PDF(Pubmed)
Abstract：
BACKGROUND: Different quickly-developed vaccines are introduced against COVID-19 with inconclusive results especially against some recent variants. Eventually, somewhere COVID-19 cases decline and in some countries it revived with some new mutant-variants (i.e. D614G, Delta and Omicron).
OBJECTIVE: Proposing a universal vaccination strategy by screening globally-conserved SARS-CoV-2 spike-epitopes.
METHODS: Presently, several conserved (186-countries) sequences including multiple-variants (ClustalX2) epitopic-regions (SVMTriP and IEDB) and in-silico mutants of SARS-CoV-2 spike-protein-fragments (Cut1-4) were screened for their stability against proteases, antigenicity (VaxiJen V2.0 and for glycosylation effects NetOGlyc-NetNGlyc), MHCI/II reactivity (IEDB-TOOLS) and CD4+ responses by molecular-docking (Haddock2.4/PatchDock). We also examined Molecular-Dynamic-Simulation (myPresto verson-5) of MHC-II 3LQZ with 3-Cuts and T-cell 2-molecules (1KGC/4JRX) with SM3-Cut. The MD-simulation was run with 5000-cycles after 300 k-heating/1-atm pressure adjustment for the system-equilibration. Finally, 1000 fs production was run.
RESULTS: The cut4-mutant (SRLFRKSNLKPFERD) showed the highest combined-score 48.23548 and Immunogenicity-Score of 92.0887. The core-sequence SRLFRKSNL showed the highest Median-Percentile-Rank (7-HLA-allele) of 19. CD4+ immunogenicity also confirms the representation of the CUT4TM2 epitope SRLFRKSNL by MHC Class II. The epitope YNYKYRLFR from CUT4 showed an IC50 of ∼30 nM with allele HLA-DRB1*11:01 and HLA-DRB5*01:01 with plenty H-bonding. Cut4 double-mutants strongly interact with the exposed T-cell surface and are facilitated by its receptors. The MD-simulation data suggest that TM2 has a maximum RMSD value of 1.7 Å, DM2 is at 1.55 Å and SM3 is at 1.5 Å. These variations correspond to structural adjustments and involve binding/unbinding chemical interactions. The RMSD plot shows that 1KGC T-cell molecule is at 2.2 Å and the 4JRX is at 1.2 Å, which increases with the simulation time.
CONCLUSIONS: Screening of conserved SARS-CoV-2 spike fragments helps to find the most stable antigenic-determinant which with some mutations showed better antigenicity. Further studies are necessary to develop global vaccination strategies against COVID-19.
OBJECTIVE: Proposing a universal vaccination strategy by screening globally-conserved SARS-CoV-2 spike-epitopes.
METHODS: Presently, several conserved (186-countries) sequences including multiple-variants (ClustalX2) epitopic-regions (SVMTriP and IEDB) and in-silico mutants of SARS-CoV-2 spike-protein-fragments (Cut1-4) were screened for their stability against proteases, antigenicity (VaxiJen V2.0 and for glycosylation effects NetOGlyc-NetNGlyc), MHCI/II reactivity (IEDB-TOOLS) and CD4+ responses by molecular-docking (Haddock2.4/PatchDock). We also examined Molecular-Dynamic-Simulation (myPresto verson-5) of MHC-II 3LQZ with 3-Cuts and T-cell 2-molecules (1KGC/4JRX) with SM3-Cut. The MD-simulation was run with 5000-cycles after 300 k-heating/1-atm pressure adjustment for the system-equilibration. Finally, 1000 fs production was run.
RESULTS: The cut4-mutant (SRLFRKSNLKPFERD) showed the highest combined-score 48.23548 and Immunogenicity-Score of 92.0887. The core-sequence SRLFRKSNL showed the highest Median-Percentile-Rank (7-HLA-allele) of 19. CD4+ immunogenicity also confirms the representation of the CUT4TM2 epitope SRLFRKSNL by MHC Class II. The epitope YNYKYRLFR from CUT4 showed an IC50 of ∼30 nM with allele HLA-DRB1*11:01 and HLA-DRB5*01:01 with plenty H-bonding. Cut4 double-mutants strongly interact with the exposed T-cell surface and are facilitated by its receptors. The MD-simulation data suggest that TM2 has a maximum RMSD value of 1.7 Å, DM2 is at 1.55 Å and SM3 is at 1.5 Å. These variations correspond to structural adjustments and involve binding/unbinding chemical interactions. The RMSD plot shows that 1KGC T-cell molecule is at 2.2 Å and the 4JRX is at 1.2 Å, which increases with the simulation time.
CONCLUSIONS: Screening of conserved SARS-CoV-2 spike fragments helps to find the most stable antigenic-determinant which with some mutations showed better antigenicity. Further studies are necessary to develop global vaccination strategies against COVID-19.
摘要：
背景：针对COVID-19引入了不同的快速开发的疫苗，但结果不确定，特别是针对一些最近的变体。最终,在某个地方，COVID-19病例下降，在一些国家，它随着一些新的突变变种而复活(即D614G，Delta和Omicron）。
目的：通过筛选全球保守的SARS-CoV-2尖峰表位，提出一种通用的疫苗接种策略。
方法：目前，筛选了几个保守的（186个国家）序列，包括多个变体（ClustalX2）表位区域（SVMTriP和IEDB）和SARS-CoV-2刺突蛋白片段（Cut1-4）的计算机突变体对蛋白酶的稳定性，抗原性（VaxiJenV2.0和糖基化效应NetOGlyc-NetNGlyc），MHCI/II反应性(IEDB-TOOLS)和通过分子对接的CD4+应答(Haddock2.4/PatchDock)。我们还检查了3切割的MHC-II3LQZ的分子动力学模拟（myPrestoverson-5）和SM3切割的T细胞2分子（1KGC/4JRX）。MD模拟在300k加热/1-atm压力调节后进行5000个循环以进行系统平衡。最后,运行了1000fs的生产。
结果：cut4突变体（SRLFRKSNLKPFERD）表现出最高的综合评分48.23548，免疫原性评分为92.0887。核心序列SRLFRKSNL显示出19的最高中位数-百分位数(7-HLA-等位基因)。CD4+免疫原性也证实了MHCII类对CUT4TM2表位SRLFRKSNL的表示。来自CUT4的表位YNYKYRLFR与等位基因HLA-DRB1*11：01和HLA-DRB5*01：01的IC50为〜30nM，具有大量的H键。Cut4双突变体与暴露的T细胞表面强烈相互作用，并由其受体促进。MD模拟数据表明TM2的最大RMSD值为1.7，DM2为1.55µ，SM3为1.5µ。这些变化对应于结构调整并且涉及结合/解结合化学相互作用。RMSD图显示1KGCT细胞分子为2.2µ，4JRX为1.2µ，随着模拟时间的增加。
结论：筛选保守的SARS-CoV-2刺突片段有助于找到最稳定的抗原决定簇，其中某些突变显示出更好的抗原性。需要进一步的研究来制定针对COVID-19的全球疫苗接种策略。
目的：通过筛选全球保守的SARS-CoV-2尖峰表位，提出一种通用的疫苗接种策略。
方法：目前，筛选了几个保守的（186个国家）序列，包括多个变体（ClustalX2）表位区域（SVMTriP和IEDB）和SARS-CoV-2刺突蛋白片段（Cut1-4）的计算机突变体对蛋白酶的稳定性，抗原性（VaxiJenV2.0和糖基化效应NetOGlyc-NetNGlyc），MHCI/II反应性(IEDB-TOOLS)和通过分子对接的CD4+应答(Haddock2.4/PatchDock)。我们还检查了3切割的MHC-II3LQZ的分子动力学模拟（myPrestoverson-5）和SM3切割的T细胞2分子（1KGC/4JRX）。MD模拟在300k加热/1-atm压力调节后进行5000个循环以进行系统平衡。最后,运行了1000fs的生产。
结果：cut4突变体（SRLFRKSNLKPFERD）表现出最高的综合评分48.23548，免疫原性评分为92.0887。核心序列SRLFRKSNL显示出19的最高中位数-百分位数(7-HLA-等位基因)。CD4+免疫原性也证实了MHCII类对CUT4TM2表位SRLFRKSNL的表示。来自CUT4的表位YNYKYRLFR与等位基因HLA-DRB1*11：01和HLA-DRB5*01：01的IC50为〜30nM，具有大量的H键。Cut4双突变体与暴露的T细胞表面强烈相互作用，并由其受体促进。MD模拟数据表明TM2的最大RMSD值为1.7，DM2为1.55µ，SM3为1.5µ。这些变化对应于结构调整并且涉及结合/解结合化学相互作用。RMSD图显示1KGCT细胞分子为2.2µ，4JRX为1.2µ，随着模拟时间的增加。
结论：筛选保守的SARS-CoV-2刺突片段有助于找到最稳定的抗原决定簇，其中某些突变显示出更好的抗原性。需要进一步的研究来制定针对COVID-19的全球疫苗接种策略。
