Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.
ACS Chem Biol. 2011 Aug 19;6(8):857-64. doi: 10.1021/cb200082d. Epub 2011 Jun 15.
Programmed -1 translational frameshifting is an essential event in the replication cycle of HIV. Frameshifting is required for expression of the viral Pol proteins, and drug-like molecules that target this process may inhibit HIV replication. A small molecule stimulator of HIV-1 frameshifting and inhibitor of viral replication, DB213 (RG501), was previously discovered from a high-throughput screen. However, the mechanistic basis for this compound's effects was unknown, and to date no structural information exists for small molecule effectors of frameshifting. Here, we investigate the binding of DB213 to the frameshift site RNA and have determined the structure of this complex by NMR. Binding of DB213 stabilizes the RNA and increases its melting temperature by 10 °C. The ligand binds to a primary site on the RNA stem-loop, although nonspecific interactions are also detected. The compound binds in the major groove and spans a distance of 9 base pairs. DB213 hydrogen bonds to phosphate groups on opposite sides of the major groove and alters the conformation of a conserved GGA bulge in the RNA. This study may provide a starting point for structure-based optimization of compounds targeting the HIV-1 frameshift site RNA.
-1 编码框架移码是 HIV 复制周期中的一个重要事件。框架移码是病毒 Pol 蛋白表达所必需的，针对该过程的类似药物的分子可能会抑制 HIV 的复制。先前从高通量筛选中发现了一种 HIV-1 框架移码的小分子刺激剂和病毒复制抑制剂 DB213（RG501）。然而，该化合物作用的机制基础尚不清楚，迄今为止，尚无框架移码小分子效应物的结构信息。在这里，我们研究了 DB213 与框架移位位点 RNA 的结合，并通过 NMR 确定了该复合物的结构。DB213 的结合稳定了 RNA，并将其熔点提高了 10°C。配体结合到 RNA 茎环的主要位点上，尽管也检测到非特异性相互作用。该化合物结合在主沟中，跨越 9 个碱基对。DB213 与主沟相对侧的磷酸基团形成氢键，并改变 RNA 中保守的 GGA 凸起的构象。这项研究可能为基于结构的针对 HIV-1 框架移位位点 RNA 的化合物的优化提供起点。
