Specific Stabilization of <i>c-MYC</i> and <i>c-KIT</i> G-Quadruplex DNA Structures by Indolylmethyleneindanone Scaffolds
作者:K. V. Diveshkumar、Saaz Sakrikar、Frédéric Rosu、S. Harikrishna、Valérie Gabelica、P. I. Pradeepkumar
DOI:10.1021/acs.biochem.6b00120
日期:2016.6.28
Stabilization of G-quadruplex DNA structures by small molecules has emerged as a promising strategy for the development of anticancer drugs. Since G-quadruplex structures can adopt various topologies, attaining specific stabilization of a G-quadruplex topology to halt a particular biological process is daunting. To achieve this, we have designed and synthesized simple structural scaffolds based on an indolylmethyleneindanone pharmacophore, which can specifically stabilize the parallel topology of promoter quadruplex DNAs (c-MYC, c-KIT1, and c-KIT2), when compared to various topologies of telomeric and duplex DNAs. The lead ligands (InEt2 and InPr2) are water-soluble and meet a number of desirable criteria for a small molecule drug. Highly specific induction and stabilization of the c-MYC and c-KIT quadruplex DNAs (ΔT1/2 up to 24 °C) over telomeric and duplex DNAs (ΔT1/2 ∼ 3.2 °C) by these ligands were further validated by isothermal titration calorimetry and electrospray ionization mass spectrometry experiments (Ka ∼ 105 to 106 M–1). Low IC50 (∼2 μM) values were emerged for these ligands from a Taq DNA polymerase stop assay with the c-MYC quadruplex forming template, whereas the telomeric DNA template showed IC50 values >120 μM. Molecular modeling and dynamics studies demonstrated the 5′- and 3′-end stacking modes for these ligands. Overall, these results demonstrate that among the >1000 quadruplex stabilizing ligands reported so far, the indolylmethyleneindanone scaffolds stand out in terms of target specificity and structural simplicity and therefore offer a new paradigm in topology specific G-quadruplex targeting for potential therapeutic and diagnostic applications.
小分子稳定 G 型四联 DNA 结构已成为开发抗癌药物的一种前景广阔的策略。由于 G-四链式结构可以采用多种拓扑结构,因此实现特定 G-四链式拓扑结构的稳定以阻止特定生物过程是一项艰巨的任务。为此,我们设计并合成了基于吲哚亚甲基茚酮药理的简单结构支架,与端粒和双链 DNA 的各种拓扑结构相比,它能特异性地稳定启动子四重 DNA(c-MYC、c-KIT1 和 c-KIT2)的平行拓扑结构。先导配体(InEt2 和 InPr2)具有水溶性,符合小分子药物的一系列理想标准。通过等温滴定量热法和电喷雾电离质谱实验(Ka ∼ 105 至 106 M-1),进一步验证了这些配体对 c-MYC 和 c-KIT 四链 DNA 的高特异性诱导和稳定作用(ΔT1/2 高达 24 °C),而对端粒和双链 DNA 的诱导和稳定作用(ΔT1/2 ∼ 3.2 °C)则没有影响。在以 c-MYC 四联体为模板的 Taq DNA 聚合酶停止实验中,这些配体的 IC50 值很低(2 μM),而端粒 DNA 模板的 IC50 值则大于 120 μM。分子建模和动力学研究证明了这些配体的 5′端和 3′端堆叠模式。总之,这些结果表明,在迄今报道的 1000 多种四链稳定配体中,吲哚亚甲基茚满酮支架在靶向特异性和结构简单性方面脱颖而出,因此为拓扑特异性 G- 四链靶向提供了一种新的范例,具有潜在的治疗和诊断应用价值。