Efficient Plasmid DNA Cleavage by Copper(II) Complexes of 1,4,7-Triazacyclononane Ligands Featuring Xylyl-Linked Guanidinium Groups

Three new metal-coordinating ligands, L1, L2, and L3, have been prepared by appending o-, m-, and p-xylylguanidine pendants, respectively, to one of the nitrogen atoms of 1,4,7-triazacyclononane (tacn). The copper(II) complexes of these ligands are able to accelerate cleavage of the P–O bonds within the model phosphodiesters bis(p-nitrophenyl)phosphate (BNPP) and [2-(hydroxypropyl)-p-nitrophenyl]phosphate (HPNPP), as well as supercoiled pBR 322 plasmid DNA. Their reactivity toward BNPP and HPNPP is not significantly different from that of the nonguanidinylated analogues, [Cu(tacn)(OH2)2]2+ and [Cu(1-benzyl-tacn)(OH2)2]2+, but they cleave plasmid DNA at considerably faster rates than either of these two complexes. The complex of L1, [Cu(L1H+)(OH2)2]3+, is the most active of the series, cleaving the supercoiled plasmid DNA (form I) to the relaxed circular form (form II) with a kobs value of (2.7 ± 0.3) × 10–4 s–1, which corresponds to a rate enhancement of 22- and 12-fold compared to those of [Cu(tacn)(OH2)2]2+ and [Cu(1-benzyl-tacn)(OH2)2]2+, respectively. Because of the relatively fast rate of plasmid DNA cleavage, an observed rate constant of (1.2 ± 0.5) × 10–5 s–1 for cleavage of form II DNA to form III was also able to be determined. The X-ray crystal structures of the copper(II) complexes of L1 and L3 show that the distorted square-pyramidal copper(II) coordination sphere is occupied by three nitrogen atoms from the tacn ring and two chloride ions. In both complexes, the protonated guanidinium pendants extend away from the metal and form hydrogen bonds with solvent molecules and counterions present in the crystal lattice. In the complex of L1, the distance between the guanidinium group and the copper(II) center is similar to that separating the adjacent phosphodiester groups in DNA (ca. 6 Å). The overall geometry of the complex is also such that if the guanidinium group were to form charge-assisted hydrogen-bonding interactions with a phosphodiester group, a metal-bound hydroxide would be well-positioned to affect the nucleophilic attack on the neighboring phosphodiester linkage. The enhanced reactivity of the complex of L1 at neutral pH appears to also be, in part, due to the relatively low pKa of 6.4 for one of the coordinated water molecules.

本研究成功合成了三种新型金属配位配体L1、L2和L3，分别通过将邻（o-）、间（m-）、对（p-）二甲苯胍侧链连接至1,4,7-三氮杂环壬烷（1,4,7-triazacyclononane，tacn）的其中一个氮原子上制得。这些配体与铜(II)形成的配合物，可催化模型磷酸二酯类底物双(对硝基苯基)磷酸酯（bis(p-nitrophenyl)phosphate，BNPP）、[2-(羟丙基)-对硝基苯基]磷酸酯（[2-(hydroxypropyl)-p-nitrophenyl]phosphate，HPNPP）以及超螺旋pBR 322质粒DNA的P-O键断裂。它们对BNPP与HPNPP的催化活性，与非胍基化的类似物[Cu(tacn)(OH₂)₂]²⁺和[Cu(1-苄基-tacn)(OH₂)₂]²⁺并无显著差异，但对质粒DNA的切割速率远高于这两种对照配合物。其中L1的铜(II)配合物[Cu(L1H⁺)(OH₂)₂]³⁺为本系列中活性最高的成员，可将超螺旋质粒DNA（I型）切割为松弛环状DNA（II型），表观速率常数kobs为(2.7 ± 0.3) × 10⁻⁴ s⁻¹，相较于[Cu(tacn)(OH₂)₂]²⁺和[Cu(1-苄基-tacn)(OH₂)₂]²⁺，速率提升分别达22倍和12倍。由于该配合物切割质粒DNA的速率较快，我们还测定了II型DNA进一步切割为III型DNA的表观速率常数，其值为(1.2 ± 0.5) × 10⁻⁵ s⁻¹。L1和L3的铜(II)配合物的X射线单晶衍射结构显示，其扭曲的四方锥配位环境由tacn环上的三个氮原子以及两个氯离子共同占据。在两种配合物中，质子化的胍基侧链均远离金属中心，并与晶格中的溶剂分子及抗衡离子形成氢键。在L1的铜(II)配合物中，胍基与铜(II)中心的间距与DNA中相邻磷酸二酯基团的间距（约6 Å）相近。该配合物的整体空间构型也满足：若胍基与磷酸二酯基团形成电荷辅助氢键相互作用，则金属配位的氢氧根将处于可对邻近磷酸二酯键进行亲核进攻的最优位置。该系列配合物在中性pH条件下活性提升的部分原因，也可归结为其中一个配位水分子的pKa较低（仅为6.4）。