Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Département de Biologie Structurale Intégrative , Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258) , 1 rue Laurent Fries , 67404 Illkirch Cedex , France.
Institute of Pharmacy , Martin-Luther-Universität Halle-Wittenberg , Wolfgang-Langenbeck-Straße 4 , 06120 Halle/Saale , Germany.
J Med Chem. 2018 Nov 21;61(22):10000-10016. doi: 10.1021/acs.jmedchem.8b01087. Epub 2018 Nov 8.
Metal-dependent histone deacetylases (HDACs) are key epigenetic regulators that represent promising therapeutic targets for the treatment of numerous human diseases. Yet the currently FDA-approved HDAC inhibitors nonspecifically target at least several of the 11 structurally similar but functionally different HDAC isozymes, which hampers their broad usage in clinical settings. Selective inhibitors targeting single HDAC isozymes are being developed, but precise understanding in molecular terms of their selectivity remains sparse. Here, we show that HDAC8-selective inhibitors adopt a L-shaped conformation required for their binding to a HDAC8-specific pocket formed by HDAC8 catalytic tyrosine and HDAC8 L1 and L6 loops. In other HDAC isozymes, a L1-L6 lock sterically prevents L-shaped inhibitor binding. Shielding of the HDAC8-specific pocket by protein engineering decreases potency of HDAC8-selective inhibitors and affects catalytic activity. Collectively, our results unravel key HDAC8 active site structural and functional determinants important for the design of next-generation chemical probes and epigenetic drugs.
金属依赖性组蛋白去乙酰化酶（HDACs）是关键的表观遗传调节剂，它们是治疗许多人类疾病的有前途的治疗靶点。然而，目前 FDA 批准的 HDAC 抑制剂不能特异性地靶向至少 11 种结构相似但功能不同的 HDAC 同工酶中的几种，这限制了它们在临床环境中的广泛应用。目前正在开发针对单个 HDAC 同工酶的选择性抑制剂，但对其选择性的分子术语的精确理解仍然很少。在这里，我们表明 HDAC8 选择性抑制剂采用 L 形构象，这是与由 HDAC8 催化酪氨酸和 HDAC8 L1 和 L6 环形成的 HDAC8 特异性口袋结合所必需的。在其他 HDAC 同工酶中，L1-L6 锁会阻碍 L 形抑制剂的结合。通过蛋白质工程屏蔽 HDAC8 特异性口袋会降低 HDAC8 选择性抑制剂的效力并影响催化活性。总的来说，我们的结果揭示了关键的 HDAC8 活性位点结构和功能决定因素，这些因素对于设计下一代化学探针和表观遗传药物很重要。
