JMIR bioinformatics and biotechnology最新文献

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Molecular Docking Using Chimera and Autodock Vina Software for Nonbioinformaticians. 非生物信息学家使用Chimera和Autodock Vina软件进行分子对接
JMIR bioinformatics and biotechnology Pub Date : 2020-06-19 DOI: 10.2196/14232
Sania Safdar Butt, Yasmin Badshah, Maria Shabbir, Mehak Rafiq
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引用次数: 0
Structural Basis for Designing Multiepitope Vaccines Against COVID-19 Infection: In Silico Vaccine Design and Validation. 设计针对 COVID-19 感染的多靶标疫苗的结构基础:硅学疫苗设计与验证。
JMIR bioinformatics and biotechnology Pub Date : 2020-06-19 eCollection Date: 2020-01-01 DOI: 10.2196/19371
Sukrit Srivastava, Sonia Verma, Mohit Kamthania, Rupinder Kaur, Ruchi Kiran Badyal, Ajay Kumar Saxena, Ho-Joon Shin, Michael Kolbe, Kailash C Pandey
{"title":"Structural Basis for Designing Multiepitope Vaccines Against COVID-19 Infection: In Silico Vaccine Design and Validation.","authors":"Sukrit Srivastava, Sonia Verma, Mohit Kamthania, Rupinder Kaur, Ruchi Kiran Badyal, Ajay Kumar Saxena, Ho-Joon Shin, Michael Kolbe, Kailash C Pandey","doi":"10.2196/19371","DOIUrl":"10.2196/19371","url":null,"abstract":"<p><strong>Background: </strong>The novel coronavirus disease (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to the ongoing 2019-2020 pandemic. SARS-CoV-2 is a positive-sense single-stranded RNA coronavirus. Effective countermeasures against SARS-CoV-2 infection require the design and development of specific and effective vaccine candidates.</p><p><strong>Objective: </strong>To address the urgent need for a SARS-CoV-2 vaccine, in the present study, we designed and validated one cytotoxic T lymphocyte (CTL) and one helper T lymphocyte (HTL) multi-epitope vaccine (MEV) against SARS-CoV-2 using various in silico methods.</p><p><strong>Methods: </strong>Both designed MEVs are composed of CTL and HTL epitopes screened from 11 Open Reading Frame (ORF), structural and nonstructural proteins of the SARS-CoV-2 proteome. Both MEVs also carry potential B-cell linear and discontinuous epitopes as well as interferon gamma-inducing epitopes. To enhance the immune response of our vaccine design, truncated (residues 10-153) <i>Onchocerca volvulus</i> activation-associated secreted protein-1 was used as an adjuvant at the N termini of both MEVs. The tertiary models for both the designed MEVs were generated, refined, and further analyzed for stable molecular interaction with toll-like receptor 3. Codon-biased complementary DNA (cDNA) was generated for both MEVs and analyzed in silico for high level expression in a mammalian (human) host cell line.</p><p><strong>Results: </strong>In the present study, we screened and shortlisted 38 CTL, 33 HTL, and 12 B cell epitopes from the 11 ORF protein sequences of the SARS-CoV-2 proteome. Moreover, the molecular interactions of the screened epitopes with their respective human leukocyte antigen allele binders and the transporter associated with antigen processing (TAP) complex were positively validated. The shortlisted screened epitopes were utilized to design two novel MEVs against SARS-CoV-2. Further molecular models of both MEVs were prepared, and their stable molecular interactions with toll-like receptor 3 were positively validated. The codon-optimized cDNAs of both MEVs were also positively analyzed for high levels of overexpression in a human cell line.</p><p><strong>Conclusions: </strong>The present study is highly significant in terms of the molecular design of prospective CTL and HTL vaccines against SARS-CoV-2 infection with potential to elicit cellular and humoral immune responses. The epitopes of the designed MEVs are predicted to cover the large human population worldwide (96.10%). Hence, both designed MEVs could be tried in vivo as potential vaccine candidates against SARS-CoV-2.</p>","PeriodicalId":73552,"journal":{"name":"JMIR bioinformatics and biotechnology","volume":"1 1","pages":"e19371"},"PeriodicalIF":0.0,"publicationDate":"2020-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7370533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38256634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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