Development of Small Molecules with a Noncanonical Binding Mode to HIV‑1 Trans Activation Response (TAR) RNA

Small molecules that bind to RNA potently and specifically are relatively rare. The study of molecules that bind to the HIV-1 transactivation response (TAR) hairpin, a cis-acting HIV genomic element, has long been an important model system for the chemistry of targeting RNA. Here we report the synthesis, biochemical, and structural evaluation of a series of molecules that bind to HIV-1 TAR RNA. A promising analogue, 15, retained the TAR binding affinity of the initial hit and displaced a Tat-derived peptide with an IC50 of 40 μM. NMR characterization of a soluble analogue, 2, revealed a noncanonical binding mode for this class of compounds. Finally, evaluation of 2 and 15 by selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) indicates specificity in binding to TAR within the context of an in vitro-synthesized 365-nt HIV-1 5′-untranslated region (UTR). Thus, these compounds exhibit a novel and specific mode of interaction with TAR, providing important suggestions for RNA ligand design.能够强效且特异性结合核糖核酸（RNA）的小分子化合物相对稀缺。针对结合HIV-1反式激活应答（TAR）发夹结构——一种顺式作用的HIV基因组元件——的分子研究，长期以来一直是RNA靶向化学领域的重要模型体系。本研究报道了一系列结合HIV-1 TAR核糖核酸（RNA）的小分子的合成、生化及结构表征与评价工作。其中一款极具潜力的类似物15，保留了初始命中化合物结合TAR的亲和力，且能以40 μM的半最大抑制浓度（IC50）置换Tat衍生肽。核磁共振波谱法（Nuclear Magnetic Resonance, NMR）对可溶性类似物2的表征结果显示，该类化合物存在一种非经典的结合模式。最后，通过基于引物延伸的选择性2'-羟基酰化分析（SHAPE）对化合物2和15进行的评估表明：在体外合成的365个核苷酸（nt）长度的HIV-1 5'-非翻译区（UTR）的语境下，二者可特异性结合TAR结构。综上，此类化合物与TAR之间存在一种全新且特异性的相互作用模式，可为RNA配体设计提供重要的指导思路。