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严重急性呼吸综合征冠状病毒2(SARS-CoV-2)与人类白细胞抗原(HLA)II类:针对新冠病毒疾病(COVID-19)防护和疫苗开发的结合亲和力的计算机模拟研究

SARS-CoV-2 Virus and Human Leukocyte Antigen (HLA) Class II: Investigation in silico of Binding Affinities for COVID-19 Protection and Vaccine Development.

作者信息

Charonis Spyros S, Tsilibary Effie-Photini, Georgopoulos Apostolos P

机构信息

Brain Sciences Center, Department of Veterans Affairs Health Care System, Minneapolis, MN 55417, USA.

Department of Neuroscience, University of Minnesota Medical School, Minneapolis, MN 55455, USA.

出版信息

J Immunol Sci. 2020 Nov 16;4(4):12-23. doi: 10.29245/2578-3009/2020/4.1198.

Abstract

SARS-CoV-2 causes COVID-19, urgently requiring the development of effective vaccine(s). Much of current efforts focus on the SARS-CoV-2 spike-glycoprotein by identifying highly antigenic epitopes as good vaccine candidates. However, high antigenicity is not sufficient, since the activation of relevant T cells depends on the presence of the complex of the antigen with a suitably matching Human Leukocyte Antigen (HLA) Class II molecule, not the antigen alone: in the absence of such a match, even a highly antigenic epitope in vitro will not elicit antibody formation in vivo. Here we assessed systematically in silico the binding affinity of epitopes of the spike-glycoprotein to 66 common HLA-Class-II alleles (frequency ≥ 0.01). We used a sliding epitope window of 22-amino-acid-width to scan the entire protein and determined the binding affinity of each subsequence to each HLA allele. DPB1 had highest binding affinities, followed by DRB1 and DQB1. Higher binding affinities were concentrated in the initial part of the glycoprotein (S1-S460), with a peak at S223-S238. This region would be well suited for effective vaccine development by ensuring high probability for successful matching of the vaccine antigen from that region to a HLA Class II molecule for CD4 T cell activation by the antigen-HLA molecule complex.

摘要

严重急性呼吸综合征冠状病毒2(SARS-CoV-2)引发2019冠状病毒病(COVID-19),因此迫切需要研发有效的疫苗。当前的许多工作都聚焦于SARS-CoV-2刺突糖蛋白,通过鉴定高度抗原性表位作为良好的疫苗候选物。然而,高抗原性并不足够,因为相关T细胞的激活取决于抗原与适当匹配的人类白细胞抗原(HLA)II类分子形成的复合物的存在,而不仅仅是抗原本身:在缺乏这种匹配的情况下,即使是体外高度抗原性的表位在体内也不会引发抗体形成。在此,我们通过计算机系统评估了刺突糖蛋白表位与66种常见HLA-II类等位基因(频率≥0.01)的结合亲和力。我们使用一个22个氨基酸宽度的滑动表位窗口扫描整个蛋白质,并确定每个子序列与每个HLA等位基因的结合亲和力。DPB1具有最高的结合亲和力,其次是DRB1和DQB1。较高的结合亲和力集中在糖蛋白的起始部分(S1-S460),在S223-S238处达到峰值。通过确保该区域的疫苗抗原与HLA II类分子成功匹配以通过抗原-HLA分子复合物激活CD4 T细胞的高概率,该区域将非常适合有效的疫苗开发。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/48d3/12077080/837df1e1e8af/nihms-2079209-f0001.jpg

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