Purdue University, College of Pharmacy, Medicinal Chemistry and Molecular Pharmacology, 575 W Stadium Ave., West Lafayette, IN 47907, USA.
College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA.
Nucleic Acids Res. 2021 Jun 4;49(10):5905-5915. doi: 10.1093/nar/gkab330.
DNA G-Quadruplexes (G4s) formed in oncogene promoters regulate transcription. The oncogene MYC promoter G4 (MycG4) is the most prevalent G4 in human cancers. However, the most studied MycG4 sequence bears a mutated 3'-residue crucial for ligand recognition. Here, we report a new drug-like small molecule PEQ without a large aromatic moiety that specifically binds MycG4. We determined the NMR solution structures of the wild-type MycG4 and its 2:1 PEQ complex, as well as the structure of the 2:1 PEQ complex of the widely used mutant MycG4. Comparison of the two complex structures demonstrates specific molecular recognition of MycG4 and shows the clear effect of the critical 3'-mutation on the drug binding interface. We performed a systematic analysis of the four available complex structures involving the same mutant MycG4, which can be considered a model system for parallel G4s, and revealed for the first time that the flexible flanking residues are recruited in a conserved and sequence-specific way, as well as unused potential for selective ligand-G4 hydrogen-bond interactions. Our results provide the true molecular basis for MycG4-targeting drugs and new critical insights into future rational design of drugs targeting MycG4 and parallel G4s that are prevalent in promoter and RNA G4s.
DNA G-四链体（G4s）在癌基因启动子中形成，调节转录。癌基因 MYC 启动子 G4（MycG4）是人类癌症中最常见的 G4。然而，研究最多的 MycG4 序列带有一个突变的 3'-残基，对于配体识别至关重要。在这里，我们报告了一种没有大芳香部分的新型类药小分子 PEQ，它可以特异性结合 MycG4。我们确定了野生型 MycG4 及其 2:1 PEQ 复合物的 NMR 溶液结构，以及广泛使用的突变 MycG4 的 2:1 PEQ 复合物的结构。两个复合物结构的比较表明了 MycG4 的特异性分子识别，并显示了关键 3'-突变对药物结合界面的明显影响。我们对涉及相同突变 MycG4 的四个可用复合物结构进行了系统分析，这些结构可以被视为平行 G4 的模型系统，首次揭示了柔性侧翼残基以保守和序列特异性的方式被募集，以及未被利用的用于选择性配体-G4 氢键相互作用的潜力。我们的结果为 MycG4 靶向药物提供了真正的分子基础，并为未来靶向 MycG4 和在启动子和 RNA G4 中普遍存在的平行 G4 的药物的合理设计提供了新的关键见解。
