novel peptide-based vaccine, MP3RT, to fight against tuberculosis (TB) infection in a mouse model. However, the consistency between the immunoinformatics predictions and the results of real-world animal experiments on the MP3RT vaccine remains unclear. Method: In this study, we predicted the antigenicity, immunogenicity, physicochemical parameters, secondary structure, and tertiary structure of MP3RT using bioinformatics technologies. The immune response properties of the MP3RT vaccine were then predicted using the C-ImmSim server. Finally, humanized mice were used to verify the characteristics of the humoral and cellular immune responses induced by the MP3RT vaccine. Results: MP3RT is a non-toxic and non-allergenic vaccine with an antigenicity index of 0.88 and an immunogenicity index of 0.61, respectively. Our results showed that the MP3RT vaccine contained 53.36% α-helix in the secondary structure, and the favored region accounted for 98.22% in the optimized tertiary structure. The binding affinities of the MP3RT vaccine to the human leukocyte antigen (HLA)-DRB1*01:01 allele, toll-like receptor-2 (TLR-2), and TLR-4 receptors were -1234.1 kcal/mol, -1066.4 kcal/mol, and -1250.4 kcal/mol, respectively. The results of the C-ImmSim server showed that the MP3RT vaccine could stimulate T and B cells to produce immune responses, such as high levels of IgM and IgG antibodies, IFN-γ, TNF-α, and IL-2 cytokines. Results from real-world animal experiments showed that the MP3RT vaccine could stimulate the humanized mice to produce high levels of IgG and IgG2a antibodies and IFN-γ+ T lymphocytes. Furthermore, the levels of IFN-γ, IL-2, and IL-6 cytokines in mice immunized with the MP3RT vaccine were significantly higher than those in the control group. Conclusion: MP3RT is a highly antigenic and immunogenic potential vaccine that can effectively induce Th1-type immune responses in silico analysis and animal experiments. This study lays the foundation for evaluating the value of computational tools and immunoinformatic techniques in reverse vaccinology research. [ABSTRACT FROM AUTHOR]

Monkeypox is a self-limiting zoonotic viral disease and causes smallpox-like symptoms. The disease has a case fatality ratio of 3–6% and, recently, a multi-country outbreak of the disease has occurred. The currently available vaccines that have provided immunization against monkeypox are classified as live attenuated vaccinia virus-based vaccines, which pose challenges of safety and efficacy in chronic infections. In this study, we have used an immunoinformatics-aided design of a multi-epitope vaccine (MEV) candidate by targeting monkeypox virus (MPXV) glycoproteins and membrane proteins. From these proteins, seven epitopes (two T-helper cell epitopes, four T-cytotoxic cell epitopes and one linear B cell epitopes) were finally selected and predicted as antigenic, non-allergic, interferon-γ activating and non-toxic. These epitopes were linked to adjuvants to design a non-allergic and antigenic candidate MPXV-MEV. Further, molecular docking and molecular dynamics simulations predicted stable interactions between predicted MEV and human receptor TLR5. Finally, the immune-simulation analysis showed that the candidate MPXV-MEV could elicit a human immune response. The results obtained from these in silico experiments are promising but require further validation through additional in vivo experiments. [ABSTRACT FROM AUTHOR]

Reports on T-cell cross-reactivity against SARS-CoV-2 epitopes in unexposed individuals have been linked with prior exposure to the human common cold coronaviruses (HCCCs). Several studies suggested that cross-reactive T-cells response to live attenuated vaccines (LAVs) such as BCG (Bacillus Calmette–Guérin), OPV (Oral Polio Vaccine), and MMR (measles, mumps, and rubella) can limit the development and severity of COVID-19. This study aims to identify potential cross-reactivity between SARS-CoV-2, HCCCs, and LAVs in the context of T-cell epitopes peptides presented by HLA (Human Leukocyte Antigen) alleles of the Indonesian population. SARS-CoV-2 derived T-cell epitopes were predicted using immunoinformatics tools and assessed for their conservancy, variability, and population coverage. Two fully conserved epitopes with 100% similarity and nine heterologous epitopes with identical T-cell receptor (TCR) contact residues were identified from the ORF1ab fragment of SARS-CoV-2 and all HCCCs. Cross-reactive epitopes from various proteins of SARS-CoV-2 and LAVs were also identified (15 epitopes from BCG, 7 epitopes from MMR, but none from OPV). A majority of the identified epitopes were observed to belong to ORF1ab, further suggesting the vital role of ORF1ab in the coronaviruses family and suggesting it as a candidate for a potential universal coronavirus vaccine that protects against severe disease by inducing cell mediated immunity. [ABSTRACT FROM AUTHOR]

Non-small-cell lung cancer (NSCLC) is the most common lung cancer which has the highest mortality rate in Indonesia. One of the trends in treating cancer is by utilizing peptide vaccines, an immunotherapeutic approach that aims to stimulate the cell-mediated adaptive immune system to recognize cancer-associated peptides. Currently, no peptide vaccines are available in the market for NSCLC treatment. Therefore, this project aims to develop a multi-epitope peptide-based vaccine for NSCLC utilizing citrullinated peptides. Citrullination is a post-translational modification that occurs in cancer cells during autophagy that functions to induce immune responses towards modified self-epitopes such as tumor cells, through activation of PAD enzymes within the APC and target cells. It was found that introducing a common citrullinated neo-antigen peptide such as vimentin and enolase to the immune system could stimulate a higher specific CD4+ T cell response against NSCLC. Moreover, carcinoembryonic antigen (CEA), an antigen that is highly expressed in cancer cells, is also added to increase the vaccine’s specificity and to mobilize both CD4+ and CD8+ T cells. These antigens bind strongly to the MHC Class II alleles such as HLA-DRB1*07:01 and HLA-DRB*11:01, which are predominant alleles in Indonesian populations. Through in silico approach, the peptides generated from CEA, citrullinated vimentin and enolase, were analyzed for their MHC binding strength, immunogenicity, ability to induce IFNγ response, and population coverage. It is expected that the immunodominant antigens presentation is able to induce a potent immune response in NSCLC patients in Indonesia, resulting in tumor eradication. [ABSTRACT FROM AUTHOR]

Background and Aim: Mycobacterium tuberculosis is a health problem in countries. Despite the global prevalence of tuberculosis and the lack of appropriate drugs, further progress is still needed with the help of modern methods of preparing epitope-based vaccines for tuberculosis. Materials and Methods: In this study, specific T and B cell epitopes required for producing chimeric vaccines with the help of servers such as IEDB were determined. The antigenicity, allergenicity, and toxicity of the selected epitopes by various other servers such as VaxiJenv2.0, AllerTOP, and Toxinpred were determined, and the vaccine of the epitope was then configured with the help of special linkers. Then, analyze the structure vaccine by some other bioinformatics servers such as PRABI, SWISS-MODEL, PROCHECK, and PEPCALC, was investigated and finally detected using docking techniques to evaluate the interaction with the epitope through MVD software. Results: The results showed that the vaccine, in terms of in silico evaluations of two-dimensional and three-dimensional structures, has a good condition. Also, the percentage of optimal placement of amino acids and bonds by PROCHECK server, % 99 percent of optimal placement of amino acids in the chimer structure was established. Also, it was non-toxic and nonallergenic and had the desired antigenicity. Conclusion: In general, the vaccine that was able to have a favorable interaction with some components of the immune system (HLA) in the docking process, which indicates the optimal identification of this structure by the humoral and cellular immune system, of course, more reliable proof of it requires clinical phase processes. [ABSTRACT FROM AUTHOR]

Gallbladder cancer (GBC) is an aggressive and difficult to treat biliary tract carcinoma with a poor survival rate. The aim of this study was to design a peptide-based multi-epitope vaccine construct against GBC using immunoinformatics approaches. Three proteins implicated in the progression of GBC were selected for B and T cell epitope prediction and the designing of the potential vaccine construct. Seven CTL, four HTL and six Bcell epitopes along with a suitable adjuvant were selected and connected using linkers for designing the vaccine construct. The secondary and tertiary models of the designed vaccine were generated and satisfactorily validated. A Ramachandran plot of the final 3D model showed more than 90% of the residues in allowed regions and only 0.4% in disallowed regions. The binding affinity of a vaccine construct with TLR 2, 3 and 4 receptors was assessed through molecular docking and simulation. The average numbers of hydrogen bonds for vaccine-TLR 2, 3 and 4 complexes in the simulation were 15.36, 16.45, and 11.98, respectively, and remained consistent over a 100 ns simulation period, which is critical for their function. The results of this study provide a strong basis for further evaluation through in vitro/in vivo experimental validation of the safety and efficacy of the designed vaccine construct. [ABSTRACT FROM AUTHOR]

After the outbreak of SARS-CoV-2 by the end of 2019, the vaccine development strategies became a worldwide priority. Furthermore, the appearances of novel SARS-CoV-2 variants challenge researchers to develop new pharmacological or preventive strategies. However, vaccines still represent an efficient way to control the SARS-CoV-2 pandemic worldwide. This review describes the importance of bioinformatic and immunoinformatic tools (in silico) for guide vaccine design. In silico strategies permit the identification of epitopes (immunogenic peptides) which could be used as potential vaccines, as well as nonacarriers such as: vector viral based vaccines, RNA-based vaccines and dendrimers through immunoinformatics. Currently, nucleic acid and protein sequential as well structural analyses through bioinformatic tools allow us to get immunogenic epitopes which can induce immune response alone or in complex with nanocarriers. One of the advantages of in silico techniques is that they facilitate the identification of epitopes, while accelerating the process and helping to economize some stages of the development of safe vaccines. [ABSTRACT FROM AUTHOR]

Monkeypox virus is the causative agent of monkeypox disease, belonging to an orthopoxvirus genus, with a disease pattern similar to that of smallpox. The number of monkeypox cases have robustly increased recently in several countries around the world, potentially causing an international threat. Therefore, serious measures are indispensable to be taken to mitigate the spread of the disease and hence, under these circumstances, vaccination is the best choice to neutralize the monkeypox virus. In the current study, we used immunoinformatic approaches to target the L1R, B5R, and A33R proteins of the monkeypox virus to screen for immunogenic cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and B-cell epitopes to construct multiepitope subunit vaccines. Various online tools predicted the best epitope from immunogenic targets (L1R, B5R, and A33R) of monkeypox virus. The predicted epitopes were joined together by different linkers and subjected to 3D structure prediction. Molecular dynamics simulation analysis confirmed the proper folding of the modeled proteins. The strong binding of the constructed vaccines with human TLR-2 was verified by the molecular docking and determination of dissociation constant values. The GC content and codon adaptation index (CAI) values confirmed the high expression of the constructed vaccines in the pET-28a (+) expression vector. The immune response simulation data delineated that the injected vaccines robustly activated the immune system, triggering the production of high titers of IgG and IgM antibodies. In conclusion, this study provided a solid base of concept to develop dynamic and effective vaccines that contain several monkeypox virus-derived highly antigenic and nonallergenic peptides to control the current pandemic of monkeypox virus. [ABSTRACT FROM AUTHOR]

The current global outbreak of monkeypox (MPX) disease, caused by Monkeypox virus (MPXV), has resulted in 16 thousand infection cases, five deaths, and has been declared a global health emergency of international concern by the World Health Organization. Given current challenges in the safety of existing vaccines, a vaccine to prevent MPX infection and/or onset of symptoms would significantly advance disease management. In this context, a multi-epitope-based vaccine could be a well-suited approach. Herein, we searched a publicly accessible database (Virus Pathogen Database and Analysis Resource) for MPXV immune epitopes from various antigens. We prioritized a group of epitopes (10 CD8+ T cells and four B-cell epitopes) using a computeraided technique based on desirable immunological and physicochemical properties, sequence conservation criteria, and non-human homology. Three multi-epitope vaccines were constructed (MPXV-1-3) by fusing finalized epitopes with the aid of appropriate linkers and adjuvant (beta-defensin 3, 50S ribosomal protein L7/L12, and Heparin-binding hemagglutinin). Codon optimization and in silico cloning in the pET28a (+) expression vector ensure the optimal expression of each construct in the Escherichia Coli system. Two and three-dimensional structures of the constructed vaccines were predicted and refined. The optimal binding mode of the construct with immune receptors [Toll-like receptors (TLR2, TLR3, and TLR4)] was explored by molecular docking, which revealed high docking energies of MPXV-1-TLR3 (-99.09 kcal/mol), MPXV-2-TLR3 (-98.68 kcal/mol), and MPXV-3-TLR2 (-85.22 kcal/mol). Conformational stability and energetically favourable binding of the vaccine-TLR2/3 complexes were assessed by performing molecular dynamics simulations and free energy calculations (Molecular Mechanics/Generalized Born Surface Area method). In silico immune simulation suggested that innate, adaptive, and humoral responses will be elicited upon administration of such potent multi-epitope vaccine constructs. The vaccine constructs are antigenic, non-allergen, non-toxic, soluble, topographically exposed, and possess favourable physicochemical characteristics. These results may help experimental vaccinologists design a potent MPX vaccine. [ABSTRACT FROM AUTHOR]

Aim: The present study aims to investigate the cluster of unexplored proteins of Staphylococcus aureususing a series of bioinformatics tools to fetch novel drug/vaccine candidates. Staphylococcus aureus, a gram-positive multidrug resistant bacteria which is easily transmitting nosocomial infections. So far, no effective vaccine exists to prevent this pathogenic infection. Materials and Methods: A total of 50 uncharacterized protein sequences of Staphylococcus aureus were retrieved from NCBI and analyzed using computational tools for studying their localization, membrane helices, physicochemical properties, virulence factors, signal peptides, antigenicity, and epitopes. These proteins were then subjected to tBLASTn to compare against human proteome for confirming that they are not human homologs in order to bypass autoimmune reactions. Results: Two potential candidate proteins possessing virulence and antigenic properties, comprising epitopes and are not human homologs were found in this study. Conclusion: Hence, these proteins could be ideal drug/vaccine targets, however, further in-depth immuno-informatics and structural biology approaches are recommended with in-vitro and in-vivo experiments for validation. [ABSTRACT FROM AUTHOR]

Aim: The present study anticipates prediction of novel drug/vaccine candidates from the group of uncharacterized proteins of Burkholderiacepaciausing a series of computational tools. B.cepacia is an emerging pulmonary pathogen in immunocompromised patients and in patients with cystic fibrosis (CS). Infections caused by these bacteria are difficult to treat due to antibiotic resistance. So far there are no drugs/vaccines against B.Cepacia. Materials and Methods: A total of 50 hypothetical proteins were retrieved from NCBI and studied using computational tools for studying their localization, membrane helices, physicochemical properties, virulence factors, signal peptides, antigenicity, and epitopes. These proteins were then subjected to BLAST to find they are matching with any human homologs to avoid autoimmune reactions. Results: Out of 50, 3 were found to be highly virulent proteins that possess antigenic properties and they are not human homologs. Conclusion: Hence, these proteins could be putative drug targets against Burkholderiacepaciainfections. Nevertheless, they require further in-vitro and in-vivo experiments for validation. [ABSTRACT FROM AUTHOR]

Helicobacter pylori is a Gram-negative bacterium estimated to infect about half of the world's population. The world health organization (WHO) has classified this bacterium in the first line of carcinogen agents; however, the only current strategy to deal with this bacterium is using antibiotics. The increase of antibiotic resistance is alarming. Vaccines could be an advantageous approach to overcome this pathogen. In this study, a multi-epitope oral vaccine was designed against H. pylori using computational approaches. GGT, BabA, HP_1453 proteins were used as antigens for finding epitopes. the two CD8+ cytolytic T lymphocyte (CTL) and seven CD4+ helper T lymphocyte (HTL) and B cell immunodominant epitopes were selected using several servers. Then, they were connected to the adjuvant (U-Omp19), COMP, and M-cell motif by GSGSG, KK and EAAAK linkers. Evaluation of the vaccine construct showed it a non-allergen, immunogen, non-toxic, and stable protein. Docking and MD results indicated its proper interaction with TLR4. Based on the obtained results, the designed vaccine, has acceptable mucosal immunogenicity besides stability in the acidic environment. It can be a proper candidate against H. pylori. However, experimental studies should be performed to confirm its stability, efficacy, and safety. [Display omitted] • Helicobacter pylori is the cunning bacterium, which can lead to gastric cancer if untreated. • The GGT, BabA, HP_1453 antigens were used to select immunodominant epitopes. • U-Omp19 adjuvant, COMP, and M-cell motif and the epitopes were joined using GSGSG, KK, and EAAAK linkers. • Computational structural and immunological studies showed the vaccine is non-allergen, immunogen, non-toxic, and stable. [ABSTRACT FROM AUTHOR]

The current study was designed to introduce an efficient epitope-based vaccine against bovine babesiosis. Four immunogenic proteins of the Babesia. bovis including Trap, msa, bov57 and 12D3 were selected from VIOLIN database, then the proteins were used for prediction of B cell and T cell epitopes. The predicted epitopes along with HBHA protein as a molecular adjuvant were used to design an epitope-based vaccine. Antigenicity, allergenicity, physicochemical features, secondary structure and tertiary structure of the designed vaccine were evaluated by VaxiJen, AllerTOP, ProtParam, SOPMA and I-TASSER servers, respectively. A molecular docking strategy was conducted by ClusPro server to investigate interaction between the designed vaccine and TLR4/MD-2. Intermolecular hydrogen bonds of the interaction were assessed by the LigPlot software and the stability of the protein-protein complex was evaluated by iMODs server. The results revealed that the designed vaccine was an antigen, non-allergen and stable protein with a molecular weight of 36 kDa which could stably bind to TLR4/MD-2 through its HBHA domain. The results showed that the DNA sequence of the vaccine could be suitably cloned in the pET21a (+) vector. According to the results, the designed vaccine can be introduced as a proper candidate to prevent bovine babesiosis. [Display omitted] • B cell and T cell epitopes of the immunogenic proteins were predicted. • An epitope-based vaccine was engineered using the predicted epitopes. • The most important parameters of the developed vaccine were assessed. • The results revealed that the engineered vaccine is a proper candidate to use. [ABSTRACT FROM AUTHOR]

Introduction: The ongoing coronavirus disease 2019 (COVID-19), which emerged in December 2019, is a serious health concern throughout the world. Despite massive COVID-19 vaccination on a global scale, there is a rising need to develop more effective vaccines and drugs to curb the spread of coronavirus. Methodology: In this study, we screened the amino acid sequence of the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 (the causative agent of COVID-19) for the identification of B and T cell epitopes using various immunoinformatic tools. These identified potent B and T cell epitopes with high antigenicity scores were linked together to design the multi-epitope vaccine construct. The physicochemical properties, overall quality, and stability of the designed vaccine construct were confirmed by suitable bioinformatic tools. Results: After proper in silico prediction and screening, we identified 3 B cell, 18 CTL, and 10 HTL epitopes from the RdRp protein sequence. The screened epitopes were non-toxic, non-allergenic, and highly antigenic in nature as revealed by appropriate servers. Molecular docking revealed stable interactions of the designed multi-epitope vaccine with human TLR3. Moreover, in silico immune simulations showed a substantial immunogenic response of the designed vaccine. Conclusions: These findings suggest that our designed multi-epitope vaccine possessing intrinsic T cell and B cell epitopes with high antigenicity scores could be considered for the ongoing development of peptide-based novel vaccines against COVID-19. However, further in vitro and in vivo studies need to be performed to confirm our in silico observations. [ABSTRACT FROM AUTHOR]

In the growing field of vaccine design for COVID and cancer research, it is essential to predict accurate peptide binding affinity and immunogenicity. We developed a comprehensive machine learning method, 'IntegralVac,' by integrating three existing deep learning tools: DeepVacPred, MHCSeqNet, and HemoPI. IntegralVac makes predictions for single and multivalent cancer and COVID-19 epitopes without manually selecting epitope prediction possibilities. We performed several rounds of optimization before integration, then re-trained IntegralVac for multiple datasets. We validated the IntegralVac with 4500 human cancer MHC I peptides obtained from the Immune Epitope Database (IEDB) and with cancer and COVID epitopes previously selected in our laboratory. The other data referenced from existing deep learning tools served as a positive control to ensure successful prediction was possible. As evidenced by increased accuracy and AUC, IntegralVac improved the prediction rate of top-ranked epitopes. We also examined the compatibility between other servers' clinical checkpoint filters and IntegralVac. This was to ensure that the other servers had a means for predicting additional checkpoint filters that we wanted to implement in IntegralVac. The clinical checkpoint filters, including allergenicity, antigenicity, and toxicity, were used as additional predictors to improve IntegralVac's prediction accuracy. We generated immunogenicity scores by cross-comparing sequence inputs with each other and determining the overlap between each individual peptide sequence. The IntegralVac increased the immunogenicity prediction accuracy to 90.1% AUC and the binding affinity accuracy to 95.4% compared to the control NetMHCPan server. The IntegralVac opens new avenues for future in silico methods, by building upon established models for continued prediction accuracy improvement. [ABSTRACT FROM AUTHOR]

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the ongoing coronavirus disease 2019 (COVID-19) pandemic which has brought a great challenge to public health. After the first emergence of novel coronavirus SARS-CoV-2 in the city of Wuhan, China, in December 2019. As of March 2020, SARS-CoV-2 was first reported in Bangladesh and since then the country has experienced a steady rise in infections, resulting in 13,355,191 cases and 29,024 deaths as of 27 February 2022. Bioinformatics techniques are used to predict B cell and T cell epitopes from the new SARS-CoV-2 spike glycoprotein in order to build a unique multiple epitope vaccine. The immunogenicity, antigenicity scores, and toxicity of these epitopes were evaluated and chosen based on their capacity to elicit an immune response. Result: The best multi-epitope of the possible immunogenic property was created by combining epitopes. EAAAK, AAY, and GPGPG linkers were used to connect the epitopes. In several computer-based immune response analyses, this vaccine design was found to be efficient, as well as having high population coverage. Conclusion: This research is entirely reliant on the development of epitope-based vaccines, and these in silico findings would represent a major step forward in the development of a vaccine that might eradicate SARS-CoV-2 in Bangladeshi patients. [ABSTRACT FROM AUTHOR]

Background: Sheep pulmonary adenocarcinoma (OPA) is a contagious lung cancer of sheep caused by the Jaagsiekte retrovirus (JSRV). OPA typically has a serious economic impact worldwide. A vaccine has yet to be developed, even though the disease has been globally spread, along with its complications. This study aimed to construct an effective multi-epitopes vaccine against JSRV eliciting B and T lymphocytes using immunoinformatics tools. Results: The designed vaccine was composed of 499 amino acids. Before the vaccine was computationally validated, all critical parameters were taken into consideration; including antigenicity, allergenicity, toxicity, and stability. The physiochemical properties of the vaccine displayed an isoelectric point of 9.88. According to the Instability Index (II), the vaccine was stable at 28.28. The vaccine scored 56.51 on the aliphatic index and -0.731 on the GRAVY, indicating that the vaccine was hydrophilic. The RaptorX server was used to predict the vaccine's tertiary structure, the GalaxyWEB server refined the structure, and the Ramachandran plot and the ProSA-web server validated the vaccine's tertiary structure. Protein-sol and the SOLPro servers showed the solubility of the vaccine. Moreover, the high mobile regions in the vaccine's structure were reduced and the vaccine's stability was improved by disulfide engineering. Also, the vaccine construct was docked with an ovine MHC-1 allele and showed efficient binding energy. Immune simulation remarkably showed high levels of immunoglobulins, T lymphocytes, and INF-γ secretions. The molecular dynamic simulation provided the stability of the constructed vaccine. Finally, the vaccine was back-transcribed into a DNA sequence and cloned into a pET-30a (+) vector to affirm the potency of translation and microbial expression. Conclusion: A novel multi-epitopes vaccine construct against JSRV, was formed from B and T lymphocytes epitopes, and was produced with potential protection. This study might help in controlling and eradicating OPA. [ABSTRACT FROM AUTHOR]

Background: Milk provides energy as well as the basic nutrients required by the body. In particular, milk is beneficial for bone growth and development in children. Based on scientific evidence, cattle milk is an excellent and highly nutritious dietary component that is abundant in vitamins, calcium, potassium, and protein, among other minerals. However, the commercial productivity of cattle milk is markedly affected by mastitis. Mastitis is an economically important disease that is characterized by inflammation of the mammary gland. This disease is frequently caused by microorganisms and is detected as abnormalities in the udder and milk. Streptococcus agalactiae is a prominent cause of mastitis. Antibiotics are rarely used to treat this infection, and other available treatments take a long time to exhibit a therapeutic effect. Vaccination is recommended to protect cattle from mastitis. Accordingly, the present study sought to design a multi-epitope vaccine using immunoinformatics. Results: The vaccine was designed to be antigenic, immunogenic, non-toxic, and non-allergic, and had a binding affinity with Toll-like receptor 2 (TLR2) and TLR4 based on structural modeling, docking, and molecular dynamics simulation studies. Besides, the designed vaccine was successfully expressed in E. coli. expression vector (pET28a) depicts its easy purification for production on a larger scale, which was determined through in silico cloning. Further, immune simulation analysis revealed the effectiveness of the vaccine with an increase in the population of B and T cells in response to vaccination. Conclusion: This multi-epitope vaccine is expected to be effective at generating an immune response, thereby paving the way for further experimental studies to combat mastitis. [ABSTRACT FROM AUTHOR]

The pandemic of COVID-19 caused by SARS-CoV-2 has made a worldwide health emergency. Despite the fact that current vaccines are readily available, several SARSCoV-2 variants affecting the existing vaccine are to be less effective due to the mutations in the structural proteins. Furthermore, the appearance of the new variants cannot be easily predicted in the future. Therefore, the attempts to construct new vaccines or to modify the current vaccines are still pivotal works for preventing the spread of the virus. In the present investigation, the computational analysis through immunoinformatics, molecular docking, and molecular dynamics (MD) simulation is employed to construct an effective vaccine against SARS-CoV2. The structural proteins of SARS-CoV2 are utilized to create a multiepitope-based vaccine (MEV). According to our findings presented by systematic procedures in the current investigation, the MEV construct may be able to trigger a strong immunological response against the virus. Therefore, the designed MEV could be a potential vaccine candidate against SARS-CoV-2, and also it is expected to be effective for other variants. [ABSTRACT FROM AUTHOR]

Background and Aim: Cutaneous leishmaniasis is a significant public health issue worldwide. Cutaneous leishmaniasis is the most prevalent in the world among the different types of leishmaniasis. Currently, available medications have had no discernible influence on the disease's progression. Up to now, there has been no approved cutaneous leishmaniasis vaccine. New developments in vaccination might be a potential way to come up with a vaccination that is successful for the treatment of cutaneous leishmaniasis. Materials and Methods: This research was conducted to learn more about an effective vaccine for Leishmania major, the ailment's primary cause of CL, which was designed using computational methods. Thus, a multiepitope protein was designed by utilizing potential immune system epitopes, including predicted MHC class I, MHC class II, Cytotoxic T lymphocytes, Bcell, and Interferon-gamma epitopes of Cysteine protease b (CPB), Leishmania homologue of activated C kinase (LACK), and Kinetoplastid membrane protein-11 (KMP-11) antigenic proteins. In order to enhance vaccine immunogenicity, two resuscitation-promoting factors of Mycobacterium tuberculosis were used as adjuvants. Final epitopes were matched with suitable linkers to construct the recombinant structure. The physicochemical and immune-based characteristics of the designed vaccine have been forecasted by using different tools. Moreover, homogeneity modeling was performed to obtain a high-quality 3D structure, followed by refinement and validation. Finally, the codon optimization based on E. coli resulted in a higher CAI value and optimal GC content, followed by combining it in the pET-14b cloning vector. Results: Evaluation of the various characteristics of the designed vaccine showed that it is an immunogenic and nonallergenic antigen that can induce immune responses against Leishmania major infection, which could be promising for cutaneous leishmaniasis. Conclusion: Research shows that a recombinant vaccine can be an effective candidate against cutaneous leishmaniasis. [ABSTRACT FROM AUTHOR]