Aminoglycoside binding to the HIV-1 RNA dimerization initiation site: thermodynamics and effect on the kissing-loop to duplex conversion.
Aminoglycoside binding to the HIV-1 RNA dimerization initiation site: thermodynamics and effect on the kissing-loop to duplex conversion.
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DOI：
10.1093/nar/gkm856
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发表时间：
2007
影响因子：
14.9
通讯作者：
Ennifar, Eric
中科院分区：
文献类型：
--
作者：
Bernacchi, Serena;Freisz, Severine;Maechling, Clarisse;Spiess, Bernard;Marquet, Roland;Dumas, Philippe;Ennifar, Eric
由于与细菌16s核糖体a位点的结构和序列惊人的相似性，HIV-1基因组RNA二聚化起始位点（DIS）形成的RNA接吻环复合物特异性结合4,5-二取代2-脱氧链胺（2-DOS）氨基糖苷类抗生素。我们使用化学探针、分子模型、等温滴定量热法（ITC）和紫外熔化来研究氨基糖苷与DIS环环复合物的结合。我们发现阿帕霉素，一种含有双环片段的氨基糖苷，也与DIS结合，但与4,5-二取代的2-DOS氨基糖苷结合的方式不同。通过对氨基糖苷类化合物热力学参数的测定，揭示了不同环在药物- rna相互作用中的作用。令人惊讶的是，我们发现利维霉素和新霉素对DIS的亲和力（Kd ~ 30 nM）明显高于在相同实验条件下对其天然靶点细菌A位点的亲和力（Kd ~ 1.6µM）。氨基糖苷提高了环-环相互作用的熔融温度，并阻断了亲和环配合物向扩展双相的转化，这与它们各自的亲和关系是一致的。综上所述，我们的数据可能有助于选择对HIV-1 DIS RNA具有更高特异性和亲和力的新分子。
Owing to a striking, and most likely fortuitous, structural and sequence similarity with the bacterial 16 S ribosomal A site, the RNA kissing-loop complex formed by the HIV-1 genomic RNA dimerization initiation site (DIS) specifically binds 4,5-disubstituted 2-deoxystreptamine (2-DOS) aminoglycoside antibiotics. We used chemical probing, molecular modeling, isothermal titration calorimetry (ITC) and UV melting to investigate aminoglycoside binding to the DIS loop–loop complex. We showed that apramycin, an aminoglycoside containing a bicyclic moiety, also binds the DIS, but in a different way than 4,5-disubstituted 2-DOS aminoglycosides. The determination of thermodynamic parameters for various aminoglycosides revealed the role of the different rings in the drug–RNA interaction. Surprisingly, we found that the affinity of lividomycin and neomycin for the DIS (Kd ∼ 30 nM) is significantly higher than that obtained in the same experimental conditions for their natural target, the bacterial A site (Kd ∼ 1.6 µM). In good agreement with their respective affinity, aminoglycoside increase the melting temperature of the loop–loop interaction and also block the conversion from kissing-loop complex to extended duplex. Taken together, our data might be useful for selecting new molecules with improved specificity and affinity toward the HIV-1 DIS RNA.