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Antonelli ACB, Almeida VP, de Castro FOF, Silva JM, Pfrimer IAH, Cunha-Neto E, Maranhão AQ, Brígido MM, Resende RO, Bocca AL, Fonseca SG. In silico construction of a multiepitope Zika virus vaccine using immunoinformatics tools. Sci Rep 2022; 12:53. [PMID: 34997041 PMCID: PMC8741764 DOI: 10.1038/s41598-021-03990-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 12/01/2021] [Indexed: 01/02/2023] Open
Abstract
Zika virus (ZIKV) is an arbovirus from the Flaviviridae family and Flavivirus genus. Neurological events have been associated with ZIKV-infected individuals, such as Guillain-Barré syndrome, an autoimmune acute neuropathy that causes nerve demyelination and can induce paralysis. With the increase of ZIKV infection incidence in 2015, malformation and microcephaly cases in newborns have grown considerably, which suggested congenital transmission. Therefore, the development of an effective vaccine against ZIKV became an urgent need. Live attenuated vaccines present some theoretical risks for administration in pregnant women. Thus, we developed an in silico multiepitope vaccine against ZIKV. All structural and non-structural proteins were investigated using immunoinformatics tools designed for the prediction of CD4 + and CD8 + T cell epitopes. We selected 13 CD8 + and 12 CD4 + T cell epitopes considering parameters such as binding affinity to HLA class I and II molecules, promiscuity based on the number of different HLA alleles that bind to the epitopes, and immunogenicity. ZIKV Envelope protein domain III (EDIII) was added to the vaccine construct, creating a hybrid protein domain-multiepitope vaccine. Three high scoring continuous and two discontinuous B cell epitopes were found in EDIII. Aiming to increase the candidate vaccine antigenicity even further, we tested secondary and tertiary structures and physicochemical parameters of the vaccine conjugated to four different protein adjuvants: flagellin, 50S ribosomal protein L7/L12, heparin-binding hemagglutinin, or RS09 synthetic peptide. The addition of the flagellin adjuvant increased the vaccine's predicted antigenicity. In silico predictions revealed that the protein is a probable antigen, non-allergenic and predicted to be stable. The vaccine’s average population coverage is estimated to be 87.86%, which indicates it can be administered worldwide. Peripheral Blood Mononuclear Cells (PBMC) of individuals with previous ZIKV infection were tested for cytokine production in response to the pool of CD4 and CD8 ZIKV peptide selected. CD4 + and CD8 + T cells showed significant production of IFN-γ upon stimulation and IL-2 production was also detected by CD8 + T cells, which indicated the potential of our peptides to be recognized by specific T cells and induce immune response. In conclusion, we developed an in silico universal vaccine predicted to induce broad and high-coverage cellular and humoral immune responses against ZIKV, which can be a good candidate for posterior in vivo validation.
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Affiliation(s)
- Ana Clara Barbosa Antonelli
- Department of Bioscience and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Rua 235 s/n, sala 335, Setor Universitário, Goiânia, GO, 74605-050, Brazil
| | - Vinnycius Pereira Almeida
- Department of Bioscience and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Rua 235 s/n, sala 335, Setor Universitário, Goiânia, GO, 74605-050, Brazil
| | - Fernanda Oliveira Feitosa de Castro
- Department of Bioscience and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Rua 235 s/n, sala 335, Setor Universitário, Goiânia, GO, 74605-050, Brazil.,Departament of Master in Environmental Sciences and Health, School of Medical, Pharmaceutical and Biomedical Sciences, Pontifical Catholic University of Goiás, Goiânia, Brazil
| | | | - Irmtraut Araci Hoffmann Pfrimer
- Departament of Master in Environmental Sciences and Health, School of Medical, Pharmaceutical and Biomedical Sciences, Pontifical Catholic University of Goiás, Goiânia, Brazil
| | - Edecio Cunha-Neto
- Heart Institute (InCor), School of Medicine, University of São Paulo, São Paulo, Brazil.,Institute for Investigation in Immunology (iii) - National Institute of Science and Technology (INCT), São Paulo, Brazil
| | - Andréa Queiroz Maranhão
- Department of Cell Biology, University of Brasília, Brasília, Brazil.,Institute for Investigation in Immunology (iii) - National Institute of Science and Technology (INCT), São Paulo, Brazil
| | - Marcelo Macedo Brígido
- Department of Cell Biology, University of Brasília, Brasília, Brazil.,Institute for Investigation in Immunology (iii) - National Institute of Science and Technology (INCT), São Paulo, Brazil
| | | | | | - Simone Gonçalves Fonseca
- Department of Bioscience and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Rua 235 s/n, sala 335, Setor Universitário, Goiânia, GO, 74605-050, Brazil. .,Institute for Investigation in Immunology (iii) - National Institute of Science and Technology (INCT), São Paulo, Brazil.
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Tsai TH, Chang CY, Wang FI. A Highly Conserved Epitope (RNNQIPQDF) of Porcine teschovirus Induced a Group-Specific Antiserum: A Bioinformatics-Predicted Model with Pan-PTV Potential. Viruses 2020; 12:v12111225. [PMID: 33138189 PMCID: PMC7693897 DOI: 10.3390/v12111225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 10/27/2020] [Indexed: 11/21/2022] Open
Abstract
Porcine teschovirus (PTV) is an OIE-listed pathogen with 13 known PTV serotypes. Heterologous PTV serotypes frequently co-circulate and co-infect with another swine pathogen, causing various symptoms in all age groups, thus highlighting the need for a pan-PTV diagnostic tool. Here, a recombinant protein composed of a highly conserved “RNNQIPQDF” epitope on the GH loop of VP1, predicted in silico, and a tandem repeat of this epitope carrying the pan DR (PADRE) and Toxin B epitopes was constructed to serve as a PTV detection tool. This recombinant GST-PADRE-(RNNQIPQDF)n-Toxin B protein was used as an immunogen, which effectively raised non-neutralizing or undetectable neutralizing antibodies against PTV in mice. The raised antiserum was reactive against all the PTV serotypes (PTV–1–7) tested, but not against members of the closely related genera Sapelovirus and Cardiovirus, and the unrelated virus controls. This potential pan-PTV diagnostic reagent may be used to differentiate naturally infected animals from vaccinated animals that have antibodies against a subunit vaccine that does not contain this epitope or to screen for PTV before further subtyping. To our knowledge, this is the first report that utilized in silico PTV epitope prediction to find a reagent broadly reactive to various PTV serotypes.
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Affiliation(s)
- Tung-Hsuan Tsai
- School of Veterinary Medicine, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan;
| | - Chia-Yi Chang
- OIE Reference Expert for CSF, Animal Health Research Institute, Council of Agriculture, Executive Yuan, No. 376, Chung Cheng Road, Tansui, New Taipei City 25158, Taiwan
- Correspondence: (C.-Y.C.); (F.-I.W.); Fax: +886-2-2366-1475 (F.-I.W.)
| | - Fun-In Wang
- School of Veterinary Medicine, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan;
- Correspondence: (C.-Y.C.); (F.-I.W.); Fax: +886-2-2366-1475 (F.-I.W.)
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Rathore AS, Sarker A, Gupta RD. Designing antibody against highly conserved region of dengue envelope protein by in silico screening of scFv mutant library. PLoS One 2019; 14:e0209576. [PMID: 30629625 PMCID: PMC6328183 DOI: 10.1371/journal.pone.0209576] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/07/2018] [Indexed: 02/08/2023] Open
Abstract
Dengue being one of the deadliest diseases of tropical regions, enforces to put continuous efforts for the development of vaccine and effective therapeutics. Most of the antibodies generated during dengue infection are non-neutralizing and cause antibody dependent enhancement. Hence, making a potent neutralizing antibody against all four dengue serotypes could be very effective for the treatment. However, designing a single antibody for all serotypes is difficult due to variation in protein sequences. Therefore, the objective is to identify conserved region of dengue envelope protein and then develop an antibody against that conserved region. Before advancing to the development of such an antibody, it is desirable to validate the interactions between antibody and dengue envelope protein. In silico analysis of such interactions provides a good platform to find out a suitable region to design and construct an antibody against it by analyzing antigen-antibody interaction before synthesizing the antibody. In this study, two highly conserved regions of dengue envelope protein were identified and an scFv was constructed against it. Both scFv and FuBc proteins were expressed in bacterial expression system and binding efficiency was analyzed by SPR analysis with KD value 2.3 μM. In order to improve binding efficiency, an in silico scFv mutant library was created which was virtually screened for higher binding efficiency. Six mutants with high binding efficiency were selected for further analysis. The binding ability of these mutants were predicted using simulation analysis which shows these mutations were stabilizing scFv-FuBc complex.
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Affiliation(s)
| | - Animesh Sarker
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, India
| | - Rinkoo Devi Gupta
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, India
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Lin CF, Jiang HK, Chen NC, Wang TY, Chen TY. Novel subunit vaccine with linear array epitope protect giant grouper against nervous necrosis virus infection. FISH & SHELLFISH IMMUNOLOGY 2018; 74:551-558. [PMID: 29355759 DOI: 10.1016/j.fsi.2018.01.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/12/2018] [Accepted: 01/16/2018] [Indexed: 06/07/2023]
Abstract
Viral nervous necrosis caused by nervous necrosis virus (NNV) is one of the most severe diseases resulting in high fish mortality rates and high economic losses in the giant grouper industry. Various NNV vaccines have been evaluated, such as inactivated viruses, virus-like particles (VLPs), recombinant coat proteins, synthetic peptides of coat proteins, and DNA vaccines. However, a cheaper manufacturing process and effective protection of NNV vaccines for commercial application are yet to be established. Hence, the present study developed a novel subunit vaccine composed of a carrier protein, receptor-binding domain of Pseudomonas exotoxin A, and tandem-repeated NNV coat protein epitopes by using the structural basis of epitope prediction and the linear array epitope (LAE) technique. On the basis of the crystal structure of the NNV coat protein, the epitope was predicted from the putative target cell receptor-binding region to elicit neutralizing immune responses. The safety of the LAE vaccine was evaluated, and all vaccinated fish survived without any physiological changes. The coat protein-specific antibody titers in the vaccinated fish increased after vaccine administration and exerted NNV-neutralizing effects. The efficacy tests revealed that the relative percent survival (RPS) of LAE antigen formulated with adjuvant was above 72% and LAE vaccine was effective for preventing NNV infection in giant grouper. This study is the first to develop an NNV vaccine by using epitope repeats, which provided effective protection to giant grouper against virus infection. The LAE construct can be used as a vaccine design platform against various pathogenic diseases.
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Affiliation(s)
- Chao-Fen Lin
- Laboratory of Molecular Genetics, Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan; Laboratory of Molecular Genetics, Institute of Biotechnology, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Han-Kai Jiang
- Laboratory of Molecular Genetics, Institute of Biotechnology, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Nai-Chi Chen
- Laboratory of Molecular Genetics, Institute of Biotechnology, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan; National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Ting-Yu Wang
- Laboratory of Molecular Genetics, Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Tzong-Yueh Chen
- Laboratory of Molecular Genetics, Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan; Laboratory of Molecular Genetics, Institute of Biotechnology, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan; Translational Center for Marine Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan; Agriculture Biotechnology Research Center, National Cheng Kung University, Tainan 70101, Taiwan.
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