1,5,18,22,25,29,36,40-Octazaoctacyclo[38.2.2.222,25.231,34.15,13.110,18.07,12.011,16]pentaconta-7,9,11(16),12,14,31(46),32,34(45)-octaene-6,17,30,35,49,50-hexone | 1606992-16-8

• 分子结构分类: 有机化合物 - 有机杂环化合物 - 吡啶及其衍生物
• 英文名称: 1,5,18,22,25,29,36,40-Octazaoctacyclo[38.2.2.222,25.231,34.15,13.110,18.07,12.011,16]pentaconta-7,9,11(16),12,14,31(46),32,34(45)-octaene-6,17,30,35,49,50-hexone
• 英文别名: 1,5,18,22,25,29,36,40-octazaoctacyclo[38.2.2.222,25.231,34.15,13.110,18.07,12.011,16]pentaconta-7,9,11(16),12,14,31(46),32,34(45)-octaene-6,17,30,35,49,50-hexone
• CAS: 1606992-16-8
• 化学式: C₄₂H₅₀N₈O₆
• 分子量: 762.909
• InChiKey: MQOXROULTDDCMM-UHFFFAOYSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  2.3
• 重原子数：
  56
• 可旋转键数：
  0
• 环数：
  23.0
• sp3杂化的碳原子比例：
  0.48
• 拓扑面积：
  146
• 氢给体数：
  2
• 氢受体数：
  10

反应信息

• 作为产物：
  描述：

  对苯二甲酸 、 N,N’-bis[[4-(3-aminopropyl)piperazinyl]propyl]naphthalene-1,4,5,8-tetracarboxylic acid diimide 在 benzotriazol-1-yloxyl-tris-(pyrrolidino)-phosphonium hexafluorophosphate 、 1-羟基苯并三唑 、 三乙胺 作用下， 以 氯仿 为溶剂， 反应 48.0h， 以10%的产率得到1,5,18,22,25,29,36,40-Octazaoctacyclo[38.2.2.222,25.231,34.15,13.110,18.07,12.011,16]pentaconta-7,9,11(16),12,14,31(46),32,34(45)-octaene-6,17,30,35,49,50-hexone
  参考文献：
  名称：

  Thermodynamics and kinetic studies in the binding interaction of cyclic naphthalene diimide derivatives with double stranded DNAs

  摘要：

  Previously, we reported our investigations of the interaction between a cyclic naphthalene diimide derivative (cNDI 1) and double stranded DNA (dsDNA) (Bioorg. Med. Chem. 2014, 22, 2593). Here, we report the synthesis of the novel cNDI 2, which has shorter linker chains than cNDI 1. We performed comparative investigations of the interactions of both cNDI 1 and cNDI 2 with different types of dsDNA, including analysis of their thermodynamics and kinetics. Interactions between the cNDIs and calf thymus DNA (CT-DNA), poly[d(A-T)](2), or poly[d(G-C)](2) were explored by physicochemical and biochemical methods, including UV-Vis spectroscopy, circular dichroism (CD) spectroscopy, stopped-flow kinetics, and a topoisomerase I assay. Upon addition of cNDIs to CT-DNA, the existence of an induced CD signal at approximately the wavelength of the naphthalene diimide chromophore and unwinding of the DNA duplex, as detected by the topoisomerase I assay, revealed that cNDIs bound to the DNA duplex. As indicated by the steric constraint in the formation of the complex, bis-threading intercalation was the more favorable binding mode. UV-Vis spectroscopic titration of the cNDIs with DNA duplexes showed affinities on the order of 10(5)-10(6) M-1, with a stoichiometry of one cNDI molecule per four DNA base pairs. Thermodynamic parameters (Delta G, Delta H, and Delta S) based on the van't Hoff equation indicated that exothermic and entropy-dependent hydrophobic interactions played a major role in the reaction. Stopped-flow association and dissociation analysis showed that cNDI interactions with poly[d(G-C)](2) were more stable and had a slower dissociation rate than their interactions with poly[d(A-T)](2) and CT-DNA. Measurement of ionic strength indicated that electrostatic attraction is also an important component of the interaction between cNDIs and CT-DNA. Because of its longer linker chain, cNDI 1 showed higher binding selectivity, a more entropically favorable interaction, and much slower dissociation from dsDNA than cNDI 2. (C) 2015 Elsevier Ltd. All rights reserved.

  DOI：

  10.1016/j.bmc.2015.05.046

文献信息

• Thermodynamics and kinetic studies in the binding interaction of cyclic naphthalene diimide derivatives with double stranded DNAs
  作者：Md. Monirul Islam、Satoshi Fujii、Shinobu Sato、Tatsuo Okauchi、Shigeori Takenaka

  DOI：10.1016/j.bmc.2015.05.046

  日期：2015.8

  Previously, we reported our investigations of the interaction between a cyclic naphthalene diimide derivative (cNDI 1) and double stranded DNA (dsDNA) (Bioorg. Med. Chem. 2014, 22, 2593). Here, we report the synthesis of the novel cNDI 2, which has shorter linker chains than cNDI 1. We performed comparative investigations of the interactions of both cNDI 1 and cNDI 2 with different types of dsDNA, including analysis of their thermodynamics and kinetics. Interactions between the cNDIs and calf thymus DNA (CT-DNA), poly[d(A-T)](2), or poly[d(G-C)](2) were explored by physicochemical and biochemical methods, including UV-Vis spectroscopy, circular dichroism (CD) spectroscopy, stopped-flow kinetics, and a topoisomerase I assay. Upon addition of cNDIs to CT-DNA, the existence of an induced CD signal at approximately the wavelength of the naphthalene diimide chromophore and unwinding of the DNA duplex, as detected by the topoisomerase I assay, revealed that cNDIs bound to the DNA duplex. As indicated by the steric constraint in the formation of the complex, bis-threading intercalation was the more favorable binding mode. UV-Vis spectroscopic titration of the cNDIs with DNA duplexes showed affinities on the order of 10(5)-10(6) M-1, with a stoichiometry of one cNDI molecule per four DNA base pairs. Thermodynamic parameters (Delta G, Delta H, and Delta S) based on the van't Hoff equation indicated that exothermic and entropy-dependent hydrophobic interactions played a major role in the reaction. Stopped-flow association and dissociation analysis showed that cNDI interactions with poly[d(G-C)](2) were more stable and had a slower dissociation rate than their interactions with poly[d(A-T)](2) and CT-DNA. Measurement of ionic strength indicated that electrostatic attraction is also an important component of the interaction between cNDIs and CT-DNA. Because of its longer linker chain, cNDI 1 showed higher binding selectivity, a more entropically favorable interaction, and much slower dissociation from dsDNA than cNDI 2. (C) 2015 Elsevier Ltd. All rights reserved.