Drug design based on the complex structure of HIV-Tat and its RNA aptamer

基于HIV-Tat及其RNA适体复杂结构的药物设计

基本信息

批准号：
12470487
负责人：
KATAHIRA Masato
金额：
$ 5.38万
依托单位：
Yokohama National University
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (B)
财政年份：
2000
资助国家：
日本
起止时间：
2000 至 2002
项目状态：
已结题

项目摘要

An RNA aptamer containing two binding sites exhibits extremely high affinity to the HIV Tat protein. We have now determined the structure of the aptamer complexed with argininamide, the simplest analogue of the Tat protein, by NMR. We found that two argininamide molecules bind per aptamer. Two adjacent U : A : U base triples were formed, which widens the major groove to make space for the two argininamide molecules. The argininamide molecules bound to the G bases through hydrogen bonds. The binding is stabilized through stacking interactions.The structure of the aptamer complexed with a Tat-derived argmine-rich peptide was also characterized. The Tat-derived peptide bound to the aptamer in a 1: 1 molar ratio. In spite of the difference in stoichiometry, similarity was noted between the argininamide- and peptide-bound forms of the aptamer in chemical shift perturbations of the aptamer upon complex formation and intermolecular contacts. These results suggest that two different arginine residues of the peptide interact with the two binding sites of the aptamer in the same way as two argininamide molecules do. Simultaneous interactions of the aptamer with two arginine residues of Tat could explain its high affinity compared to the authentic TAR RNA. The formation of the two adjacent base triples makes the simultaneous interactions possible by creating space for the accommodation of two arginine residues and linking residues of Tat, and also contributes to the stabilization of the binding through stacking interactions.The elucidated structure of the aptamer gives clues to rationally design a new aptamer that exhibits even higher affinity to Tat. The way to design a new aptamer with a less side effect is also provided by the elucidated structure.

包含两个结合位点的RNA适体对HIV TAT蛋白表现出极高的亲和力。现在，我们已经确定了NMR与Argininamide（TAT蛋白的最简单类似物）复合的适体的结构。我们发现两个精氨酸分子每个适体结合。形成了两个相邻的u：a：u碱基三元，这扩大了主要的凹槽，以腾出两个精氨酸分子的空间。精氨酸分子通过氢键结合到G碱基。结合通过堆叠相互作用稳定。适体的结构与富含TAT的富含Argmine的肽复合在一起。 TAT衍生的肽以1：1摩尔比结合到适体。尽管化学计量学的差异差异，但在复合物形成和分子间接触时，在适体的化学移动扰动中，精氨酸胺和肽结合的适体的形式之间存在相似性。这些结果表明，肽的两个不同的精氨酸残基与适体的两个结合位点相互作用，其方式与两个精氨酸分子相同。与真实的Tar RNA相比，适体与两个精氨酸残基的同时相互作用可以解释其高亲和力。两个相邻的基本三元组的形成使同时相互作用通过为可容纳两个精氨酸残基和将TAT的残基链接起来的空间而成为可能，并且还有助于通过堆叠相互作用稳定结合的稳定。Aptamer的阐明结构为Aptamer提供了线索，从而使其在更高的Aptamer上设计了更高的Achamer，该恰当的aptamer均具有更高的亲密关系。阐明结构还提供了设计具有较小副作用的新适体的方法。