Design of a Novel Multi-Epitope Vaccine Against Echinococcus granulosus in Immunoinformatics

Yu, Mingkai; Zhu, Yuejie; Li, Yujiao; Chen, Zhiqiang; Sha, Tong; Li, Zhiwei; Zhang, Fengbo; Ding, Jianbing

doi:10.3389/fimmu.2021.668492

Cited by 25 publications

(26 citation statements)

References 35 publications

(33 reference statements)

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“…For instance, they do not require microbial culture, saving time and cost; highly promiscuous epitopes can be recognized and combined by multiple alleles at a time to overcome the differences of alleles among the human population; biological harmfulness and toxicity reversion of traditional inactivated or attenuated vaccines can be avoided. At present, multi-epitope vaccines for different diseases, such as HIV-1 (20), cancer (21), Chlamydia trachomatis (22), and parasites (23), have been investigated.…”

Section: Introductionmentioning

confidence: 99%

Immunoinformatics Approach Toward the Introduction of a Novel Multi-Epitope Vaccine Against Clostridium difficile

et al. 2022

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Clostridium difficile (C.difficile) is an exclusively anaerobic, spore-forming, and Gram-positive pathogen that is the most common cause of nosocomial diarrhea and is becoming increasingly prevalent in the community. Because C. difficile is strictly anaerobic, spores that can survive for months in the external environment contribute to the persistence and diffusion of C. difficile within the healthcare environment and community. Antimicrobial therapy disrupts the natural intestinal flora, allowing spores to develop into propagules that colonize the colon and produce toxins, thus leading to antibiotic-associated diarrhea and pseudomembranous enteritis. However, there is no licensed vaccine to prevent Clostridium difficile infection (CDI). In this study, a multi-epitope vaccine was designed using modern computer methods. Two target proteins, CdeC, affecting spore germination, and fliD, affecting propagule colonization, were chosen to construct the vaccine so that it could simultaneously induce the immune response against two different forms (spore and propagule) of C. difficile. We obtained the protein sequences from the National Center for Biotechnology Information (NCBI) database. After the layers of filtration, 5 cytotoxic T-cell lymphocyte (CTL) epitopes, 5 helper T lymphocyte (HTL) epitopes, and 7 B-cell linear epitopes were finally selected for vaccine construction. Then, to enhance the immunogenicity of the designed vaccine, an adjuvant was added to construct the vaccine. The Prabi and RaptorX servers were used to predict the vaccine’s two- and three-dimensional (3D) structures, respectively. Additionally, we refined and validated the structures of the vaccine construct. Molecular docking and molecular dynamics (MD) simulation were performed to check the interaction model of the vaccine–Toll-like receptor (TLR) complexes, vaccine–major histocompatibility complex (MHC) complexes, and vaccine–B-cell receptor (BCR) complex. Furthermore, immune stimulation, population coverage, and in silico molecular cloning were also conducted. The foregoing findings suggest that the final formulated vaccine is promising against the pathogen, but more researchers are needed to verify it.

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Section: Introductionmentioning

confidence: 99%

Immunoinformatics Approach Toward the Introduction of a Novel Multi-Epitope Vaccine Against Clostridium difficile

et al. 2022

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“…HLA allele frequency is specific in Xinjiang because of geographical location and population factors. Therefore, we selected three groups of alleles, HLA‐A*0301, HLA‐A*0201, and HLA‐A*1101, with high frequency in Xinjiang 28–30 . Cytotoxic T lymphocytes (CTLs) can secrete various cytokines to play an immune function role and kill some target cells with viruses and cancers, and to constitute the body's antiviral, antineoplastic immunity defense line with natural killer cells (NK cells), we used EpiJen (http://www.ddg-pharmfac.net/epijen/EpiJen/EpiJen.htm) 31 and NetCTLpan (https://services.healthtech.dtu.dk/service.php?NetCTLpan-1.1) 32 online software for prediction.…”

Section: Methodsmentioning

confidence: 99%

“…To analyze the interaction between the multi‐epitope vaccine of H. pylori and human TLR‐2 and 4, as well as B7‐1 and B7‐2, TLR‐2 (PDB ID 2Z7X), TLR‐4 (PDB ID 2Z63), B7‐1 (PDB ID 1DR9), and B7‐2 (PDB ID 1NCN) 3D models were searched using the Protein Data Bank (PDB) (https://www.rcsb.org/). Because most of the results were compounds, we used Discovery Studio software to separate the complexes and obtain the final model 29 . Molecular docking was performed using the LZerD Web Server (https://lzerd.kiharalab.org/upload/upload/), an advanced molecular docking server, which can flexibly model the protein–protein complex.…”

Section: Methodsmentioning

confidence: 99%

“…Therefore, we selected three groups of alleles, HLA-A*0301, HLA-A*0201, and HLA-A*1101, with high frequency in Xinjiang. [28][29][30] Cytotoxic T lymphocytes (CTLs) can secrete various cytokines to play an immune…”

Section: Cytotoxic T Lymphocyte Epitope Predictionmentioning

confidence: 99%

“…Because most of the results were compounds, we used Discovery Studio software to separate the complexes and obtain the final model. 29 Molecular docking was performed using the LZerD Web Server (https://lzerd.kihar alab.org/uploa d/ uploa d/), an advanced molecular docking server, which can flexibly model the protein-protein complex. The advantage of the software is that the models it generates are sorted by a scoring system that ranks in the top of Capri; moreover, users can specify interacting and non-interacting residue constraints in a flexible way.…”

Section: Molecular Dockingmentioning

confidence: 99%

See 2 more Smart Citations

Immmunoinformatics‐based design of a multi‐epitope vaccine with CTLA‐4 extracellular domain to combat Helicobacter pylori

Zhu

et al. 2022

The FASEB Journal

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In view of the high infection rate of Helicobacter pylori, a safe and effective vaccine is urgently needed. Recent trends in vaccine design have shifted toward safe and specific epitope‐based vaccines. In this study, by using different immunoinformatics approaches, a total of eight linear B cell epitopes, four HTL and three CTL epitopes of FlaA and UreB proteins of H. pylori G27 strain were screened out, we also predicted the conformational epitopes of the two proteins. Then, the dominant epitopes were sequentially linked by appropriate linkers, and the cytotoxic T lymphocyte–associated antigen 4 extracellular domain was attached to the N‐terminal of the epitope sequence. Meanwhile, molecular docking, molecular dynamics simulations and principal component analysis were performed to show that the multi‐epitope vaccine structure had strong interactions with B7 (B7‐1, B7‐2) and Toll‐like receptors (TLR‐2, ‐4). Eventually, the effectiveness of the vaccine was validated using in silico cloning. These analyses suggested that the designed vaccine could target antigen‐presenting cells and had high potency against H. pylori, which could provide a reference for the future development of efficient H. pylori vaccines.

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Immunoinformatic prediction of potential immunodominant epitopes from cagW in order to investigate protection against Helicobacter pylori infection based on experimental consequences

Chehelgerdi

Heidarnia

Dehkordi

et al. 2023

Funct Integr Genomics

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Helicobacter pylori is a leading cause of stomach cancer and peptic ulcers. Thus, identifying epitopes in H. pylori antigens is important for disease etiology, immunological surveillance, enhancing early detection tests, and developing optimal epitope-based vaccines. We used immunoinformatic and computational methods to create a potential CagW epitope candidate for H. pylori protection. The cagW gene of H. pylori was amplified and cloned into pcDNA3.1 (+) for injection into the muscles of healthy BALB/c mice to assess the impact of the DNA vaccine on interleukin levels. The results will be compared to a control group of mice that received PBS or cagW-pcDNA3.1 (+) vaccinations. An analysis of CagW protein antigens revealed 8 CTL and 7 HTL epitopes linked with AYY and GPGPG, which were enhanced by adding B-defensins to the N-terminus. The vaccine’s immunogenicity, allergenicity, and physiochemistry were validated, and its strong activation of TLRs (1, 2, 3, 4, and 10) suggests it is antigenic. An in-silico cloning and immune response model confirmed the vaccine’s expression efficiency and predicted its impact on the immune system. An immunofluorescence experiment showed stable and bioactive cagW gene expression in HDF cells after cloning the whole genome into pcDNA3.1 (+). In vivo vaccination showed that pcDNA3.1 (+)-cagW-immunized mice had stronger immune responses and a longer plasmid DNA release window than control-plasmid-immunized mice. After that, bioinformatics methods predicted, developed, and validated the three-dimensional structure. Many online services docked it with Toll-like receptors. The vaccine was refined using allergenicity, antigenicity, solubility, physicochemical properties, and molecular docking scores. Virtual-reality immune system simulations showed an impressive reaction. Codon optimization and in-silico cloning produced E. coli-expressed vaccines. This study suggests a CagW epitopes-protected H. pylori infection. These studies show that the proposed immunization may elicit particular immune responses against H. pylori , but laboratory confirmation is needed to verify its safety and immunogenicity.

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Design of a Novel Multi-Epitope Vaccine Against Echinococcus granulosus in Immunoinformatics

Cited by 25 publications

References 35 publications

Immunoinformatics Approach Toward the Introduction of a Novel Multi-Epitope Vaccine Against Clostridium difficile

Immunoinformatics Approach Toward the Introduction of a Novel Multi-Epitope Vaccine Against Clostridium difficile

Immmunoinformatics‐based design of a multi‐epitope vaccine with CTLA‐4 extracellular domain to combat Helicobacter pylori

Immunoinformatic prediction of potential immunodominant epitopes from cagW in order to investigate protection against Helicobacter pylori infection based on experimental consequences

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