scholarly journals Proteome-Wide Mapping and Reverse Vaccinology Approaches to Design a Multi-Epitope Vaccine against Clostridium perfringens

Vaccines ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 1079
Author(s):  
Fahad M. Aldakheel ◽  
Amna Abrar ◽  
Samman Munir ◽  
Sehar Aslam ◽  
Khaled S. Allemailem ◽  
...  
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Epitope Vaccine ◽  
Ifn Gamma ◽  
Cellular Immune Responses ◽  
Medical Control ◽  
Food Borne ◽  
Food Borne Illness ◽  
Cellular Immune ◽  
The Brain

C. perfringens is a highly versatile bacteria of livestock and humans, causing enteritis (a common food-borne illness in humans), enterotoxaemia (in which toxins are formed in the intestine which damage and destroy organs, i.e., the brain), and gangrene (wound infection). There is no particular cure for the toxins of C. perfringens. Supportive care (medical control of pain, intravenous fluids) is the standard treatment. Therefore, a multiple-epitope vaccine (MEV) should be designed to battle against C. perfringens infection. Furthermore, the main objective of this in silico investigation is to design an MEV that targets C. perfringens. For this purpose, we selected the top three proteins that were highly antigenic using immuno-informatics approaches, including molecular docking. B-cells, IFN-gamma, and T cells for target proteins were predicted and the most conserved epitopes were selected for further investigation. For the development of the final MEV, epitopes of LBL5, CTL17, and HTL13 were linked to GPGPG, AAY, and KK linkers. The vaccine N-end was joined to an adjuvant through an EAAK linker to improve immunogenicity. After the attachment of linkers and adjuvants, the final construct was 415 amino acids. B-cell and IFN-gamma epitopes demonstrate that the model structure is enhanced for humoral and cellular immune responses. To validate the immunogenicity and safety of the final construct, various physicochemical properties, and other properties such as antigenicity and non-allergens, were evaluated. Furthermore, molecular docking was carried out for verification of vaccine compatibility with the receptor, evaluated in silico. Also, in silico cloning was employed for the verification of the proper expression and credibility of the construct.

scholarly journals In Silico Characterization of Toxin-Antitoxin Systems in Campylobacter Isolates Recovered from Food Sources and Sporadic Human Illness

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 72
Author(s):  
Bishoy Wadie ◽  
Mohamed A. Abdel-Fattah ◽  
Alshymaa Yousef ◽  
Shaimaa F. Mouftah ◽  
Mohamed Elhadidy ◽  
...  
Keyword(s):  
Environmental Conditions ◽  
In Silico ◽  
Antimicrobial Agents ◽  
Food Sources ◽  
Model Organisms ◽  
Food Borne ◽  
Food Borne Illness ◽  
Human Illness ◽  
Clonal Population Structure ◽  
In Silico Characterization

Campylobacter spp. represents the most common cause of gastroenteritis worldwide with the potential to cause serious sequelae. The ability of Campylobacter to survive stressful environmental conditions has been directly linked with food-borne illness. Toxin-antitoxin (TA) modules play an important role as defense systems against antimicrobial agents and are considered an invaluable strategy harnessed by bacterial pathogens to survive in stressful environments. Although TA modules have been extensively studied in model organisms such as Escherichia coli K12, the TA landscape in Campylobacter remains largely unexplored. Therefore, in this study, a comprehensive in silico screen of 111 Campylobacter (90 C.jejuni and 21 C.coli) isolates recovered from different food and clinical sources was performed. We identified 10 type II TA systems belonging to four TA families predicted in Campylobacter genomes. Furthermore, there was a significant association between the clonal population structure and distribution of TA modules; more specifically, most (12/13) of the Campylobacter isolates belonging to ST-21 isolates possess HicB-HicA TA modules. Finally, we observed a high degree of shared synteny among isolates bearing certain TA systems or even coexisting pairs of TA systems. Collectively, these findings provide useful insights about the distribution of TA modules in a heterogeneous pool of Campylobacter isolates from different sources, thus developing a better understanding regarding the mechanisms by which these pathogens survive stressful environmental conditions, which will further aid in the future designing of more targeted antimicrobials.

scholarly journals CD171 multi‑epitope peptide design based on immunoinformatics approach as a cancer vaccine candidate for glioblastoma

2021 ◽  
Author(s):  
Seyed Amir Hossein Mohammadzadeh Hosseini Moghri ◽  
Arefeh Abbasian
Keyword(s):  
Tertiary Structure ◽  
Vaccine Development ◽  
T Cell Epitopes ◽  
Epitope Peptide ◽  
Primary Malignancy ◽  
Cellular Immune Responses ◽  
The Central Nervous System ◽  
Cellular Immune ◽  
Informatics Tools ◽  
The Brain

Abstract Glioblastoma (GB) is a common primary malignancy of the central nervous system, and one of the highly lethal brain tumors. GB cells can promote therapeutic resistance and tumor angiogenesis. The CD171 is an adhesion molecule in neuronal cells that is expressed in glioma cells; it is a regulator of the brain development. CD171 is one of the immunoglobulin-like CAMs (cell adhesion molecules) families that can be associated with prognosis in a variety of human tumors. The multi-epitope peptide vaccines are based on synthetic peptides with a combination of both B-cell epitopes and T-cell epitopes, which can induce specific humoral or cellular immune responses. In the present study, several immune-informatics tools were used for analyzing the CD171 sequence and studying the important characteristics of a designed vaccine. The results included the prediction and validation of the secondary and tertiary structure, physicochemical properties, solubility, conservancy, toxicity as well as antigenicity and allergenicity of the promising candidate for a vaccine against CD171. The immunoinformatic analysis suggested 12 predicted multi-epitope peptides, whose construction consists of 582 residues long. Therewith, cloning adaptation of designed vaccine was performed and eventually sequence was inserted into pET30a (+) vector for the application of the anti-glioblastoma vaccine development.

scholarly journals Yersinia pestis Antigen F1 but Not LcrV Induced Humoral and Cellular Immune Responses in Humans Immunized with Live Plague Vaccine—Comparison of Immunoinformatic and Immunological Approaches

Vaccines ◽  
2020 ◽  
Vol 8 (4) ◽  
pp. 698
Author(s):  
Valentina A. Feodorova ◽  
Anna M. Lyapina ◽  
Maria A. Khizhnyakova ◽  
Sergey S. Zaitsev ◽  
Yury V. Saltykov ◽  
...  
Keyword(s):  
Immune Responses ◽  
B Cell ◽  
Yersinia Pestis ◽  
In Silico ◽  
Rational Design ◽  
Limited Information ◽  
B Cell Epitopes ◽  
Cellular Immune Responses ◽  
Cellular Immune ◽  
Plague Vaccine

The recent progress in immunoinformatics provided the basis for an accelerated development of target-specific peptide vaccines as an alternative to the traditional vaccine concept. However, there is still limited information on whether the in silico predicted immunoreactive epitopes correspond to those obtained from the actual experiments. Here, humoral and cellular immune responses to two major Yersinia pestis protective antigens, F1 and LcrV, were studied in human donors immunized with the live plague vaccine (LPV) based on the attenuated Y. pestis strain EV line NIIEG. The F1 antigen provided modest specific cellular (mixed T helper 1 (Th1)/Th2 type) and humoral immune responses in vaccinees irrespective of the amount of annual vaccinations and duration of the post-vaccination period. The probing of the F1 overlapping peptide library with the F1-positive sera revealed the presence of seven linear B cell epitopes, which were all also predicted by in silico assay. The immunoinformatics study evaluated their antigenicity, toxicity, and allergenic properties. The epitope TSQDGNNH was mostly recognized by the sera from recently vaccinated donors rather than antibodies from those immunized decades ago, suggesting the usefulness of this peptide for differentiation between recent and long-term vaccinations. The in silico analysis predicted nine linear LcrV-specific B-cell epitopes; however, weak antibody and cellular immune responses prevented their experimental evaluation, indicating that LcrV is a poor marker of successful vaccination. No specific Th17 immune response to either F1 or LcrV was detected, and there were no detectable serum levels of F1-specific immunoglobulin A (IgA) in vaccinees. Overall, the general approach validated in the LPV model could be valuable for the rational design of vaccines against other neglected and novel emerging infections with high pandemic potency.

scholarly journals CNLAC1 Is Required for Extrapulmonary Dissemination of Cryptococcus neoformans but Not Pulmonary Persistence

2004 ◽  
Vol 72 (3) ◽  
pp. 1693-1699 ◽  
Author(s):  
Mairi C. Noverr ◽  
Peter R. Williamson ◽  
Ryan S. Fajardo ◽  
Gary B. Huffnagle
Keyword(s):  
Respiratory Tract ◽  
Cryptococcus Neoformans ◽  
Random Mutagenesis ◽  
Pathogenic Yeast ◽  
Infectious Dose ◽  
Cellular Immune Responses ◽  
Laccase Enzyme ◽  
Cellular Immune ◽  
The Brain

ABSTRACT The pathogenic yeast Cryptococcus neoformans produces a laccase enzyme (CNLAC1), which catalyzes the synthesis of melanin in the presence of phenolic compounds. A number of genes have been implicated in the regulation of laccase and melanization, including IPC1, GPA1, MET3, and STE12. Albino mutants derived from random mutagenesis techniques may contain mutations in genes that regulate multiple virulence factors, including CNLAC1. The goal of our study is to investigate the role of CNLAC1 in virulence and evasion of pulmonary host defenses after infection via the respiratory tract. Using a set of congenic laccase-positive (2E-TUC-4) and laccase-deficient (2E-TU-4) strains, we found that both strains are avirulent at a lower dose (104 CFU/mouse) in mice. After the infectious dose was increased to 106 CFU/mouse, 70% mortality was observed in mice infected with 2E-TUC-4 compared to no mortality in mice infected with 2E-TU-4 at day 30 postinfection. This observation confirms the requirement for CNLAC1 in virulence. Interestingly, we observed no differences between the two strains in pulmonary growth or in elicitation of cellular immune responses in the lung. The only measurable defect of 2E-TU-4 was in dissemination to extrapulmonary sites. To examine the role of CNLAC1 in dissemination, mice were infected intravenously. By week 3 postinfection, equal numbers of strains 2E-TUC-4 and 2E-TU-4 were recovered from the brain and spleen. This observation indicates that CNLAC1 facilitates escape from the lung, but not growth in the lungs or brain, and suggests a novel role for CNLAC1 in virulence during an infection aquired via the respiratory tract.

scholarly journals 326 SARS-CoV-2 specific T-cells in TIL from patients with epithelial cancer

2020 ◽  
Vol 8 (Suppl 3) ◽  
pp. A352-A352
Author(s):  
Pedro Noronha ◽  
Georgia Paraschoudi ◽  
Eric Sousa ◽  
Jéssica Kamiki ◽  
Patrícia António ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Immune Responses ◽  
T Cell Activation ◽  
T Cell Responses ◽  
T Cell Epitopes ◽  
Ifn Gamma ◽  
Cell Responses ◽  
Cellular Immune Responses ◽  
Cellular Immune

BackgroundSARS-CoV-2 primarily infects the upper and lower airway system, yet also endothelial cells and multiple tissues/organ systems. Anti-SARS-CoV-2 directed cellular immune responses may be deleterious or may confer immune protection – more research is needed in order to link epitope-specific T-cell responses with clinically relevant endpoints.1 Analysis of epitope reactivity in blood from healthy individuals showed pre-existing (CD4+) reactivity most likely due to previous exposure to the common old coronavirus species HCoV-OC43, HCoV-229E, - NL63 or HKU1, or – not mutually exclusive - cross-reactive T-cell responses that would recognize SARS-CoV-2, yet also other non-SARS-CoV-2 targets.2,3 Detailed single cell analysis in PBMCs from patients with COVID-19 showed strong T-cell activation and expansion of TCR gamma – delta T-cells in patients with fast recovery or mild clinical symptoms.4 Previous studies examining antigen-specific T-cell responses in tumor-infiltrating T-cells (TIL) showed that EBV or CMV-specific cellular immune responses in TIL from patients with melanoma or pancreatic cancer. Such virus -specific T-cells may represent ‘bystander’ T-cell activation, yet they may also impact on the quality and quantity of anti-tumor directed immune responses. We tested therefore TIL expanded from 5 patients with gastrointestinal cancer, who underwent elective tumor surgery during the COVID-19 pandemic for recognition of a comprehensive panel of SARS-CoV-2 T-cell epitopes and compared the reactivity, defined by IFN-gamma production to TIL reactivity in TIL harvested from patients in 2018, prior to the pandemic.MethodsA set of 187 individual T-cell epitopes were tested for TIL recognition using 100IU IL-2 and 100 IU IL-15. Different peptide epitopes were selected: i) all epitopes were not shared with the 4 common old coronavirus species, ii) some peptides were unique for SARS-CoV-2, and iii) others were shared with SARS-CoV-1. Antigen targets were either 15 mers or 9mers for MHC class II or class I epitopes, respectively, derived from the nucleocapsid, membrane, spike protein, ORF8 or the ORF3a. The amount of IFN-gamma production was reported as pg/10e4 cells/epitope/5 days. Controls included CMV and EBV peptides.ResultsWe detected strong IFN-gamma production directed against antigenic ‘hotspots’ including the ORF3a, epitopes from the SARS-CoV-2 nucleocapsid and spike protein with a range of 12 up to 30 targets being recognized/TIL.ConclusionsSARS-CoV-2 epitope recognition, defined by IFN production, can be readily detected in TIL from patients who underwent surgery during the pandemic, which is not the case for TIL harvested prior to the circulating SARS-CoV-2. This suggests a broader exposure of individuals to SARS-CoV-2 and shows that SARS-CoV-2 responses may shape the quality and quantity of anti-cancer directed cellular immune responses in patients with solid epithelial malignancies.AcknowledgementsWe thank the Surgery, Pathology and Vivarium Units of Champalimaud Clinical Center (N. Figueiredo, A. Brandl, A. Beltran, M. Castillo, C. Silva ).Ethics ApprovalThis study was approved by the Champalimaud Foundation Ethics Committee.ConsentAll donors provided written consent and the study was approved by the local ethics committee. The study is in compliance with the Declaration of Helsinki.ReferencesGrifoni, A., Weiskopf, D., Ramirez, S. I., Mateus, J., Dan, J. M., Moderbacher, C. R., Rawlings, S. A., Sutherland, A., Premkumar, L., Jadi, R. S., Marrama, D., de Silva, A. M., Frazier, A., Carlin, A. F., Greenbaum, J. A., Peters, B., Krammer, F., Smith, D. M., Crotty, S., & Sette, A. ( 2020). Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals. Cell, 181(7), 1489–1501.e15. https://doi.org/10.1016/j.cell.2020.05.015Mateus, J., Grifoni, A., Tarke, A., Sidney, J., Ramirez, S. I., Dan, J. M., Burger, Z. C., Rawlings, S. A., Smith, D. M., Phillips, E., Mallal, S., Lammers, M., Rubiro, P., Quiambao, L., Sutherland, A., Yu, E. D., da Silva Antunes, R., Greenbaum, J., Frazier, A., … Weiskopf, D. ( 2020). Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans. Science, eabd3871. https://doi.org/10.1126/science.abd3871Le Bert, N., Tan, A. T., Kunasegaran, K., Tham, C. Y. L., Hafezi, M., Chia, A., Chng, M. H. Y., Lin, M., Tan, N., Linster, M., Chia, W. N., Chen, M. I.-C., Wang, L.-F., Ooi, E. E., Kalimuddin, S., Tambyah, P. A., Low, J. G.-H., Tan, Y.-J., & Bertoletti, A. ( 2020). SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls. Nature, 584(7821), 457–462. https://doi.org/10.1038/s41586-020-2550-zZhang, J., Wang, X., Xing, X. et al. Single-cell landscape of immunological responses in patients with COVID-19. Nat Immunol 2020;21:1107–1118. https://doi.org/10.1038/s41590-020-0762-x

scholarly journals Designing A Candidate Multi-Epitope Vaccine Against SARS-CoV-2 Using Reverse Vaccinology Approach

2021 ◽  
Author(s):  
Amir Atapour ◽  
Ali Golestan
Keyword(s):  
Molecular Docking ◽  
B Cell ◽  
In Silico ◽  
Md Simulation ◽  
Peptide Sequence ◽  
Reverse Vaccinology ◽  
Effective Vaccine ◽  
Epitope Vaccine ◽  
B Cell Epitopes

Abstract Coronavirus 2019 (COVID-19) infection is a global epidemic that is spreading dramatically from day today. Currently, many efforts have been made against COVID-19 through the designing or developing of specific vaccines or drugs, worldwide. Unfortunately, to date, it has not been successful. Therefore, an effective vaccine against COVID-19 is mandatory. In this study, we used the bioinformatics approach to design an effective multi-epitope vaccine against COVID-19 based on Spike protein. Here, we implemented in silico tools to identify potential T and B cell epitopes that can induce cellular and humoral immunity. Then, the peptide sequence of potential T, B cell epitopes, and flagellin (as an adjuvant molecule) was joined together by suitable linkers to construct of candidate multi-epitope vaccine (MEV). Subsequently, immunological and structural evaluations such as antigenicity, 3D modeling, etc. were performed. In the following, molecular docking of vaccine constructs with Toll-Like Receptors 5 (TLR5), Molecular Dynamics (MD) simulation as well as in silico cloning were carried out. Immunological and structural computational data showed that designed MEV potentially has proper capacity for inducing cellular and humoral immune responses against COVID-19. Based on the preliminary results, in vitro and in vivo experiments are required for validation in the future. Keywords: COVID-19, Vaccine, Reverse Vaccinology, Multi-epitope, Molecular docking, MD Simulation.

scholarly journals In Silico Defined SARS-CoV2 Epitopes May Not Predict Immunogenicity to COVID19

2021 ◽  
Author(s):  
Ke Pan ◽  
Yulun Chiu ◽  
Michelle Chen ◽  
Junmei Wang ◽  
Ivy Lai ◽  
...  
Keyword(s):  
T Cell ◽  
In Silico ◽  
T Cell Responses ◽  
T Cell Response ◽  
Binding Affinities ◽  
Cell Responses ◽  
Cellular Immune Responses ◽  
Humoral Responses ◽  
Cellular Immune ◽  
In Silico Methods

SARS-CoV-2 infections elicit both humoral and cellular immune responses. For the prevention and treatment of COVID19, the disease caused by SARS-CoV-2, it has become increasingly apparent that T cell responses are equally, if not more important than humoral responses in mediating recovery and immune-protection. One of the major challenges in developing T cell-based therapies for infectious and malignant diseases has been the identification of immunogenic epitopes that can elicit a meaningful T cell response. Traditionally, this has been achieved using sophisticated in silico methods to predict putative epitopes deduced from binding affinities and consensus data. Our studies find that, in contrast to current dogma, immunodominant SARS-CoV-2 peptides defined by such in silico methods often fail to elicit T cell responses recognizing naturally presented SARS-CoV-2 epitopes.

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