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用于在巴西利什曼原虫蛋白质组中寻找潜在CD4(+)和CD8(+) T细胞表位的计算机方法组合

Combination of In Silico Methods in the Search for Potential CD4(+) and CD8(+) T Cell Epitopes in the Proteome of Leishmania braziliensis.

作者信息

E Silva Rafael de Freitas, Ferreira Luiz Felipe Gomes Rebello, Hernandes Marcelo Zaldini, de Brito Maria Edileuza Felinto, de Oliveira Beatriz Coutinho, da Silva Ailton Alvaro, de-Melo-Neto Osvaldo Pompílio, Rezende Antônio Mauro, Pereira Valéria Rêgo Alves

机构信息

Department of Natural Sciences, Universidade de Pernambuco, Garanhuns, Pernambuco, Brazil; Department of Immunology, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil.

Department of Pharmaceutical Sciences, Universidade Federal de Pernambuco , Recife, Pernambuco , Brazil.

出版信息

Front Immunol. 2016 Aug 29;7:327. doi: 10.3389/fimmu.2016.00327. eCollection 2016.


DOI:10.3389/fimmu.2016.00327
PMID:27621732
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5002431/
Abstract

The leishmaniases are neglected tropical diseases widespread throughout the globe, which are caused by protozoans from the genus Leishmania and are transmitted by infected phlebotomine flies. The development of a safe and effective vaccine against these diseases has been seen as the best alternative to control and reduce the number of cases. To support vaccine development, this work has applied an in silico approach to search for high potential peptide epitopes able to bind to different major histocompatibility complex Class I and Class II (MHC I and MHC II) molecules from different human populations. First, the predicted proteome of Leishmania braziliensis was compared and analyzed by modern linear programs to find epitopes with the capacity to trigger an immune response. This approach resulted in thousands of epitopes derived from 8,000 proteins conserved among different Leishmania species. Epitopes from proteins similar to those found in host species were excluded, and epitopes from proteins conserved between different Leishmania species and belonging to surface proteins were preferentially selected. The resulting epitopes were then clustered, to avoid redundancies, resulting in a total of 230 individual epitopes for MHC I and 2,319 for MHC II. These were used for molecular modeling and docking with MHC structures retrieved from the Protein Data Bank. Molecular docking then ranked epitopes based on their predicted binding affinity to both MHC I and II. Peptides corresponding to the top 10 ranked epitopes were synthesized and evaluated in vitro for their capacity to stimulate peripheral blood mononuclear cells (PBMC) from post-treated cutaneous leishmaniasis patients, with PBMC from healthy donors used as control. From the 10 peptides tested, 50% showed to be immunogenic and capable to stimulate the proliferation of lymphocytes from recovered individuals.

摘要

利什曼病是全球广泛分布的被忽视的热带病,由利什曼原虫属的原生动物引起,通过受感染的白蛉传播。开发一种安全有效的针对这些疾病的疫苗被视为控制和减少病例数的最佳选择。为支持疫苗开发,本研究采用了一种计算机模拟方法来寻找能够与来自不同人群的不同主要组织相容性复合体I类和II类(MHC I和MHC II)分子结合的高潜力肽表位。首先,通过现代线性程序对巴西利什曼原虫的预测蛋白质组进行比较和分析,以找到能够引发免疫反应的表位。这种方法产生了数千个源自8000种不同利什曼原虫物种中保守蛋白质的表位。与宿主物种中发现的蛋白质相似的蛋白质的表位被排除,优先选择不同利什曼原虫物种之间保守且属于表面蛋白的蛋白质的表位。然后对所得表位进行聚类,以避免冗余,最终得到230个MHC I的单个表位和2319个MHC II的单个表位。这些表位被用于分子建模以及与从蛋白质数据库检索到的MHC结构进行对接。分子对接随后根据表位对MHC I和II的预测结合亲和力对其进行排名。合成了与排名前十的表位相对应的肽,并在体外评估它们刺激皮肤利什曼病治疗后患者外周血单核细胞(PBMC)的能力,以健康供体的PBMC作为对照。在所测试的10种肽中,50%显示具有免疫原性,能够刺激康复个体的淋巴细胞增殖。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bdc5/5002431/0ac0035218e6/fimmu-07-00327-g007a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bdc5/5002431/73fc750b103c/fimmu-07-00327-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bdc5/5002431/181b7027adce/fimmu-07-00327-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bdc5/5002431/a90fa42be20f/fimmu-07-00327-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bdc5/5002431/d7dfe44bda2a/fimmu-07-00327-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bdc5/5002431/d746bc00a080/fimmu-07-00327-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bdc5/5002431/12234a75fb78/fimmu-07-00327-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bdc5/5002431/0ac0035218e6/fimmu-07-00327-g007a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bdc5/5002431/73fc750b103c/fimmu-07-00327-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bdc5/5002431/181b7027adce/fimmu-07-00327-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bdc5/5002431/a90fa42be20f/fimmu-07-00327-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bdc5/5002431/d7dfe44bda2a/fimmu-07-00327-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bdc5/5002431/d746bc00a080/fimmu-07-00327-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bdc5/5002431/12234a75fb78/fimmu-07-00327-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bdc5/5002431/0ac0035218e6/fimmu-07-00327-g007a.jpg

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[6]
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[10]
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本文引用的文献

[1]
American tegumentary leishmaniasis: mRNA expression for Th1 and Treg mediators are predominant in patients with recent active disease.

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Front Immunol. 2014-6-10

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