Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94158 , United States.
Department of Pharmaceutical Chemistry , National and Kapodistrian University of Athens , 15771 Athens , Greece.
J Am Chem Soc. 2018 Nov 14;140(45):15219-15226. doi: 10.1021/jacs.8b06741. Epub 2018 Sep 12.
Water-mediated interactions play key roles in drug binding. In protein sites with sparse polar functionality, a small-molecule approach is often viewed as insufficient to achieve high affinity and specificity. Here we show that small molecules can enable potent inhibition by targeting key waters. The M2 proton channel of influenza A is the target of the antiviral drugs amantadine and rimantadine. Structural studies of drug binding to the channel using X-ray crystallography have been limited because of the challenging nature of the target, with the one previously solved crystal structure limited to 3.5 Å resolution. Here we describe crystal structures of amantadine bound to M2 in the Inward conformation (2.00 Å), rimantadine bound to M2 in both the Inward (2.00 Å) and Inward (2.25 Å) conformations, and a spiro-adamantyl amine inhibitor bound to M2 in the Inward conformation (2.63 Å). These X-ray crystal structures of the M2 proton channel with bound inhibitors reveal that ammonium groups bind to water-lined sites that are hypothesized to stabilize transient hydronium ions formed in the proton-conduction mechanism. Furthermore, the ammonium and adamantyl groups of the adamantyl-amine class of drugs are free to rotate in the channel, minimizing the entropic cost of binding. These drug-bound complexes provide the first high-resolution structures of drugs that interact with and disrupt networks of hydrogen-bonded waters that are widely utilized throughout nature to facilitate proton diffusion within proteins.
水介导的相互作用在药物结合中起着关键作用。在极性功能稀疏的蛋白质部位，小分子方法通常被认为不足以实现高亲和力和特异性。在这里，我们表明小分子可以通过靶向关键水来实现有效的抑制。流感 A 病毒的 M2 质子通道是抗病毒药物金刚烷胺和金刚乙胺的作用靶点。使用 X 射线晶体学研究药物与通道的结合受到目标挑战性的限制，以前解决的晶体结构分辨率仅为 3.5 Å。在这里，我们描述了金刚烷胺结合到 M2 的向内构象（2.00 Å）、金刚乙胺结合到 M2 的向内构象（2.00 Å）和向内构象（2.25 Å）以及金刚烷胺结合到 M2 的螺旋 - 金刚烷胺抑制剂的晶体结构向内构象（2.63 Å）。这些与抑制剂结合的 M2 质子通道的 X 射线晶体结构揭示了铵基团结合到假设稳定质子传导机制中形成的瞬态质子化氢离子的水线位置。此外，金刚烷胺类药物的铵和金刚烷基与通道中的水自由旋转，使结合的熵成本最小化。这些与药物结合的复合物提供了与氢键结合的水分子网络相互作用并破坏的药物的第一个高分辨率结构，这些水分子网络在自然界中被广泛用于促进蛋白质内的质子扩散。
