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对抗替加环素耐药鲍曼不动杆菌:迈向基于多表位疫苗发现的一大步。

Combating tigecycline resistant Acinetobacter baumannii: A leap forward towards multi-epitope based vaccine discovery.

机构信息

Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan.

Centre for Computational Chemistry, University of Bristol, Bristol, United Kingdom.

出版信息

Eur J Pharm Sci. 2019 Apr 30;132:1-17. doi: 10.1016/j.ejps.2019.02.023. Epub 2019 Feb 21.

Abstract

Global emergence of Tigecycline resistant Acinetobacter baumannii (TRAB) is on the horizon and poses a very serious threat to human health. There is a pressing demand for suitable therapeutics against this pathogen, particularly a vaccine to protect against TRAB infections. We present a comprehensive investigation of the complete proteome of a TRAB AB031 strain to predict promiscuous antigenic, non-allergenic, virulent B-cell derived T-cell epitopes and formulate a multi-epitope vaccine against the pathogen. We identified epitopes from three proteins: outer membrane protein assembly factor (BamA), fimbrial biogenesis outer membrane usher protein (FimD) and type IV secretion protein (Rhs) that are appropriate for vaccine design. These proteins constitute the core proteome of the pathogen, are essential, localized at the pathogen surface, non-homologous to humans, mice and to the beneficial probiotic bacteria that reside the human gut. Moreover, these proteins are ideal candidates for experimental investigation as they have favorable physicochemical properties and have strong cellular interacting networks. The predicted epitopes: FPLNDKPGD (BamA), FVHAEEAAA (FimD) and YVVAGTAAA (Rhs) have exo-membrane topology for efficient recognition of the host immune system and high affinity for the most prevalent allele in human populations, the DRB*0101. These epitopes were linked and attached to an adjuvant to enhance its antigenicity. The multi-epitope vaccine-construct was docked with the TLR4 receptor to assess its affinity for the protein and thus its presentation to the host immune system. Docking results were validated through molecular dynamics simulations and binding free energies were calculated using the molecular mechanics/generalized Born (MM-GBSA) method. In conclusion, we expect the designed chimeric vaccine is highly likely to be effective against infections caused by TRAB.

摘要

全球范围内替加环素耐药鲍曼不动杆菌(TRAB)的出现迫在眉睫,对人类健康构成了严重威胁。迫切需要针对这种病原体的合适疗法,特别是针对 TRAB 感染的疫苗。我们全面研究了一株 TRAB AB031 菌株的完整蛋白质组,以预测具有混杂抗原性、非变应原性、毒力的 B 细胞衍生 T 细胞表位,并制定针对该病原体的多表位疫苗。我们从三种蛋白质中鉴定出了表位:外膜蛋白组装因子(BamA)、菌毛生物发生外膜导蛋白(FimD)和 IV 型分泌蛋白(Rhs),这些蛋白适合疫苗设计。这些蛋白构成了病原体的核心蛋白质组,是必需的,位于病原体表面,与人类、小鼠以及居住在人类肠道中的有益益生菌没有同源性。此外,这些蛋白是实验研究的理想候选物,因为它们具有良好的物理化学特性和强大的细胞相互作用网络。预测的表位:FPLNDKPGD(BamA)、FVHAEEAAA(FimD)和 YVVAGTAAA(Rhs)具有外膜拓扑结构,可有效识别宿主免疫系统,并与人类群体中最常见的等位基因 DRB*0101 具有高亲和力。这些表位被连接并附着到佐剂上,以增强其抗原性。多表位疫苗构建体与 TLR4 受体对接,以评估其与蛋白质的亲和力,从而将其呈递给宿主免疫系统。通过分子动力学模拟对接结果进行了验证,并使用分子力学/广义 Born(MM-GBSA)方法计算了结合自由能。总之,我们预计设计的嵌合疫苗极有可能对 TRAB 引起的感染有效。

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