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Ojha R, Singh S, Gupta N, Kumar K, Padhi AK, Prajapati VK. Multi-pathogen based chimeric vaccine to fight against COVID-19 and concomitant coinfections. Biotechnol Lett 2023:10.1007/s10529-023-03380-0. [PMID: 37148345 PMCID: PMC10163573 DOI: 10.1007/s10529-023-03380-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/21/2022] [Accepted: 04/11/2023] [Indexed: 05/08/2023]
Abstract
BACKGROUND COVID-19 has proved to be a fatal disease of the year 2020, due to which thousands of people globally have lost their lives, and still, the infection cases are at a high rate. Experimental studies suggested that SARS-CoV-2 interacts with various microorganisms, and this coinfection is accountable for the augmentation of infection severity. METHODS AND RESULTS In this study, we have designed a multi-pathogen vaccine by involving the immunogenic proteins from S. pneumonia, H. influenza, and M. tuberculosis, as they are dominantly associated with SARS-CoV-2. A total of 8 antigenic protein sequences were selected to predict B-cell, HTL, and CTL epitopes restricted to the most prevalent HLA alleles. The selected epitopes were antigenic, non-allergenic, and non-toxic and were linked with adjuvant and linkers to make the vaccine protein more immunogenic, stable, and flexible. The tertiary structure, Ramachandran plot, and discontinuous B-cell epitopes were predicted. Docking and MD simulation study has shown efficient binding of the chimeric vaccine with the TLR4 receptor. CONCLUSION The in silico immune simulation analysis has shown a high level of cytokines and IgG after a three-dose injection. Hence, this strategy could be a better way to decrease the disease's severity and could be used as a weapon to prevent this pandemic.
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Affiliation(s)
- Rupal Ojha
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Ajmer, Kishangarh, 305817, Rajasthan, India
| | - Satyendra Singh
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Ajmer, Kishangarh, 305817, Rajasthan, India
| | - Nidhi Gupta
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Ajmer, Kishangarh, 305817, Rajasthan, India
| | - Ketan Kumar
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Ajmer, Kishangarh, 305817, Rajasthan, India
| | - Aditya K Padhi
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU) Varanasi, Varanasi, 221005, Uttar Pradesh, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Ajmer, Kishangarh, 305817, Rajasthan, India.
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bhatinda, Punjab, India.
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Jin X, Ding Y, Sun S, Wang X, Zhou Z, Liu X, Li M, Chen X, Shen A, Wu Y, Liu B, Zhang J, Li J, Yang Y, Qiu H, Shen C, He Y, Zhao G. Screening HLA-A-restricted T cell epitopes of SARS-CoV-2 and the induction of CD8 + T cell responses in HLA-A transgenic mice. Cell Mol Immunol 2021; 18:2588-2608. [PMID: 34728796 PMCID: PMC8561351 DOI: 10.1038/s41423-021-00784-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 09/23/2021] [Indexed: 11/22/2022] Open
Abstract
Since severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-specific T cells have been found to play essential roles in host immune protection and pathology in patients with coronavirus disease 2019 (COVID-19), this study focused on the functional validation of T cell epitopes and the development of vaccines that induce specific T cell responses. A total of 120 CD8+ T cell epitopes from the E, M, N, S, and RdRp proteins were functionally validated. Among these, 110, 15, 6, 14, and 12 epitopes were highly homologous with SARS-CoV, OC43, NL63, HKU1, and 229E, respectively; in addition, four epitopes from the S protein displayed one amino acid that was distinct from the current SARS-CoV-2 variants. Then, 31 epitopes restricted by the HLA-A2 molecule were used to generate peptide cocktail vaccines in combination with Poly(I:C), R848 or poly (lactic-co-glycolic acid) nanoparticles, and these vaccines elicited robust and specific CD8+ T cell responses in HLA-A2/DR1 transgenic mice as well as wild-type mice. In contrast to previous research, this study established a modified DC-peptide-PBL cell coculture system using healthy donor PBMCs to validate the in silico predicted epitopes, provided an epitope library restricted by nine of the most prevalent HLA-A allotypes covering broad Asian populations, and identified the HLA-A restrictions of these validated epitopes using competitive peptide binding experiments with HMy2.CIR cell lines expressing the indicated HLA-A allotype, which initially confirmed the in vivo feasibility of 9- or 10-mer peptide cocktail vaccines against SARS-CoV-2. These data will facilitate the design and development of vaccines that induce antiviral CD8+ T cell responses in COVID-19 patients.
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Affiliation(s)
- Xiaoxiao Jin
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Yan Ding
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Shihui Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Xinyi Wang
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Zining Zhou
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Xiaotao Liu
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Miaomiao Li
- Blood Component Preparation Section, Jiangsu Province Blood Center, Nanjing, 210042, Jiangsu, China
| | - Xian Chen
- Blood Component Preparation Section, Jiangsu Province Blood Center, Nanjing, 210042, Jiangsu, China
| | - Anran Shen
- Institute of Nephrology, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Yandan Wu
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Bicheng Liu
- Institute of Nephrology, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Jianqiong Zhang
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Jian Li
- Life Science & Technology School of Southeast University, Nanjing, 210096, Jiangsu, China
| | - Yi Yang
- Jiangsu Province Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Haibo Qiu
- Jiangsu Province Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Chuanlai Shen
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China.
- Jiangsu Province Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China.
| | - Yuxian He
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Guangyu Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
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Viana Invenção MDC, Melo ARDS, de Macêdo LS, da Costa Neves TSP, de Melo CML, Cordeiro MN, de Aragão Batista MV, de Freitas AC. Development of synthetic antigen vaccines for COVID-19. Hum Vaccin Immunother 2021; 17:3855-3870. [PMID: 34613880 PMCID: PMC8506811 DOI: 10.1080/21645515.2021.1974288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/04/2021] [Accepted: 08/24/2021] [Indexed: 11/04/2022] Open
Abstract
The current pandemic called COVID-19 caused by the SARS-CoV-2 virus brought the need for the search for fast alternatives to both control and fight the SARS-CoV-2 infection. Therefore, a race for a vaccine against COVID-19 took place, and some vaccines have been approved for emergency use in several countries in a record time. Ongoing prophylactic research has sought faster, safer, and precise alternatives by redirecting knowledge of other vaccines, and/or the development of new strategies using available tools, mainly in the areas of genomics and bioinformatics. The current review highlights the development of synthetic antigen vaccines, focusing on the usage of bioinformatics tools for the selection and construction of antigens on the different vaccine constructions under development, as well as strategies to optimize vaccines for COVID-19.
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Affiliation(s)
- Maria da Conceição Viana Invenção
- Laboratory of Molecular Studies and Experimental Therapy - LEMTE, Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Alanne Rayssa da Silva Melo
- Laboratory of Molecular Studies and Experimental Therapy - LEMTE, Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Larissa Silva de Macêdo
- Laboratory of Molecular Studies and Experimental Therapy - LEMTE, Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Thaís Souto Paula da Costa Neves
- Laboratory of Molecular Studies and Experimental Therapy - LEMTE, Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Cristiane Moutinho Lagos de Melo
- Laboratory of Immunological and Antitumor Analysis, Department of Antibiotics, Bioscience Center, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Marcelo Nazário Cordeiro
- Laboratory of Molecular Studies and Experimental Therapy - LEMTE, Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Marcus Vinicius de Aragão Batista
- Laboratory of Molecular Genetics and Biotechnology, Department of Biology, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
| | - Antonio Carlos de Freitas
- Laboratory of Molecular Studies and Experimental Therapy - LEMTE, Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco, Brazil
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