DNA cleavage induced by [Cu(L)x(NO3)2] (L=2,2′-dipyridylamine, 2,2′-bipyridine, dipicolylamine, x=1 or 2): Effect of the ligand structure

Probing DNA-Cleavage Efficiencies of Copper(II) Complexes: A Computational Perspective

Theoretical studies on DNA-cleavage efficiencies of Cu(II) complexes 1-3 were carried out using density functional theory (DFT). The optimized Cu(II) complexes were allowed to bind to glutathiones (GSH) and ascorbic acids (VC) by the docking program so that corresponding docking structures can be obtained. To predict DNA-cleavage efficiencies, the docking structures of Cu(II) complexes with GSH and VC were further optimized by DFT. The activation energies of electrons from GSH to complexes, the redox potentials of these complexes, and binding energies of these complexes with GSH and VC were calculated. The efficiencies of complexes cleaving DNA were predicted and found to be in agreement with the experimental results. Finally, three occupied molecular orbitals of docking structures (GSH-complexes) were analyzed, and the DNA-cleavage abilities of complexes were also explained by the electron distribution on the three occupied orbitals. This work has important implications understanding the DNA-cleavage mechanism of Cu(II) complexes, which might be helpful for designing novel anticancer Cu(II) complexes for the future.

Ditopic binuclear copper(II) complexes for DNA cleavage

Herein we present the synthesis of two ligands containing two di(2-picolyl)amine (DPA) units linked by either a 1,1'-(pyridine-2,6-diyl)bis(3-ethylurea) (L1) or a 1,1'-(1,3-phenylene)bis(3-ethylurea) (L2) spacer. The corresponding binuclear Cu^II and Zn^II complexes were prepared and isolated. The X-ray structures of the L1 ligand and the [Cu₂L1Cl₂]²⁺ complex evidence an unusual cis/trans conformation of one of the urea groups stabilized by an intramolecular hydrogen bond with the nitrogen atom of the pyridyl spacer. The Cu^II complexes form rather strong ternary complexes with phosphorylated anions. The [Cu₂L1]⁴⁺ complex presents a rather high affinity for pyrophosphate (logK₁₁ = 8.19 at pH 7, 25 °C), while [Cu₂L2]⁴⁺ stands out because of its strong binding to AMP^2- (logK₁₁ = 9.3 at pH 7, 25 °C). The interaction of the Cu^II complexes with deoxyribonucleic acid from calf thymus (ct-DNA) was monitored using circular dichroism (CD) and luminescence spectroscopies. These studies revealed a quite strong interaction of the complexes with ct-DNA (K_b = (6.4 ± 0.7) × 10³ for [Cu₂L1]⁴⁺ and K_b = (6.3 ± 1.0) × 10³ for [Cu₂L2]⁴⁺). Competition experiments carried out in the presence of methyl green and BAPPA (N¹,N³-Bis(4-amidinophenyl)propane-1,3-diamine) as major and minor groove competitors, respectively, confirm that the interaction of both complexes with DNA takes place through the minor groove, in agreement with docking studies. The [Cu₂L2]⁴⁺ complex is quite efficient in promoting the cleavage of the double-stranded pUC19 plasmid DNA, by favoring the conversion of the supercoiled form to the nicked form following a hydrolytic mechanism.

Theoretical study on the DNA interaction properties of copper(II) complexes

Theoretical studies on DNA-cleavage and DNA-binding properties of a series of Cu(II) complexes [Cu(bimda)(diimine)] 1-5 have been carried out by density functional theory (DFT). The optimized structures of Cu(II) complexes were docked into parallel, antiparallel and mixed G-quadruplexes, with which the binding energies of complexes 1-5 were obtained. The cytotoxicities of these complexes can be predicted preliminarily by the binding energies. To explore the energy changes of Cu(II) complexes in duplex DNA, the optimized structures of these complexes were docked into the duplex DNA, and the obtained docking models were further optimized using QM/MM method. The DNA-cleavage abilities of complexes 1-5 can be predicted accurately and explained reasonably by the computed intra-molecular reorganization energies of these complexes. This work reported here has implications for the understanding of the interaction Cu(II) complexes with the DNA, which might be helpful for the future directing the design of novel anticancer Cu(II) complexes.

Oxidative Assets Toward Biomolecules and Cytotoxicity of New Oxindolimine-Copper(II) and Zinc(II) Complexes

A new oxindolimine ligand derived from isatin (1H-indole-2,3-dione) and 2-aminomethylbenzimidazole was synthesized, leading to two novel complexes after metalation with copper(II) perchlorate or zinc(II) chloride, [Cu(isambz)2](ClO4)2 (complex 1) and [Zn(isambz)Cl2] (complex 2). This new ligand was designed as a more lipophilic compound, in a series of oxindolimine–metal complexes with antitumor properties, having DNA, mitochondria, and some proteins, such as CDK1 kinase and topoisomerase IB, as key targets. The new complexes had their reactivity to human serum albumin (HSA) and DNA, and their cytotoxicity toward tumor cells investigated. The binding to CT-DNA was monitored by circular dichroism (CD) spectroscopy and fluorescence measurements using ethidium bromide in a competitive assay. Consequent DNA cleavage was verified by gel electrophoresis with complex 1, in nmolar concentrations, with formation of linear DNA (form III) after 60 min incubation at 37 °C, in the presence of hydrogen peroxide, which acts as a reducing agent. Formation of reactive oxygen species (ROS) was observed, monitored by spin trapping EPR. Interaction with HSA lead to α-helix structure disturbance, and formation of a stable radical species (HSA–Tyr·) and carbonyl groups in the protein. Despite showing oxidative ability to damage vital biomolecules such as HSA and DNA, these new complexes showed moderate cytotoxicity against hepatocellular carcinoma (HepG2) and neuroblastoma (SHSY5Y) cells, similarly to previous compounds in this series. These results confirm DNA as an important target for these compounds, and additionally indicate that oxidative damage is not the leading mechanism responsible for their cytotoxicity. Additionally, this work emphasizes the importance of ligand characteristics and of speciation in activity of metal complexes.

Oxidative DNA cleavage by Cu(II) complexes: Effect of periphery substituent groups

A series of structurally-related [Cu(R-benzyl-dipicolylamine)(NO3)2] complexes, where R=methoxy- (1), methyl- (2), H- (3), fluoro- (4), and nitro-group (5), were synthesized, and their activity on DNA cleavage was investigated by linear dichroism (LD) and electrophoresis. The addition of a benzyl group to the dipicolylamine ligand of the [Cu(dipicolylamine)(NO3)2] complex (A), i.e., the [Cu(benzyl-dipicolylamine)(NO3)2] complex (3), caused significant enhancement in the efficiency of oxidative cleavage of both super-coiled (sc) and double stranded (ds) DNA, as evidenced by the electrophoresis pattern and faster decrease in the LD intensity at 260nm. The efficiency in DNA cleavage was also altered with further modifications of the benzyl group by the introduction of various substituents at the para-position. The cleavage efficiency appeared to be the largest when the methyl group was attached. The order of efficiency in DNA cleavage was methyl>methoxy≈H>fluoro≈nitro group. When an electron-withdrawing group was introduced, the cleavage efficiency decreased remarkably. The reactive oxygen species involved in the cleavage process were the superoxide radical and singlet oxygen. A possible mechanism for this variation in the DNA cleavage efficiency was proposed.

Synthesis, DNA binding profile and DNA cleavage pathway of divalent metal complexes

Divalent metal complexes of dipyridylamine ligand with an anthracene moiety induced considerable oxidative DNA cleavage in the presence hydrogen peroxide and dioxygen.

Targeted water soluble copper–tetrazolate complexes: interactions with biomolecules and catecholase like activities

Two new copper–tetrazolate complexes are synthesized and their interaction with DNA, bovine serum albumin (BSA) and catecholase like activity are explored. Interactions of the complexes with DNA are also investigated using DFT.

Lanthanide-Based Polymers with Charged Ligand Backbones: Triple-Stranded Chain Structures and their DNA Cleavage Studies

Four rare-earth metal complexes, [Ln(Ccbp)3(H2O)3]n (Ln = La (1), Ce (2), Pr (3) and Nd (4)) are synthesised from the ligand H2CcbpBr (H2CcbpBr = 4-carboxy-1-(4-carboxybenzyl)pyridinium bromide) and the respective lanthanide metal ions. Complexes 1–4 are isostructural in that every three Ccbp– ligands juxtapose two Ln3+ ions in a monodentate coordination mode to form triple-stranded one-dimensional chain structures. Each central Ln3+ atom further associates with three H2O molecules, furnishing a monocapped square-antiprism geometry. Agarose gel electrophoresis studies indicate that 1–4 are capable of cleaving DNA in the presence of H2O2, most probably via an oxidative cleavage mechanism. Complexes 1 and 2 exhibited catalytic efficiencies (kmax/KM) of 37.69 and 34.11 h–1 mM–1, and are approx. 15- and 20-fold more effective than those of complexes 3 (kmax/KM = 1.75 h–1 mM–1) and 4 (kmax/KM = 2.21 h–1 mM–1).

Efficient hydrolytic cleavage of plasmid DNA by chloro-cobalt(II) complexes based on sterically hindered pyridyl tripod tetraamine ligands: synthesis, crystal structure and DNA cleavage

Four new cobalt(ii) complexes [Co(6-MeTPA)Cl]ClO4/PF6 (2/2a), [Co(6-Me2TPA)Cl]ClO4/PF6 (3/3a), [Co(BPQA)Cl]ClO4/PF6 (4/4a) and [Co(BQPA)Cl]ClO4/PF6 (5/5a) as well as [Co(TPA)Cl]ClO4 (1) where TPA = tris(2-pyridylmethyl)amine, 6-MeTPA = ((6-methyl-2-pyridyl)methyl)bis(2-pyridylmethyl)amine, 6-Me2TPA = bis(6-methyl-2-pyridyl)methyl)-(2-pyridylmethyl)amine, BPQA = bis(2-pyridylmethyl)-(2-quinolylmethyl)-amine and BQPA = bis(2-quinolylmethyl)-(2-pyridylmethyl)amine were synthesized and structurally characterized. Single crystal X-ray crystallography confirmed the distorted trigonal bipyramidal geometries of complexes 2a-5a. Spectrophotometric titrations and conductivity measurements of the complexes in the CH3CN-H2O mixture showed that the chloro complexes exist in equilibrium with the corresponding hydrolyzed aqua species, [Co(L)(H2O)](2+). The pKa values of the coordinated H2O in aqua complexes vary from 8.4 to 8.7 (37 °C). The interactions of the complexes (1-5) with DNA have been investigated at pH = 7.0 and 9.0 (10 mM Tris-HCl buffer) and 37 °C where very high catalytic cleavage was observed. Under pseudo Michaelis-Menten kinetic conditions, the catalytic rate constants, kcat, decrease in the order 4>2>5>1>3. At pH 7.0 (10 mM Tris-HCl buffer) and 37 °C, the kcat value for complex 4 (6.02 h(-1)), where [Co(BPQA)(H2O)](2+) is the major species, corresponds to 170 million rate enhancement over the non-catalyzed DNA. Electrophoretic experiments conducted in the presence and absence of radical scavengers (DMSO, KI, NaN3) ruled out the oxidative mechanistic pathway of the reaction and suggested that the hydrolytic mechanism is the preferred one. This finding was in agreement with the observed increase in the kcat values at pH 9.0 compared to the corresponding values at pH 7.0 as a result of the increased concentration of the reactive hydroxo species, [Co(L)(OH)](+). The reactivity of the synthesized complexes in catalyzing the DNA cleavage is discussed in relation to the steric effect imposed by the coordinated pyridyl ligand around the central cobalt(ii) center.