Structure-based optimization of FDA-approved drug methylene blue as a c-myc G-quadruplex DNA stabilizer
Structure-based optimization of FDA-approved drug methylene blue as a c-myc G-quadruplex DNA stabilizer
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DOI：
10.1016/j.biochi.2011.02.013
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发表时间：
2011-06-01
期刊：
影响因子：
3.9
通讯作者：
Ma, Dik-Lung
中科院分区：
文献类型：
--
作者：
Chan, Daniel Shiu-Hin;Yang, Hui;Ma, Dik-Lung
G-四链体是非典型的 DNA 二级结构，推测存在于人类基因组中癌基因的启动子区域。靶向启动子 G 四链体结构来抑制癌基因转录是一种潜在的抗癌策略。在这里，我们使用高通量虚拟筛选来鉴定 FDA 批准的药物亚甲蓝 (MB) 作为结合 c-myc 癌基因 G-四链体 DNA 的有前途的支架。基于MB与c-myc G-四链体的分子对接分析，我们设计并筛选了50个含有可与G-四链体凹槽相互作用的侧链的MB衍生物。作为概念验证，合成了得分最高的化合物，并使用 FID 测定研究了与 c-myc G-四联体的相互作用。结果表明，与已知的G-四链体结合配体结晶紫相比，亚甲基蓝衍生物6a-c能够以更大的结合亲和力与c-myc G-四链体结合。从 FID 测定中鉴定出的最有效的化合物 6b 的活性，作为聚合酶驱动 DNA 延伸的抑制剂，使用 PCR 停止测定进行检查，并与母体化合物亚甲蓝的活性进行比较。 PCR终止测定的结果表明，与母体化合物相比，侧链的添加提高了衍生物作为抑制剂的活性。 MB 衍生物 6b 比双链 DNA 和其他细胞生物学模型对 c-myc G-四链体具有高度选择性，并且与母体化合物 MB 相比，对人肝癌细胞表现出更高的细胞毒性。分别使用紫外-可见光谱和质谱法进行生物学相关的 G-四链体。 MB 衍生物 6b 可以在无细胞和 (C) 2011 Elsevier Masson SAS 中诱导或稳定 c-myc G-四联体形成。版权所有。
G-quadruplexes are non-canonical DNA secondary structures putatively present in the promoter regions of oncogenes in the human genome. The targeting of promoter G-quadruplex structures to repress oncogene transcription represents a potential anticancer strategy. Here, we have used high-throughput virtual screening to identify FDA-approved drug methylene blue (MB) as a promising scaffold for binding the c-myc oncogene G-quadruplex DNA. Based on molecular docking analysis of MB to the c-myc G-quadruplex, we designed and screened 50 MB derivatives containing side chains that could interact with the G-quadruplex grooves. As a proof-of-concept, the highest-scoring compounds were synthesized and the interactions with the c-myc G-quadruplex were investigated using the FID assay. The results showed that the methylene blue derivatives 6a-c were able to bind to the c-myc G-quadruplex with greater binding affinity compared to the known G-quadruplex binding ligand, crystal violet. The activity of the most potent compound identified from the FID assay, 6b, as an inhibitor for polymerase-drive DNA extension was examined using a PCR-stop assay and compared against that of the parent compound methylene blue. The results of the PCR-stop assay showed that the addition of the side chain improved the activity of the derivatives as an inhibitor compared to the parent compound. The MB derivative 6b was shown to be highly selective towards c-myc G-quadruplex over double-stranded DNA and other cellular biological models, and displayed higher cytoxicity against human hepatocarcinoma cells compared to the parent compound, MB. biologically relevant G-quadruplexes using UV-visible spectroscopy and mass spectrometry, respectively. The MB derivative 6b could induce or stabilize c-myc G-quadruplex formation in both cell-free and (C) 2011 Elsevier Masson SAS. All rights reserved.