State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University, Beijing, 100191, China.
Eur J Med Chem. 2019 Nov 15;182:111656. doi: 10.1016/j.ejmech.2019.111656. Epub 2019 Aug 31.
Chemical probes of epigenetic 'readers' of histone post-translational modifications (PTMs) have become powerful tools for mechanistic and functional studies of their target proteins in physiology and pathology. However, only limited 'reader' probes have been developed, which restricted our understanding towards these macromolecules and their roles in cells or animals. Here, we reported a structure-guided approach to develop and characterize benzo [d]oxazol-2(3H)-one analogs as the first potent and selective small-molecule inhibitors of chromodomain Y-like (CDYL), a histone methyllysine reader protein. The binding conformation between the chromodomain of CDYL and the modified peptidomimetics was studied via molecular docking and dynamic simulations, facilitating subsequent virtual screening of tens of hits from Specs chemical library validated by SPR technique (K values: from 271.1 μM to 5.4 μM). Further design and synthesis of 43 compounds helped to interpret the structure-activity relationship (SAR) that lead to the discovery of novel small-molecule inhibitors of CDYL. Compound D03 (K: 0.5 μM) was discovered and showed excellent selectivity among other chromodomain proteins, including CDYL2 (>140 folds), CDY1 (no observed binding) and CBX7 (>32 folds). Moreover, we demonstrated that D03 engaged with endogenous CDYL in a dose-dependent manner, and perturbed the recruitment of CDYL onto chromatin, resulting in transcriptional derepression of its target genes. Finally, the results showed that D03 promoted the development and branching of neurodendrites by inhibiting CDYL in hippocampal and cortical cultured neurons. This study not only discovers the first selective small-molecule inhibitors of CDYL, but provids a new chemical tool to intervene the dynamic nature of bio-macromolecules involved in epigenetic mechanism.
化学探针可用于研究组蛋白翻译后修饰（PTMs）的表观遗传学“读取器”，这已成为研究其在生理和病理条件下靶蛋白的机制和功能的有力工具。然而，目前仅开发了有限的“读取器”探针，这限制了我们对这些大分子及其在细胞或动物中作用的理解。在这里，我们报道了一种基于结构的方法，用于开发和表征苯并 [d] 恶唑-2(3H)-酮类似物，作为第一个有效的、选择性的组蛋白甲基赖氨酸读取器蛋白 chromodomain Y-like（CDYL）的小分子抑制剂。通过分子对接和动态模拟研究了 CDYL 的 chromodomain 与修饰肽模拟物之间的结合构象，随后通过 SPR 技术（K 值：从 271.1μM 到 5.4μM）验证了来自 Specs 化学文库的数十个命中物的虚拟筛选。进一步设计和合成 43 种化合物有助于解释结构-活性关系（SAR），从而发现了 CDYL 的新型小分子抑制剂。化合物 D03（K：0.5μM）被发现，对其他 chromodomain 蛋白（包括 CDYL2（>140 倍）、CDY1（无观察到结合）和 CBX7（>32 倍））具有优异的选择性。此外，我们证明 D03 以剂量依赖的方式与内源性 CDYL 结合，并干扰 CDYL 与染色质的募集，导致其靶基因的转录去抑制。最后，结果表明，D03 通过抑制海马和皮质培养神经元中的 CDYL 促进神经树突的发育和分支。这项研究不仅发现了第一个选择性的 CDYL 小分子抑制剂，而且为干预涉及表观遗传机制的生物大分子的动态性质提供了新的化学工具。
