必须声明标量变量 "@Script_ID"。  新型冠状病毒SARS-CoV-2棘突蛋白免疫原性分析及其多肽疫苗设计研究-《赣南医学院学报》

[1]许志强,鲁陈,胡晓军,等. 新型冠状病毒SARS-CoV-2棘突蛋白免疫原性分析及其多肽疫苗设计研究[J].赣南医学院学报,2020,40(03):1.
 XU Zhi-qiang,LU Chen,HU Xiao-jun,et al. Epitope-based peptide vaccine design and immunogenicity analysis of the spike protein from SARS-CoV-2[J].,2020,40(03):1.
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 新型冠状病毒SARS-CoV-2棘突蛋白免疫原性分析及其多肽疫苗设计研究()
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《赣南医学院学报》[ISSN:1001-5779/CN:36-1154/R]

卷:
40
期数:
2020年03期
页码:
1
栏目:
新型冠状病毒专题
出版日期:
2020-04-30

文章信息/Info

Title:
 Epitope-based peptide vaccine design and immunogenicity analysis of the spike protein from SARS-CoV-2
作者:
许志强1鲁陈2胡晓军3郭有2胡巧丽1朱颖24
1.南京医科大学第一附属医院,江苏 南京 210000;2.赣南医学院第一附属医院,江西 赣州 341000;3.赣州市疾病预防控制中心,江西 赣州 341000;4.南昌大学生命科学学院,江西 南昌 330031
Author(s):
 XU Zhi-qiang1 LU Chen2 HU Xiao-jun3 GUO You2 HU Qiao-li1 ZHU Ying24
 1.The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210000; 2.The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000; 3.Ganzhou Center for Disease Control and Prevention, Ganzhou, Jiangxi 341000; 4.School of Life Science, Nanchang University, Nanchang, Jiangxi 330031
关键词:
 SARS-CoV-2COVID-19三维结构模拟B细胞表位
Keywords:
 SARS-CoV-2 COVID-19 modelling of 3D structure B-cell epitopes
分类号:
R392.11
文献标志码:
A
摘要:
目的:分析SARS-CoV-2表面棘突蛋白的结构和B细胞表位。方法:首先利用Protparam对SARS-CoV-2棘突蛋白的物理化学性质特征进行分析。随后通过Clustal软件,对SARS-CoV-2和SARS-CoV棘突蛋白中的功能区域进行分析,并结合同源模拟,明确棘突蛋白的空间结构和折叠特征。综合DNAStar、ABCpred和BepiPred结果,筛选2019-CoV 棘突蛋白的线性B细胞表位,同时利用ElliPro、DiscoTope、SEPPA对棘突蛋白的构象B细胞表位进行综合预测。结果:通过同源模拟,SARS-CoV-2的棘突蛋白是同源三聚体结构,并且与SARS-CoV的棘突蛋白相似,也具有两种受体结合区域构象。通过综合多种免疫信息学工具及进一步筛选,11条线性表位(B9-B14和B27-B31)及5条构象表位(CB4-CB8)被筛出。结论:本研究筛选出的SARS-CoV-2棘突蛋白的16条B细胞表位,包括11条线性表位(B9-B14和B27-B31)及5条构象表位(CB4-CB8),可作为潜在的新型冠状病毒肺炎免疫原疫苗研发的候选表位。
Abstract:
Objective: To analyse the structure and B-cell epitope of spike protein from SARS-CoV-2 surface. Methods: Firstly, the physiochemical properties of the SARS-Cov-2 spike protein were analyzed by the Protparam.Subsequently, the architecture of the SARS-CoV-2 spike protein was compared with that of SARS-CoV by sequence alignment in Clustal. The tertiary structure of SARS-CoV-2 spike protein was built by homologous modelling. Finally, both linear and conformational epitopes in spike protein were predicted by different immunoinformatic approaches including DNAStar,ABCpred, BepiPred, ElliPro, DiscoTope and SEPPA. Results: Through homologous simulation, the spike protein on SARS-CoV-2 was a homo trimer and had two different conformations of receptor binding domain which was similar with SARS-CoV. By combining multiple immunoinformatics tools and further screening, eleven linear epitopes (B9-B14 and B27-B31) and five conformational epitopes (CB4-CB8) were screened out. Conclusions: Sixteen B cell epitopes of SARS-CoV-2 spike protein, including eleven linear epitopes (B9-B14 and B27-B31) and five conformational epitopes (CB4-CB8), were suggested to be the potential candidate epitopes for the development of novel coronavirus pneumonia immunogenicity vaccine in the study.

参考文献/References:

[1]XU X, CHEN P, WANG J, et al. Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission[J]. Sci China Life Sci, 2020,63(3):457-460.
[2]LI GD, CLERCQ ED. Therapeutic options for the 2019 novel coronavirus (2019-nCoV)[J]. Nat Rev Drug Discov, 2020, 19(3):149-150.
[3]LU H. Drug treatment options for the 2019-new coronavirus (2019-nCoV)[J]. Bioscience trends, 2020. doi:10.5582/bst.2020.01020.
[4]YUAN Y, CAO D, ZHANG Y, et al. Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains[J]. Nat Commun, 2017, 8:15092.
[5]KROGH A, LARSSON B, VON HEIJNE G, et al. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes[J]. J Mol Biol, 2001, 305(3):567-580.
[6]WATERHOUSE A, BERTONI M, BIENERT S, et al. SWISS-MODEL: homology modelling of protein structures and complexes[J]. Nucleic Acids Res, 2018, 46(W1):W296-W303. [7]DELANO W L. Pymol: An open-source molecular graphics tool[J]. CCP4 Newsletter on protein crystallography, 2002, 40(1): 82-92.
[8]SAHA S, RAGHAVA GP. Prediction of continuous B-cell epitopes in an antigen using recurrent neural network[J]. Proteins, 2006, 65(1):40-8.
[9]JESPERSEN MC, PETERS B, NIELSEN M, et al. BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes[J]. Nucleic Acids Res, 2017, 45 (W1):W24-W29.
 [10]PONOMARENKO J, BUI HH, LI W, et al. ElliPro: a new structure-based tool for the prediction of antibody epitopes[J]. BMC Bioinformatics, 2008, 9:514.
[11]KRINGELUM JV, LUNDEGAARD C, LUND O, et al. Reliable B cell epitope predictions: impacts of method development and improved benchmarking[J]. PLoS Comput Biol, 2012, 8(12): e1002829.
[12]ZHOU C, CHEN Z, ZHANG L, et al. SEPPA 3.0-enhanced spatial epitope prediction enabling glycoprotein antigens[J]. Nucleic Acids Res, 2019, 47(W1): W388-W394.
[13]CHAN J F W, KOK K H, ZHU Z, et al. Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan[J]. Emerging Microbes & Infections, 2020, 9(1): 221-236.
[14]GUI M, SONG W, ZHOU H, et al. Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding[J]. Cell Res, 2017, 27(1):119-129.
[15]WRAPP D, WANG N, CORBETT K S, et al. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation[J]. Science, 2020.
[16]DUAN J, YAN X, GUO X, et al. A human SARS-CoV neutralizing antibody against epitope on S2 protein[J]. Biochem Biophys Res Commun, 2005, 333(1):186-193.
[17]CHOU TH, WANG S, SAKHATSKYY PV, et al. Epitope mapping and biological function analysis of antibodies produced by immunization of mice with an inactivated Chinese isolate of severe acute respiratory syndrome-associated coronavirus (SARS-CoV)[J]. Virology, 2005, 334(1):134-143.
[18]WANG Q, ZHANG L, KUWAHARA K, et al. Immunodominant SARS Coronavirus Epitopes in Humans Elicited both Enhancing and Neutralizing Effects on Infection in Non-human Primates[J]. ACS Infect Dis, 2016, 2(5):361-376.
[19]BARUAH V, BOSE S. Immunoinformatics-aided identification of T cell and B cell epitopes in the surface glycoprotein of 2019-nCoV[J]. J Med Virol, 2020. doi:10.1002/jmv.25698.

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备注/Memo

备注/Memo:
 基金项目:赣南医学院COVID-19应急项目(YJ202014)
作者简介:许志强,男,硕士,药师,研究方向:药学。E-mail:xu.zhiqiang@outlook.com
通信作者:朱颖,女,硕士,副主任医师,研究方向:生物化学与分子生物学。E-mail:pink-shadow@163.com
收稿日期:2020-02-17
更新日期/Last Update: 2020-03-18