Contriving Multi-Epitope Subunit of Vaccine for COVID-19: Immunoinformatics Approaches
COVID-19 has recently become the most serious threat to public health, and its prevalence has been increasing at an alarming rate. The incubation period for the virus is ~1–14 days and all age groups may be susceptible to a fatality rate of about 5.9%. COVID-19 is caused by a novel single-stranded,...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-07-01
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| Series: | Frontiers in Immunology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fimmu.2020.01784/full |
| _version_ | 1817986626869002240 |
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| author | Rong Dong Rong Dong Rong Dong Zhugang Chu Fuxun Yu Yan Zha Yan Zha Yan Zha |
| author_facet | Rong Dong Rong Dong Rong Dong Zhugang Chu Fuxun Yu Yan Zha Yan Zha Yan Zha |
| author_sort | Rong Dong |
| collection | DOAJ |
| description | COVID-19 has recently become the most serious threat to public health, and its prevalence has been increasing at an alarming rate. The incubation period for the virus is ~1–14 days and all age groups may be susceptible to a fatality rate of about 5.9%. COVID-19 is caused by a novel single-stranded, positive (+) sense RNA beta coronavirus. The development of a vaccine for SARS-CoV-2 is an urgent need worldwide. Immunoinformatics approaches are both cost-effective and convenient, as in silico predictions can reduce the number of experiments needed. In this study, with the aid of immunoinformatics tools, we tried to design a multi-epitope vaccine that can be used for the prevention and treatment of COVID-19. The epitopes were computed by using B cells, cytotoxic T lymphocytes (CTL), and helper T lymphocytes (HTL) base on the proteins of SARS-CoV-2. A vaccine was devised by fusing together the B cell, HTL, and CTL epitopes with linkers. To enhance the immunogenicity, the β-defensin (45 mer) amino acid sequence, and pan-HLA DR binding epitopes (13aa) were adjoined to the N-terminal of the vaccine with the help of the EAAAK linker. To enable the intracellular delivery of the modeled vaccine, a TAT sequence (11aa) was appended to C-terminal. Linkers play vital roles in producing an extended conformation (flexibility), protein folding, and separation of functional domains, and therefore, make the protein structure more stable. The secondary and three-dimensional (3D) structure of the final vaccine was then predicted. Furthermore, the complex between the final vaccine and immune receptors (toll-like receptor-3 (TLR-3), major histocompatibility complex (MHC-I), and MHC-II) were evaluated by molecular docking. Lastly, to confirm the expression of the designed vaccine, the mRNA of the vaccine was enhanced with the aid of the Java Codon Adaptation Tool, and the secondary structure was generated from Mfold. Then we performed in silico cloning. The final vaccine requires experimental validation to determine its safety and efficacy in controlling SARS-CoV-2 infections. |
| first_indexed | 2024-04-14T00:11:40Z |
| format | Article |
| id | doaj.art-9d4de0a6542c443993b5493a9b647a18 |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-04-14T00:11:40Z |
| publishDate | 2020-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-9d4de0a6542c443993b5493a9b647a182022-12-22T02:23:19ZengFrontiers Media S.A.Frontiers in Immunology1664-32242020-07-011110.3389/fimmu.2020.01784544029Contriving Multi-Epitope Subunit of Vaccine for COVID-19: Immunoinformatics ApproachesRong Dong0Rong Dong1Rong Dong2Zhugang Chu3Fuxun Yu4Yan Zha5Yan Zha6Yan Zha7Department of Biomedicine, Guizhou University School of Medicine, Guiyang, ChinaDepartment of Nephrology, Guizhou Provincial People's Hospital, Guiyang, ChinaNHC Key Laboratory of Pulmonary Immunological Diseases (Guizhou Provincial People's Hospital), Guiyang, ChinaDepartment of Urinary Surgery, Guizhou Provincial People's Hospital, Guiyang, ChinaNHC Key Laboratory of Pulmonary Immunological Diseases (Guizhou Provincial People's Hospital), Guiyang, ChinaDepartment of Biomedicine, Guizhou University School of Medicine, Guiyang, ChinaDepartment of Nephrology, Guizhou Provincial People's Hospital, Guiyang, ChinaNHC Key Laboratory of Pulmonary Immunological Diseases (Guizhou Provincial People's Hospital), Guiyang, ChinaCOVID-19 has recently become the most serious threat to public health, and its prevalence has been increasing at an alarming rate. The incubation period for the virus is ~1–14 days and all age groups may be susceptible to a fatality rate of about 5.9%. COVID-19 is caused by a novel single-stranded, positive (+) sense RNA beta coronavirus. The development of a vaccine for SARS-CoV-2 is an urgent need worldwide. Immunoinformatics approaches are both cost-effective and convenient, as in silico predictions can reduce the number of experiments needed. In this study, with the aid of immunoinformatics tools, we tried to design a multi-epitope vaccine that can be used for the prevention and treatment of COVID-19. The epitopes were computed by using B cells, cytotoxic T lymphocytes (CTL), and helper T lymphocytes (HTL) base on the proteins of SARS-CoV-2. A vaccine was devised by fusing together the B cell, HTL, and CTL epitopes with linkers. To enhance the immunogenicity, the β-defensin (45 mer) amino acid sequence, and pan-HLA DR binding epitopes (13aa) were adjoined to the N-terminal of the vaccine with the help of the EAAAK linker. To enable the intracellular delivery of the modeled vaccine, a TAT sequence (11aa) was appended to C-terminal. Linkers play vital roles in producing an extended conformation (flexibility), protein folding, and separation of functional domains, and therefore, make the protein structure more stable. The secondary and three-dimensional (3D) structure of the final vaccine was then predicted. Furthermore, the complex between the final vaccine and immune receptors (toll-like receptor-3 (TLR-3), major histocompatibility complex (MHC-I), and MHC-II) were evaluated by molecular docking. Lastly, to confirm the expression of the designed vaccine, the mRNA of the vaccine was enhanced with the aid of the Java Codon Adaptation Tool, and the secondary structure was generated from Mfold. Then we performed in silico cloning. The final vaccine requires experimental validation to determine its safety and efficacy in controlling SARS-CoV-2 infections.https://www.frontiersin.org/article/10.3389/fimmu.2020.01784/fullimmunoinformaticsepitope predictionCOVID-19SARS-CoV-2vaccine |
| spellingShingle | Rong Dong Rong Dong Rong Dong Zhugang Chu Fuxun Yu Yan Zha Yan Zha Yan Zha Contriving Multi-Epitope Subunit of Vaccine for COVID-19: Immunoinformatics Approaches Frontiers in Immunology immunoinformatics epitope prediction COVID-19 SARS-CoV-2 vaccine |
| title | Contriving Multi-Epitope Subunit of Vaccine for COVID-19: Immunoinformatics Approaches |
| title_full | Contriving Multi-Epitope Subunit of Vaccine for COVID-19: Immunoinformatics Approaches |
| title_fullStr | Contriving Multi-Epitope Subunit of Vaccine for COVID-19: Immunoinformatics Approaches |
| title_full_unstemmed | Contriving Multi-Epitope Subunit of Vaccine for COVID-19: Immunoinformatics Approaches |
| title_short | Contriving Multi-Epitope Subunit of Vaccine for COVID-19: Immunoinformatics Approaches |
| title_sort | contriving multi epitope subunit of vaccine for covid 19 immunoinformatics approaches |
| topic | immunoinformatics epitope prediction COVID-19 SARS-CoV-2 vaccine |
| url | https://www.frontiersin.org/article/10.3389/fimmu.2020.01784/full |
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