Rational design of inhibitors of HIV-1 TAR RNA through the stabilisation of electrostatic "hot spots"
Rational design of inhibitors of HIV-1 TAR RNA through the stabilisation of electrostatic "hot spots"
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DOI：
10.1016/j.jmb.2003.12.046
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发表时间：
2004-02-13
影响因子：
5.6
通讯作者：
Aboul-ela, F
中科院分区：
文献类型：
--
作者：
Davis, B;Afshar, M;Aboul-ela, F
迄今为止，用于设计新型抗病毒化合物的RNA靶向研究在很大程度上没有结合基于结构的设计方法的直接输入，部分原因是缺乏结构数据，以及底物灵活性引起的复杂性。我们提出了一个范式来解释配体诱导的人免疫缺陷病毒1型（HIV-1）反式激活反应元件（TAR RNA）重折叠的物理机制。基于Poisson-Boltzmann分析的TAR结构，作为绑定的肽衍生自转录激活蛋白，达特，我们的假设表明，两个特定的静电相互作用是必要的，以稳定的构象。这一结果与以下观点相矛盾：单个烟酰胺残基负责稳定TAR折叠，以及与RNA的静电相互作用是非特异性的或由磷酸盐主导的传统观点。我们测试这一假设，通过使用NMR和计算方法来模拟一系列新的抑制剂的体外RNA结合活性的肽来自达特的相互作用。一个子集的抑制剂，包括双胍化合物rbt 203及其类似物，诱导TAR的构象类似于所带来的蛋白质。这些配体中的两个与RNA的相互作用和在化合物系列内观察到的结构-活性关系的比较，证实了两个特定的静电相互作用在稳定Tat结合的RNA构象中的重要性。这项工作说明了如何使用药物化学和结构分析可以提供一个合理的基础预测配体诱导的构象变化，一个必要的步骤，对应用基于结构的方法在设计新的RNA或蛋白质结合药物。(C)2003 Elsevier Ltd.保留所有权利。
The targeting of RNA for the design of novel anti-viral compounds has until now proceeded largely without incorporating direct input from structure-based design methodology, partly because of lack of structural data, and complications arising from substrate flexibility. We propose a paradigm to explain the physical mechanism for ligand-induced refolding of trans-activation response element (TAR RNA) from human immunodeficiency virus 1 (HIV-1). Based upon Poisson-Boltzmann analysis of the TAR structure, as bound by a peptide derived from the transcriptional activator protein, Tat, our hypothesis shows that two specific electrostatic interactions are necessary to stabilise the conformation. This result contradicts the belief that a single argininamide residue is responsible for stabilising the TAR fold, as well as the conventional wisdom that electrostatic interactions with RNA are non-specific or dominated by phosphates. We test this hypothesis by using NMR and computational methods to model the interaction of a series of novel inhibitors of the in vitro RNA-binding activities for a peptide derived from Tat. A subset of inhibitors, including the bis-guanidine compound rbt203 and its analogues, induce a conformation in TAR similar to that brought about by the protein. Comparison of the interactions of two of these ligands with the RNA and structure-activity relationships observed within the compound series, confirm the importance of the two specific electrostatic interactions in the stabilisation of the Tat-bound RNA conformation. This work illustrates how the use of medicinal chemistry and structural analysis can provide a rational basis for prediction of ligand-induced conformational change, a necessary step towards the application of structure-based methods in the design of novel RNA or protein-binding drugs. (C) 2003 Elsevier Ltd. All rights reserved.