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Pumchan A, Proespraiwong P, Sawatdichaikul O, Phurahong T, Hirono I, Unajak S. Computational design of novel chimeric multiepitope vaccine against bacterial and viral disease in tilapia (Oreochromis sp.). Sci Rep 2024; 14:14048. [PMID: 38890454 PMCID: PMC11189486 DOI: 10.1038/s41598-024-64383-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
Regarding several infectious diseases in fish, multiple vaccinations are not favorable. The chimeric multiepitope vaccine (CMEV) harboring several antigens for multi-disease prevention would enhance vaccine efficiency in terms of multiple disease prevention. Herein, the immunogens of tilapia's seven pathogens including E. tarda, F. columnare, F. noatunensis, S. iniae, S. agalactiae, A. hydrophila, and TiLV were used for CMEV design. After shuffling and annotating the B-cell epitopes, 5,040 CMEV primary protein structures were obtained. Secondary and tertiary protein structures were predicted by AlphaFold2 creating 25,200 CMEV. Proper amino acid alignment in the secondary structures was achieved by the Ramachandran plot. In silico determination of physiochemical and other properties including allergenicity, antigenicity, glycosylation, and conformational B-cell epitopes were determined. The selected CMEV (OSLM0467, OSLM2629, and OSLM4294) showed a predicted molecular weight (MW) of 70 kDa, with feasible sites of N- and O-glycosylation, and a number of potentially conformational B-cell epitope residues. Molecular docking, codon optimization, and in-silico cloning were tested to evaluate the possibility of protein expression. Those CMEVs will further elucidate in vitro and in vivo to evaluate the efficacy and specific immune response. This research will highlight the new era of vaccines designed based on in silico structural vaccine design.
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Affiliation(s)
- Ansaya Pumchan
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, 10900, Bangkok, Thailand
- Kasetsart Vaccines and Bio-Product Innovation Centre, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, 10900, Bangkok, Thailand
| | - Porranee Proespraiwong
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, 10900, Bangkok, Thailand
- Kasetsart Vaccines and Bio-Product Innovation Centre, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, 10900, Bangkok, Thailand
| | - Orathai Sawatdichaikul
- Department of Nutrition and Health, Institute of Food Research and Product Development, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, 10900, Bangkok, Thailand
| | - Thararat Phurahong
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, 10900, Bangkok, Thailand
- Kasetsart Vaccines and Bio-Product Innovation Centre, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, 10900, Bangkok, Thailand
| | - Ikuo Hirono
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-KU, Tokyo, 108-8477, Japan
| | - Sasimanas Unajak
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, 10900, Bangkok, Thailand.
- Kasetsart Vaccines and Bio-Product Innovation Centre, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, 10900, Bangkok, Thailand.
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Shafaghi M, Bahadori Z, Barzi SM, Afshari E, Madanchi H, Mousavi SF, Shabani AA. A new candidate epitope-based vaccine against PspA PhtD of Streptococcus pneumoniae: a computational experimental approach. Front Cell Infect Microbiol 2023; 13:1271143. [PMID: 38035337 PMCID: PMC10684780 DOI: 10.3389/fcimb.2023.1271143] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/26/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction Pneumococcus is an important respiratory pathogen that is associated with high rates of death in newborn children and the elderly. Given the disadvantages of current polysaccharide-based vaccines, the most promising alternative for developing improved vaccines may be to use protein antigens with different roles in pneumococcus virulence. PspA and PhtD, highly immunogenic surface proteins expressed by almost all pneumococcal strains, are capable of eliciting protective immunity against lethal infections. Methods In this study using immunoinformatics approaches, we constructed one fusion construct (called PAD) by fusing the immunodominant regions of PspA from families 1 & 2 (PA) to the immunodominant regions of PhtD (PD). The objective of this project was to test the immunogenicity of the fusion protein PAD and to compare its protective activity against S. pneumoniae infection with PA or PD alone and a combination of PA and PD. The prediction of physicochemical properties, antigenicity, allergenicity, toxicity, and 3D-structure of the constructs, as well as molecular docking with HLA receptor and immune simulation were performed using computational tools. Finally, mice were immunized and the serum levels of antibodies/cytokines and functionality of antibodies in vitro were evaluated after immunization. The mice survival rates and decrease of bacterial loads in the blood/spleen were examined following the challenge. Results The computational analyses indicated the proposed constructs could be antigenic, non-allergenic, non-toxic, soluble and able to elicit robust immune responses. The results of actual animal experiments revealed the candidate vaccines could induce the mice to produce high levels of antibodies and cytokines. The complement-mediated bactericidal activity of antibodies was confirmed and the antibodies provided favorable survival in immunized mice after bacterial challenge. In general, the experimental results verified the immunoinformatics studies. Conclusion For the first time this report presents novel peptide-based vaccine candidates consisting of immunodominant regions of PspA and PhtD antigens. The obtained findings confirmed that the fusion formulation could be relatively more efficient than the individual and combination formulations. The results propose that the fusion protein alone could be used as a serotype-independent pneumococcal vaccine or as an effective partner protein for a conjugate polysaccharide vaccine.
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Affiliation(s)
- Mona Shafaghi
- Department of Medical Biotechnology, faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Zohreh Bahadori
- Department of Medical Biotechnology, faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Elnaz Afshari
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Hamid Madanchi
- Department of Medical Biotechnology, faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
- Drug Design and Bioinformatics Unit, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | - Ali Akbar Shabani
- Department of Medical Biotechnology, faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
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Hou W, Wu H, Wang S, Wang W, Wang B, Wang H. Designing a multi-epitope vaccine to control porcine epidemic diarrhea virus infection using immunoinformatics approaches. Front Microbiol 2023; 14:1264612. [PMID: 37779715 PMCID: PMC10538973 DOI: 10.3389/fmicb.2023.1264612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023] Open
Abstract
Porcine epidemic diarrhea virus (PEDV), a continuously evolving pathogen, causes severe diarrhea in piglets with high mortality rates. However, current vaccines cannot provide complete protection against PEDV, so vaccine development is still necessary and urgent. Here, with the help of immunoinformatics approaches, we attempted to design a multi-epitope vaccine named rPMEV to prevent and control PEDV infection. The epitopes of rPMEV were constructed by 9 cytotoxic T lymphocyte epitopes (CTLs), 11 helper T lymphocyte epitopes (HTLs), 6 linear B cell epitopes (LBEs), and 4 conformational B cell epitopes (CBEs) based on the S proteins from the four representative PEDV G2 strains. To enhance immunogenicity, porcine β-defensin-2 (PBD-2) was adjoined to the N-terminal of the vaccine as an adjuvant. All of the epitopes and PBD-2 were joined by corresponding linkers and recombined into the multivalent vaccine, which is stable, antigenic, and non-allergenic. Furthermore, we adopted molecular docking and molecular dynamics simulation methods to analyze the interaction of rPMEV with the Toll-like receptor 4 (TLR4): a stable interaction between them created by 13 hydrogen bonds. In addition, the results of the immune simulation showed that rPMEV could stimulate both cellular and humoral immune responses. Finally, to raise the expression efficiency, the sequence of the vaccine protein was cloned into the pET28a (+) vector after the codon optimization. These studies indicate that the designed multi-epitope vaccine has a potential protective effect, providing a theoretical basis for further confirmation of its protective effect against PEDV infection in vitro and in vivo studies.
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Affiliation(s)
- Wei Hou
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Heqiong Wu
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Sibei Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Wenting Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Bin Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
- Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing, China
| | - Haidong Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
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Guo WH, Zhu YJ, Haimiti G, Xie XR, Niu C, Li M, Shi J, Yin ZW, Yu MK, Ding JB, Zhang FB. Bioinformatics-based design of a fusion vaccine with CTLA-4 variable region to combat Brucella. Braz J Med Biol Res 2023; 56:e12938. [PMID: 37493775 PMCID: PMC10361638 DOI: 10.1590/1414-431x2023e12938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/16/2023] [Indexed: 07/27/2023] Open
Abstract
Brucellosis has become a global zoonotic disease, seriously endangering the health of people all over the world. Vaccination is an effective strategy for protection against Brucella infection in livestock in developed countries. However, current vaccines are pathogenic to humans and pregnant animals, which limits their use. Therefore, it is very important to improve the safety and immune protection of Brucella vaccine. In this study, different bioinformatics approaches were carried out to predict the physicochemical properties, T/B epitope, and tertiary structure of Omp2b and Omp31. Then, these two proteins were sequentially linked, and the Cytotoxic T lymphocyte associated antigen-4 (CTLA-4) variable region was fused to the N-terminal of the epitope sequence. In addition, molecular docking was performed to show that the structure of the fusion protein vaccine had strong affinity with B7 (B7-1, B7-2). This study showed that the designed vaccine containing CTLA-4 had high potency against Brucella, which could provide a reference for the future development of efficient brucellosis vaccines.
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Affiliation(s)
- W H Guo
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Y J Zhu
- Department of Reproductive Assistance, Center for Reproductive Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - G Haimiti
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - X R Xie
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - C Niu
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - M Li
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - J Shi
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Z W Yin
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - M K Yu
- School of Life Science and Technology, Southeast University, Nanjing, China
| | - J B Ding
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
- State Key Laboratory of Pathogenesis, Prevention, and Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - F B Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
- State Key Laboratory of Pathogenesis, Prevention, and Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
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Gaiya DD, Muhammad A, Aimola IA, Udu SK, Balarabe SA, Auta R, Ekpa E, Sheyin A. Potential of Onchocerca ochengi inosine-5'-monophosphate dehydrogenase (IMPDH) and guanosine-5'-monophosphate oxidoreductase (GMPR) as druggable and vaccine candidates: immunoinformatics screening. J Biomol Struct Dyn 2023; 41:14832-14848. [PMID: 36866624 DOI: 10.1080/07391102.2023.2184171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 02/18/2023] [Indexed: 03/04/2023]
Abstract
Onchocerciasis is a vector-borne disease caused by the filarial nematode Onchocerca volvulus, which is responsible for most of the visual impairments recorded in Africa, Asia and the Americas. It is known that O. volvulus has similar molecular and biological characteristics as Onchocerca ochengi in cattle. This study was designed to screen for immunogenic epitopes and binding pockets of O. ochengi IMPDH and GMPR ligands using immunoinformatic approaches. In this study, a total of 23 B cell epitopes for IMPDH and 7 B cell epitopes for GMPR were predicted using ABCpred tool, Bepipred 2.0 and Kolaskar and Tongaonkar methods. The CD4+ Th computational results showed 16 antigenic epitopes from IMPDH with strong binding affinity for DRB1_0301, DRB3_0101, DRB1_0103 and DRB1_1501 MHC II alleles while 8 antigenic epitopes from GMPR were predicted to bind DRB1_0101 and DRB1_0401 MHC II alleles, respectively. For the CD8+ CTLs analysis, 8 antigenic epitopes from IMPDH showed strong binding affinity to human leukocyte antigen HLA-A*26:01, HLA-A*03:01, HLA-A*24:02 and HLA-A*01:01 MHC I alleles while 2 antigenic epitopes from GMPR showed strong binding affinity to HLA-A*01:01 allele, respectively. The immunogenic B cell and T cell epitopes were further evaluated for antigenicity, non-alllergernicity, toxicity, IFN-gamma, IL4 and IL10. The docking score revealed favorable binding free energy with IMP and MYD scoring the highest binding affinity at -6.6 kcal/mol with IMPDH and -8.3 kcal/mol with GMPR. This study provides valuable insight on IMPDH and GMPR as potential drug targets and for the development of multiple epitope vaccine candidates.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Daniel Danladi Gaiya
- Biology Unit, Faculty of Science, Air Force Institute of Technology, Nigerian Air Force Base, Kawo, Kaduna State, Nigeria
| | - Aliyu Muhammad
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Samaru Zaria, Kaduna State, Nigeria
| | - Idowu Asegame Aimola
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Samaru Zaria, Kaduna State, Nigeria
| | - Stella Kuyet Udu
- Biology Unit, Faculty of Science, Air Force Institute of Technology, Nigerian Air Force Base, Kawo, Kaduna State, Nigeria
| | - Sallau Abdullahi Balarabe
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Samaru Zaria, Kaduna State, Nigeria
| | - Richard Auta
- Department of Biochemistry, Faculty of Science, Kaduna State University, Kaduna, Kaduna State, Nigeria
| | - Emmanuel Ekpa
- Biology Unit, Faculty of Science, Air Force Institute of Technology, Nigerian Air Force Base, Kawo, Kaduna State, Nigeria
| | - Abraham Sheyin
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Samaru Zaria, Kaduna State, Nigeria
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Shafaghi M, Bahadori Z, Madanchi H, Ranjbar MM, Shabani AA, Mousavi SF. Immunoinformatics-aided design of a new multi-epitope vaccine adjuvanted with domain 4 of pneumolysin against Streptococcus pneumoniae strains. BMC Bioinformatics 2023; 24:67. [PMID: 36829109 PMCID: PMC9951839 DOI: 10.1186/s12859-023-05175-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 02/06/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Streptococcus pneumoniae (Pneumococcus) has remained a leading cause of fatal infections such as pneumonia, meningitis, and sepsis. Moreover, this pathogen plays a major role in bacterial co-infection in patients with life-threatening respiratory virus diseases such as influenza and COVID-19. High morbidity and mortality in over one million cases, especially in very young children and the elderly, are the main motivations for pneumococcal vaccine development. Due to the limitations of the currently marketed polysaccharide-based vaccines, non-serotype-specific protein-based vaccines have received wide research interest in recent years. One step further is to identify high antigenic regions within multiple highly-conserved proteins in order to develop peptide vaccines that can affect various stages of pneumococcal infection, providing broader serotype coverage and more effective protection. In this study, immunoinformatics tools were used to design an effective multi-epitope vaccine in order to elicit neutralizing antibodies against multiple strains of pneumococcus. RESULTS The B- and T-cell epitopes from highly protective antigens PspA (clades 1-5) and PhtD were predicted and immunodominant peptides were linked to each other with proper linkers. The domain 4 of Ply, as a potential TLR4 agonist adjuvant candidate, was attached to the end of the construct to enhance the immunogenicity of the epitope vaccine. The evaluation of the physicochemical and immunological properties showed that the final construct was stable, soluble, antigenic, and non-allergenic. Furthermore, the protein was found to be acidic and hydrophilic in nature. The protein 3D-structure was built and refined, and the Ramachandran plot, ProSA-web, ERRAT, and Verify3D validated the quality of the final model. Molecular docking analysis showed that the designed construct via Ply domain 4 had a strong interaction with TLR4. The structural stability of the docked complex was confirmed by molecular dynamics. Finally, codon optimization was performed for gene expression in E. coli, followed by in silico cloning in the pET28a(+) vector. CONCLUSION The computational analysis of the construct showed acceptable results, however, the suggested vaccine needs to be experimentally verified in laboratory to ensure its safety and immunogenicity.
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Affiliation(s)
- Mona Shafaghi
- grid.486769.20000 0004 0384 8779Department of Medical Biotechnology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran ,grid.486769.20000 0004 0384 8779Research Center of Biotechnology, Semnan University of Medical Sciences, Semnan, Iran ,grid.420169.80000 0000 9562 2611Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Zohreh Bahadori
- grid.486769.20000 0004 0384 8779Department of Medical Biotechnology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran ,grid.486769.20000 0004 0384 8779Research Center of Biotechnology, Semnan University of Medical Sciences, Semnan, Iran ,grid.420169.80000 0000 9562 2611Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Hamid Madanchi
- grid.486769.20000 0004 0384 8779Department of Medical Biotechnology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran ,grid.486769.20000 0004 0384 8779Research Center of Biotechnology, Semnan University of Medical Sciences, Semnan, Iran ,grid.420169.80000 0000 9562 2611Drug Design and Bioinformatics Unit, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Mehdi Ranjbar
- grid.418970.3Agricultural Research, Education, and Extension Organization (AREEO), Razi Vaccine and Serum Research Institute, Karaj, Iran
| | - Ali Akbar Shabani
- Department of Medical Biotechnology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran. .,Research Center of Biotechnology, Semnan University of Medical Sciences, Semnan, Iran.
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Zhou Y, Zhao S, Li Y, Yu M, Zheng J, Gong Q, Cao C, Ding J, Zhou X. Design and functional preliminary investigation of recombinant antigen EgG1Y162-EgG1Y162 against Echinococcus granulosus. Open Life Sci 2023; 18:20220558. [PMID: 36941829 PMCID: PMC10024343 DOI: 10.1515/biol-2022-0558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 12/02/2022] [Accepted: 01/02/2023] [Indexed: 03/15/2023] Open
Abstract
In the early stage, our research group cloned Echinococcus granulosus-specific antigen, EgG1Y162, from protoscolex and adult worms of E. granulosus. In order to enhance the immunogenicity of the vaccine, we prepared a recombinant vaccine by tandemly linking EgG1Y162, splicing the protein and linker at the gene level. This approach is expected to improve the immunogenicity of the vaccine by enhancing the molecular weight of the protein and increasing the antigenic epitopes. Bioinformatics was used to predict the physicochemical properties, transmembrane domain, protein structure, and T-/B-cell antigenic epitope of different recombinant proteins, EgG1Y162-linker-EgG1Y162. Finally, the linker sequence, "GGGGSGGG," which had the least influence on the migration of recombinant protein T/B epitope and can fold normally in series with EgG1Y162, was selected to design the recombinant vaccine. The plasmid was produced using genetic engineering techniques, and the recombinant protein, EGG1Y162-GGGGSGGG-EgG1Y162, was induced to be expressed and purified. EgG1Y162-GGGGSGGG-EgG1Y162 was identified to be correctly expressed with 100% specificity. Compared with EgG1Y162, EgG1Y162-GGGGSGGG-EgG1Y162 was more likely to promote dendritic cell maturation. EgG1Y162-GGGGSGGG-EgG1Y162 was speculated to have the potential to improve antigen immunogenicity by increasing the molecular weight and antigenic epitope.
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Affiliation(s)
- Yanxia Zhou
- Department of Immunology, Basic Medical College, Xinjiang Medical University, Xinjiang830011, Urumqi, China
- Department of Anesthesiology, Zhanjiang Central Hospital, Zhanjiang, 524037, Guangdong, China
| | - Shangqi Zhao
- Department of Immunology, Basic Medical College, Xinjiang Medical University, Xinjiang830011, Urumqi, China
- Xinjiang Key Laboratory of Molecular Biology for Endemic Diseases, Xinjiang830011, Urumqi, China
| | - Yanmin Li
- Department of Immunology, Basic Medical College, Xinjiang Medical University, Xinjiang830011, Urumqi, China
- Xinjiang Key Laboratory of Molecular Biology for Endemic Diseases, Xinjiang830011, Urumqi, China
| | - Mingkai Yu
- Department of Immunology, Basic Medical College, Xinjiang Medical University, Xinjiang830011, Urumqi, China
- Xinjiang Key Laboratory of Molecular Biology for Endemic Diseases, Xinjiang830011, Urumqi, China
| | - Jia Zheng
- Department of Immunology, Basic Medical College, Xinjiang Medical University, Xinjiang830011, Urumqi, China
- Xinjiang Key Laboratory of Molecular Biology for Endemic Diseases, Xinjiang830011, Urumqi, China
| | - Qiaoqiao Gong
- Department of Immunology, Basic Medical College, Xinjiang Medical University, Xinjiang830011, Urumqi, China
- Xinjiang Key Laboratory of Molecular Biology for Endemic Diseases, Xinjiang830011, Urumqi, China
| | - Chunbao Cao
- Department of Immunology, Basic Medical College, Xinjiang Medical University, Xinjiang830011, Urumqi, China
- Xinjiang Key Laboratory of Molecular Biology for Endemic Diseases, Xinjiang830011, Urumqi, China
| | - Jianbing Ding
- Department of Immunology, Basic Medical College, Xinjiang Medical University, Xinjiang830011, Urumqi, China
- Xinjiang Key Laboratory of Molecular Biology for Endemic Diseases, Xinjiang830011, Urumqi, China
| | - Xiaotao Zhou
- Department of Immunology, Basic Medical College, Xinjiang Medical University, Xinjiang830011, Urumqi, China
- Xinjiang Key Laboratory of Molecular Biology for Endemic Diseases, Xinjiang830011, Urumqi, China
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Designing a novel multi‑epitope vaccine against Ebola virus using reverse vaccinology approach. Sci Rep 2022; 12:7757. [PMID: 35545650 PMCID: PMC9094136 DOI: 10.1038/s41598-022-11851-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 04/19/2022] [Indexed: 12/18/2022] Open
Abstract
Ebola virus (EBOV) is a dangerous zoonotic infectious disease. To date, more than 25 EBOV outbreaks have been documented, the majority of which have occurred in Central Africa. The rVSVG-ZEBOV-GP vaccine (ERVEBO), a live attenuated vaccine, has been approved by the US Food and Drug Administration (FDA) to combat EBOV. Because of the several drawbacks of live attenuated vaccines, multi-epitope vaccines probably appear to be safer than live attenuated vaccines. In this work, we employed immunoinformatics tools to design a multi-epitope vaccine against EBOV. We collected sequences of VP35, VP24, VP30, VP40, GP, and NP proteins from the NCBI database. T-cell and linear B-cell epitopes from target proteins were identified and tested for antigenicity, toxicity, allergenicity, and conservancy. The selected epitopes were then linked together in the vaccine's primary structure using appropriate linkers, and the 50S ribosomal L7/L12 (Locus RL7 MYCTU) sequence was added as an adjuvant to the vaccine construct's N-terminal. The physicochemical, antigenicity, and allergenicity parameters of the vaccine were all found to be satisfactory. The 3D model of the vaccine was predicted, refined, and validated. The vaccine construct had a stable and strong interaction with toll-like receptor 4 (TLR4) based on molecular docking and molecular dynamic simulation (MD) analysis. The results of codon optimization and in silico cloning revealed that the proposed vaccine was highly expressed in Escherichia coli (E. coli). The findings of this study are promising; however, experimental validations should be carried out to confirm these findings.
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Yu M, Zhu Y, Li Y, Chen Z, Li Z, Wang J, Li Z, Zhang F, Ding J. Design of a Recombinant Multivalent Epitope Vaccine Based on SARS-CoV-2 and Its Variants in Immunoinformatics Approaches. Front Immunol 2022; 13:884433. [PMID: 35603198 PMCID: PMC9120605 DOI: 10.3389/fimmu.2022.884433] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/12/2022] [Indexed: 01/08/2023] Open
Abstract
The development of an effective multivalent vaccine against SARS-CoV-2 variants is an important means to improve the global public health situation caused by COVID-19. In this study, we identified the antigen epitopes of the main global epidemic SARS-CoV-2 and mutated virus strains using immunoinformatics approach, and screened out 8 cytotoxic T lymphocyte epitopes (CTLEs), 17 helper T lymphocyte epitopes (HTLEs), 9 linear B-cell epitopes (LBEs) and 4 conformational B-cell epitopes (CBEs). The global population coverage of CTLEs and HTLEs was 93.16% and 99.9% respectively. These epitopes were spliced together by corresponding linkers and recombined into multivalent vaccine. In silico tests, the vaccine protein was a non-allergen and the docking with TLR-3 molecule showed a strong interaction. The results of immune simulation showed that the vaccine may be helpful to initiate both cellular and humoral immunity against all VOC. The optimistic immunogenicity of the vaccine was confirmed in vivo and in vitro finally. Therefore, our vaccine may have potential protection against SARS-CoV-2 and its variants.
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Affiliation(s)
- Mingkai Yu
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Xinjiang Key Molecular Biology Laboratory of Endemic Disease, Xinjiang Medical University, Urumqi, China
| | - Yuejie Zhu
- Reproductive Medicine Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yujiao Li
- Department of Blood Transfusion, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Zhiqiang Chen
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Xinjiang Key Molecular Biology Laboratory of Endemic Disease, Xinjiang Medical University, Urumqi, China
| | - Zhiwei Li
- Clinical Laboratory Center, Xinjiang Uygur Autonomous Region People’s Hospital, Urumqi, China
| | - Jing Wang
- Xinjiang Laboratory of Respiratory Disease Research, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumqi, China
| | - Zheng Li
- Xinjiang Laboratory of Respiratory Disease Research, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumqi, China
| | - Fengbo Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- *Correspondence: Jianbing Ding, ; Fengbo Zhang,
| | - Jianbing Ding
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Xinjiang Key Molecular Biology Laboratory of Endemic Disease, Xinjiang Medical University, Urumqi, China
- *Correspondence: Jianbing Ding, ; Fengbo Zhang,
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10
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Du X, Zhu M, Zhang T, Wang C, Tao J, Yang S, Zhu Y, Zhao W. The Recombinant Eg.P29-Mediated miR-126a-5p Promotes the Differentiation of Mouse Naive CD4 + T Cells via DLK1-Mediated Notch1 Signal Pathway. Front Immunol 2022; 13:773276. [PMID: 35211114 PMCID: PMC8861942 DOI: 10.3389/fimmu.2022.773276] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/18/2022] [Indexed: 12/12/2022] Open
Abstract
Cystic echinococcosis (CE) is a zoonotic parasitic disease spread worldwide caused by Echinococcus granulosus (Eg), which sometimes causes serious damage; however, in many cases, people are not aware that they are infected. A number of recombinant vaccines based on Eg are used to evaluate their effectiveness against the infection. Our previous report showed that recombinant Eg.P29 (rEg.P29) has a marvelous immunoprotection and can induce Th1 immune response. Furthermore, data of miRNA microarray in mice spleen CD4+ T cells showed that miR-126a-5p was significantly elevated 1 week after immunization by using rEg.P29. Therefore, in this perspective, we discussed the role of miR-126a-5p in the differentiation of naive CD4+ T cells into Th1/Th2 under rEg.P29 immunization and determined the mechanisms associated with delta-like 1 homolog (DLK1) and Notch1 signaling pathway. One week after P29 immunization of mice, we found that miR-126a-5p was significantly increased and DLK1 expression was decreased, while Notch1 pathway activation was enhanced and Th1 response was significantly stronger. The identical conclusion was obtained by overexpression of mmu-miR-126a-5p in primary naive CD4+ T cells in mice. Intriguingly, mmu-miR-126a-5p was significantly raised in serum from mice infected with protoscolex in the early stages of infection and markedly declined in the late stages of infection, while has-miR-126-5p expression was dramatically reduced in serum from CE patients. Taken together, we show that miR-126a-5p functions as a positive regulator of Notch1-mediated differentiation of CD4+ T cells into Th1 through downregulating DLK1 in vivo and in vitro. Hsa-miR-126-5p is potentially a very promising diagnostic biomarker for CE.
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Affiliation(s)
- Xiancai Du
- School of Basic Medical Science of Ningxia Medical University, Yinchuan, China.,Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, Yinchuan, China
| | - Mingxing Zhu
- Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, Yinchuan, China.,Center of Scientific Technology of Ningxia Medical University, Yinchuan, China
| | - Tingrui Zhang
- School of Basic Medical Science of Ningxia Medical University, Yinchuan, China.,Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, Yinchuan, China
| | - Chan Wang
- School of Basic Medical Science of Ningxia Medical University, Yinchuan, China.,Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, Yinchuan, China
| | - Jia Tao
- School of Basic Medical Science of Ningxia Medical University, Yinchuan, China.,Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, Yinchuan, China
| | - Songhao Yang
- School of Basic Medical Science of Ningxia Medical University, Yinchuan, China.,Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, Yinchuan, China
| | - Yazhou Zhu
- School of Basic Medical Science of Ningxia Medical University, Yinchuan, China.,Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, Yinchuan, China
| | - Wei Zhao
- Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, Yinchuan, China.,Center of Scientific Technology of Ningxia Medical University, Yinchuan, China
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11
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The current state of the issues of diagnosis and surgical treatment of liver echinococcosis (literature review). ACTA BIOMEDICA SCIENTIFICA 2022. [DOI: 10.29413/abs.2022-7.1.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The article presents a review of literature data in order to study current problems in the diagnosis and surgical treatment of liver echinococcosis. At the present stage of technological progress, it is possible to study the genetic, anatomical and pathophysiological aspects of echinococcosis. The article highlights the advantages and disadvantages of surgical operations performed in patients with echinococcal liver damage. Methods and results of surgical treatment in various clinics are considered. The main surgical directions in the treatment of parasitic liver damage have been determined. These are more radical anatomical and extensive liver resections and minimally invasive, including laparoscopic and robotic techniques. Each of the methods used has its own niche of application and its own limitations. An opinion is expressed about the prospects for the development of minimally invasive methods of surgical treatment. The authors note the actual absence of a unified standardized tactics of surgical treatment at the moment. It is noted that the literature contains only fragmentary data on the possibility of combining minimally invasive and classical methods of surgical treatment. Despite the introduction of new methods of treatment, the percentage of complications and mortality are still high. Thus, the lack of uniform diagnostic standards and principles for determining surgical tactics testifies to the urgency of the problem of treating parasitic liver damage and determines the search for new solutions in order to improve the results of surgical treatment of this pathology.
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12
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Yu M, Zhu Y, Li Y, Chen Z, Sha T, Li Z, Zhang F, Ding J. Design of a Novel Multi-Epitope Vaccine Against Echinococcus granulosus in Immunoinformatics. Front Immunol 2021; 12:668492. [PMID: 34456902 PMCID: PMC8388843 DOI: 10.3389/fimmu.2021.668492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/15/2021] [Indexed: 12/18/2022] Open
Abstract
All the time, echinococcosis is a global zoonotic disease which seriously endangers public health all over the world. In order to speed up the development process of anti-Echinococcus granulosus vaccine, at the same time, it can also save economic cost. In this study, immunoinformatics tools and molecular docking methods were used to predict and screen the antigen epitopes of Echinococcus granulosus, to design a multi-epitope vaccine containing B- and T-cell epitopes. The multi-epitope vaccine could activate B lymphocytes to produce specific antibodies theoretically, which could protect the human body against Echinococcus granulosus infection. It also could activate T lymphocytes and clear the infected parasites in the body. In this study, four CD8+ T-cell epitopes, three CD4+ T-cell epitopes and four B-cell epitopes of Protein EgTeg were identified by immunoinformatics methods. Meanwhile, three CD8+ T-cell epitopes, two CD4+ T-cell epitopes and four B-cell epitopes of Protein EgFABP1 were identified. We constructed the multi-epitope vaccine using linker proteins. The study based on the traditional methods of antigen epitope prediction, further optimized the prediction results combined with molecular docking technology and improved the precision and accuracy of the results. Finally, in vivo and in vitro experiments had verified that the vaccine designed in this study had good antigenicity and immunogenicity.
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MESH Headings
- Adolescent
- Adult
- Animals
- Antibodies, Helminth/blood
- Antigens, Helminth/immunology
- Antigens, Helminth/pharmacology
- B-Lymphocytes/immunology
- B-Lymphocytes/parasitology
- Cells, Cultured
- Computer-Aided Design
- Disease Models, Animal
- Drug Design
- Echinococcosis/blood
- Echinococcosis/immunology
- Echinococcosis/parasitology
- Echinococcosis/prevention & control
- Echinococcus granulosus/immunology
- Epitopes, B-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/immunology
- Fatty Acid-Binding Proteins/immunology
- Fatty Acid-Binding Proteins/pharmacology
- Humans
- Immunity, Humoral
- Immunogenicity, Vaccine
- Lymphocyte Activation
- Mice, Inbred BALB C
- Middle Aged
- Molecular Docking Simulation
- T-Lymphocytes/immunology
- T-Lymphocytes/parasitology
- Vaccines, DNA/immunology
- Vaccines, DNA/pharmacology
- Vaccines, Subunit/immunology
- Vaccines, Subunit/pharmacology
- Young Adult
- Mice
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Affiliation(s)
- Mingkai Yu
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Yuejie Zhu
- Reproductive Medicine Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yujiao Li
- Department of Blood Transfusion, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Zhiqiang Chen
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Tong Sha
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Zhiwei Li
- Clinical Laboratory Center, Xinjiang Uygur Autonomous Region People's Hospital, Urumqi, China
| | - Fengbo Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Jianbing Ding
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
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13
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Li Y, Zhu Y, Sha T, Chen Z, Yu M, Zhang F, Ding J. A Multi-Epitope Chitosan Nanoparticles Vaccine of Canine Against Echinococcus granulosus. J Biomed Nanotechnol 2021; 17:910-920. [PMID: 34082876 DOI: 10.1166/jbn.2021.3065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cystic Echinococcosis (CE) is caused by Echinococcus granulosus (Eg), which endangers the health of the intermediate host. Therefore, effective canid vaccines against Eg infection are urgently needed to reduce the incidence of this disease. In the present work, the aim was to predict epitopes in four vaccine candidate antigens (VCAs) in Eg as a basis to design a multi-epitope canine-directed vaccine. This vaccine is based on chitosan nanoparticles (CS-NPs) and is directed against Eg infection in the definitive host. The canine-directed vaccine was designed based on Eg antigens EgM9, Eg_10196, EgA31 and EgG1Y162. Several tools in online servers were used to predict VCAs information, which was combined with B cell, CTL and Th epitopes. Considering that acquiring experimental information in canids is difficult, and that it may be possible to perform future experiments in mice, we predicted both canine and murine T cell epitopes. The multi-epitope vaccine was synthetically prepared by ionic crosslinking method, and CS-NPs was used as adjuvant. The mice were immunized by oral gavage and laser scanning confocal microscopy was used to localize the fluorescein- labeled multi-epitope peptide in the intestinal tract. The final multi-epitope vaccine was construct consist of Co1 targeting peptide, four B-cell epitopes, four canine-directed CTL epitopes and four murine-directed Th epitopes. It has been proven experimentally by this research that multi-epitope antigen concentration merged with microfold cells was high in the CS-NPs vaccine group. The present bioinformatics study is a first step towards the construction of a canine-specific multiepitope vaccine against Eg with twelve predicted epitopes. CS-NPs is a potential adjuvant with relatively safe penetration enhancement delivery and a potent immunostimulant.
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Affiliation(s)
- Yujiao Li
- School of Public Health, Xinjiang Medical University, Xinjiang 830011, PR China
| | - Yuejie Zhu
- Department of Blood Transfusion, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang 830011, PR China
| | - Tong Sha
- Department of Immunology, College of Basic Medicine, Xinjiang Medical University, Xinjiang 830011, PR China
| | - Zhiqiang Chen
- Department of Immunology, College of Basic Medicine, Xinjiang Medical University, Xinjiang 830011, PR China
| | - Mingkai Yu
- Department of Immunology, College of Basic Medicine, Xinjiang Medical University, Xinjiang 830011, PR China
| | - Fengbo Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang 830011, PR China
| | - Jianbing Ding
- Department of Immunology, College of Basic Medicine, Xinjiang Medical University, Xinjiang 830011, PR China
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Huang L, Shao Y, Li X, Li H, Liu Y, Zhu G. Designing Multi-epitope Diagnosis of Gal d 5 and Gal d 6 Based on Immunoinformatics Approaches Against Egg Yolk Allergy. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10192-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Majidiani H, Dalimi A, Ghaffarifar F, Pirestani M, Ghaffari AD. Computational probing of Toxoplasma gondii major surface antigen 1 (SAG1) for enhanced vaccine design against toxoplasmosis. Microb Pathog 2020; 147:104386. [DOI: 10.1016/j.micpath.2020.104386] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/18/2020] [Accepted: 07/06/2020] [Indexed: 01/14/2023]
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16
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Sunita, Singhvi N, Singh Y, Shukla P. Computational approaches in epitope design using DNA binding proteins as vaccine candidate in Mycobacterium tuberculosis. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 83:104357. [PMID: 32438080 DOI: 10.1016/j.meegid.2020.104357] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/04/2020] [Accepted: 05/07/2020] [Indexed: 12/28/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is a successful pathogen in the history of mankind. A high rate of mortality and morbidity raises the need for vaccine development. Mechanism of pathogenesis, survival strategy and virulence determinant are needed to be explored well for this pathogen. The involvement of DNA binding proteins in the regulation of virulence genes, transcription, DNA replication, repair make them more significant. In present work, we have identified 1453 DNA binding proteins (DBPs) in the 4173 genes of Mtb through the DNABIND tool and they were subjected for further screening by incorporating different bioinformatics tools. The eighteen DBPs were selected for the B-cell epitope prediction by using ABCpred server. Moreover, the B-cell epitope bearing the antigenic and non- allergenic property were selected for T-cell epitope prediction using ProPredI, and ProPred server. Finally, DGIGSAVSV (Rv1088), IRALPSSRH (Rv3923c), LTISPIANS (Rv3235), VQPSGKGGL (Rv2871) VPRPGPRPG (Rv2731) and VGQKINPHG (Rv0707) were identified as T-cell epitopes. The structural modelling of these epitopes and DBPs was performed to ensure the localization of these epitopes on the respective proteins. The interaction studies of these epitopes with human HLA confirmed their validation to be used as potential vaccine candidates. Collectively, these results revealed that the DBPs- Rv2731, Rv3235, Rv1088, Rv0707, Rv3923c and Rv2871 are the most appropriate vaccine candidates. In our knowledge, it is the first report of using the DBPs of Mtb for epitope prediction. Significantly, this study also provides evidence to be useful for designing a peptide-based vaccine against tuberculosis.
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Affiliation(s)
- Sunita
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India; Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Nirjara Singhvi
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Yogendra Singh
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
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17
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Sha T, Li Z, Zhang C, Zhao X, Chen Z, Zhang F, Ding J. Bioinformatics analysis of candidate proteins Omp2b, P39 and BLS for Brucella multivalent epitope vaccines. Microb Pathog 2020; 147:104318. [PMID: 32531499 DOI: 10.1016/j.micpath.2020.104318] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/02/2020] [Accepted: 06/02/2020] [Indexed: 12/11/2022]
Abstract
This study focuses on analyzing the physicochemical properties, structural characteristics and dominant epitopes of Brucella outer membrane protein 2b (Omp2b), periplasmic binding protein (P39) and Brucella lumazine synthase (BLS) proteins by bioinformatics methods, and to provide a theoretical basis for constructing multi-epitope vaccines. The amino acid sequences of three kinds of proteins were obtained from the UniProt database. The highest frequency alleles in northern China were obtained from the AlleleFrequencies database. Analysis of the physicochemical properties of the proteins by ProtParam online software. Analysis of the secondary structure of the proteins were predicted by SOMPA online software. Using SWISS-MODEL online software constructed and analyzed the tertiary structure of the proteins. Using ABCpred, BepiPred, BCPred and SVMTrip online software analyzed linear B cell epitopes of proteins, The T cell dominant epitope of the protein was analyzed using SYFPEITHI, RANKPEP and IEDB online software. Omp2b was identified three linear B cell dominant epitopes, five CD8+ T cell dominant epitopes, and three CD4+ T cell dominant epitopes. P39 was identified three linear B cell dominant epitopes, two CD8+ T cell dominant epitopes, and two CD4+ T cell dominant epitopes. BLS was identified one linear B cell dominant epitope, one CD8+ T cell dominant epitope, and two CD4+ T cell dominant epitopes. The results indicated that epitope prediction of three Brucella vaccine candidate proteins can provide a theoretical basis for the construction of an ideal multivalent epitope vaccine against Brucella.
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Affiliation(s)
- Tong Sha
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China; Basic Medical College, Xinjiang Medical University, Urumqi, China
| | - Zhiwei Li
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China; Clinical Laboratory Center, Xinjiang Uygur Autonomous Region People's Hospital, Urumqi, China
| | - Chuntao Zhang
- Basic Medical College, Xinjiang Medical University, Urumqi, China
| | - Xiao Zhao
- Basic Medical College, Xinjiang Medical University, Urumqi, China
| | - Zhiqiang Chen
- Basic Medical College, Xinjiang Medical University, Urumqi, China
| | - Fengbo Zhang
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China; Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China.
| | - Jianbing Ding
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China; Basic Medical College, Xinjiang Medical University, Urumqi, China.
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18
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Nourmohammadi H, Javanmardi E, Shams M, Shamsinia S, Nosrati MC, Yousefi A, Nemati T, Fatollahzadeh M, Ghasemi E, Kordi B, Majidiani H, Irannejad H. Multi-epitope vaccine against cystic echinococcosis using immunodominant epitopes from EgA31 and EgG1Y162 antigens. INFORMATICS IN MEDICINE UNLOCKED 2020. [DOI: 10.1016/j.imu.2020.100464] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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