Instituto de Investigación Viña Giner, Universidad Católica de Valencia, C/Quevedo 2, 46001 Valencia, Spain.
Biopolymers. 2012 Dec;97(12):974-87. doi: 10.1002/bip.22114.
The bisnaphthalimide cytotoxic agent elinafide exhibits a mixed DNA binding mode including groove-association and intercalation. We have compared the interaction of elinafide and two bisnaphthalimide analogues with various natural and modified DNA sequences using solution NMR and UV-melting methods and surface plasmon resonance (SPR) experiments at different pH conditions. The combined data obtained with these techniques established a high-affinity binding mode comprising intercalation and strong electrostatic contacts with guanine bases in the major groove, and a weaker interaction with A·T pairs likely involving groove association. However, the SPR binding constants and the NMR and UV-melting binding parameters responded differently to variations in DNA bases and ligand intercalating moieties. The rates and equilibrium constants determined by SPR clearly responded to changes in pH and DNA groove composition, but were rather insensitive to alterations in drug rings and DNA bases affecting the intercalation process. Conversely, the intermolecular stacking interactions detected by NMR and the ligand-induced thermal stabilizations measured by UV depended on both sets of factors and were controlled by the sequence-dependent properties of the DNA helices, indicating that these data were modulated by naphthalimide stacking in addition to groove association. A two-step binding process where a groove-bound state is required prior to intercalation is proposed as an explanation for these observations. These findings may be useful for studying other classes of DNA- and RNA-binding drugs, which frequently combine groove-binding and stacking moieties.
双萘嵌苯类细胞毒剂依利那非显示出一种混合的 DNA 结合模式，包括沟结合和嵌入。我们使用溶液 NMR 和 UV 融解方法以及不同 pH 条件下的表面等离子体共振（SPR）实验比较了依利那非和两种双萘嵌苯类似物与各种天然和修饰的 DNA 序列的相互作用。这些技术的综合数据确定了一种高亲和力的结合模式，包括嵌入和与大沟中鸟嘌呤碱基的强静电接触，以及与 A·T 对的较弱相互作用，可能涉及沟结合。然而，SPR 结合常数和 NMR 和 UV 融解的结合参数对 DNA 碱基和配体嵌入部分的变化有不同的响应。SPR 确定的速率和平衡常数清楚地响应 pH 和 DNA 沟组成的变化，但对影响嵌入过程的药物环和 DNA 碱基的改变相当不敏感。相反，通过 NMR 检测到的分子间堆积相互作用和通过 UV 测量的配体诱导的热稳定性依赖于这两组因素，并受 DNA 螺旋的序列依赖性特性控制，表明这些数据除了沟结合外还受到萘嵌苯堆积的调节。提出了一个两步结合过程，其中需要一个沟结合态才能进行嵌入，以解释这些观察结果。这些发现可能对研究其他类 DNA 和 RNA 结合药物有用，这些药物通常结合沟结合和堆积部分。
