Targeting topoisomerase II with the chiral DNA-intercalating ruthenium(II) polypyridyl complexes

Many antitumor drugs act as topoisomerase inhibitors, and the inhibitions are usually related to DNA binding. Here we designed and synthesized DNA-intercalating Ru(II) polypyridyl complexes Δ--[Ru(bpy)₂(uip)]²⁺ and Λ-[Ru(bpy)₂(uip)]²⁺ (bpy is 2,2′-bipyridyl, uip is 2-(5-uracil)-1H-imidazo[4,5-f][1,10]phenanthroline). The DNA binding, photocleavage, topoisomerase inhibition, and cytotoxicity of the complexes were studied. As we expected, the synthesized Ru(II) complexes can intercalate into DNA base pairs and cleave the pBR322 DNA with high activity upon irradiation. The mechanism studies reveal that singlet oxygen (¹O₂) and superoxide anion radical (O₂^•−) may play an important role in the photocleavage. The inhibition of topoisomerases I and II by the Ru(II) complexes has been studied. The results suggest that both complexes are efficient inhibitors towards topoisomerase II by interference with the DNA religation and direct topoisomerase II binding. Both complexes show antitumor activity towards HELA, hepG2, BEL-7402, and CNE-1 tumor cells. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Synthesis, GC selective DNA binding and topoisomerase II inhibition activities of ruthenium(II) polypyridyl complex containing 11-aminopteridino[6,7-f][1,10]phenanthrolin-13(12H)-one

A DNA-intercalating Ru(II) polypyridyl complex [Ru(bpy)₂(appo)]²⁺ (bpy = 2,2′-bipyridine, appo = 11-aminopteridino[6,7-f][1,10]phenanthrolin-13(12H)-one) has been synthesized and characterized by elemental analysis, electrospray mass spectra, ¹H NMR, UV/Vis spectrum, fluorescent spectrum and electrochemistry. The DNA-binding, photocleavage, and topoisomerase inhibition of the complex was studied. Interestingly, the complex binds to DNA via an intercalative mode with preference for GC sequences and cleaves the pBR322 DNA upon irradiation. In addition, the complex shows high inhibition activity against topoisomerase II by interfere the DNA religation.     

A theoretical study of Ru(II) polypyridyl DNA intercalators: Structure and electronic absorption spectroscopy of [Ru(phen)2(dppz)] and [Ru(tap)2(dppz)] complexes intercalated in guanine-cytosine base pairs

The structural and spectroscopic properties of [Ru(phen)₂(dppz)]²⁺ and [Ru(tap)₂(dppz)]²⁺ (phen = 1,10-phenanthroline; tap = 1,4,5,8-tetraazaphenanthrene; dppz = dipyridophenazine ) have been investigated by means of density functional theory (DFT), time-dependent DFT (TD-DFT) within the polarized continuum model (IEF-PCM) and quantum mechanics/molecular mechanics (QM/MM) calculations. The model of the Δ and Λ enantiomers of Ru(II) intercalated in DNA in the minor and major grooves is limited to the metal complexes intercalated in two guanine-cytosine base pairs. The main experimental spectral features of these complexes reported in DNA or synthetic polynucleotides are better reproduced by the theoretical absorption spectra of the Δ enantiomers regardless of intercalation mode (major or minor groove). This is especially true for [Ru(phen)₂(dppz)]²⁺. The visible absorption of [Ru(tap)₂(dppz)]²⁺ is governed by the MLCT_tap transitions regardless of the environment (water, acetonitrile or bases pair), the visible absorption of [Ru(phen)₂(dppz)]²⁺ is characterized by transitions to metal-to-ligand-charge-transfer MLCT_dppz in water and acetonitrile and to MLCT_phen when intercalated in DNA. The response of the IL_dppz state to the environment is very sensitive. In vacuum, water and acetonitrile these transitions are characterized by significant oscillator strengths and their positions depend significantly on the medium with blue shifts of about 80 nm when going from vacuum to solvent. When the complex is intercalated in the guanine-cytosine base pairs the ¹IL_dppz transition contributes mainly to the band at 370 nm observed in the spectrum of [Ru(phen)₂(dppz)]²⁺ and to the band at 362 nm observed in the spectrum of [Ru(tap)₂(dppz)]²⁺.     

Chiral ruthenium(II) anthraquinone complexes as dual inhibitors of topoisomerases I and II

Abstract  

DNA topoisomerases (I and II) have been one of the excellent targets in anticancer drug development. Here two chiral ruthenium(II) anthraquinone complexes, Δ- and Λ-[Ru(bpy)₂(ipad)]²⁺, where bpy is 2,2′-bipyridine and ipad is 2-(anthracene-9,10-dione-2-yl)imidazo[4,5-f][1,10]phenanthroline, were synthesized and characterized. As expected, both of the Ru(II) complexes intercalate into DNA base pairs and possess an obviously greater affinity with DNA. Topoisomerase inhibition and DNA strand passage assay confirmed that the two complexes are efficient dual inhibitors of topoisomerases I and II by interference with the DNA religation. In MTT cytotoxicity studies, two Ru(II) complexes exhibited antitumor activity against HeLa, MCF-7, HepG2 and BEL-7402 tumor cell lines. Flow cytometry analysis shows an increase in the percentage of cells with apoptotic morphological features in the sub-G1 phase for Ru(II) complexes. Nuclear chromatin cleavage has also been observed from AO/EB staining assay and alkaline single-cell gel electrophoresis (comet assay). The results demonstrated that Δ- and Λ-[Ru(bpy)₂(ipad)]²⁺ act as dual inhibitors of topoisomerases I and II, and cause DNA damage that can lead to cell cycle arrest and/or cell death by apoptosis.     

pH- and DNA-induced dual molecular light switches based on a novel ruthenium(II) complex

A novel Ru(II) complex, [Ru(bpy)₂(btppz)]Cl₂, where bpy = 2,2′-bipyridine and btppz = benzo[h]tripyrido[3,2-a:2′,3′-c:2″,3″-j]phenazine, has been synthesized and characterized. The pH effects on UV-visible (UV-vis) absorption and emission spectra of the complex have been studied and ground- and excited-state ionization constants of the complex have been derived. The calf thymus DNA (ct-DNA) binding properties of the complex were investigated with UV-vis absorption and luminescence spectrophotometric titrations, steady-state emission quenching by [Fe(CN)₆]⁴⁻, DNA competitive binding with ethidium bromide, DNA melting experiments, reverse salt titrations and viscosity measurements. The complex was demonstrated to act as dual molecular switches: pH-induced “on-off” emission switch with an on-off intensity ratio of ∼54 which is favorably compared with those reported for structurally analogous Ru(II) complexes, and a DNA molecular light switch with a luminescence enhancement factor of 22 as it intercalatively bound to the DNA.     

The relationship between the structures of periphery ligands and the DNA binding mode of [Ru(II)(1,10-phenanthroline)(L1L2)dipyrido[3,2-a:2',3'-c]phenazine](n+) (L1=Cl or pyridine and L2=pyridine, n=1,2)

The binding modes of the [Ru(II)(1,10-phenanthroline)(L₁L₂) dipyrido[3,2-a:2′,3′-c]phenazine]²⁺ {[Ru(phen)(py) Cl dppz]⁺ (L₁ = Cl, L₂ = pyridine) and ([Ru(phen)(py)₂dppz]²⁺ (L₁ = L₂ = pyridine)} to native DNA is compared to that of the [Ru(II)(1,10-phenanthroline)₂dipyrido[3,2-a:2′,3′-c]phenazine]²⁺ complex ([Ru(phen)₂dppz]²⁺) by various spectroscopic and hydrodynamic methods including electric absorption, linear dichroism (LD), fluorescence spectroscopy, and viscometric titration. All measured properties, including red-shift and hypochromism in the dppz absorption band, nearly perpendicular molecular plane of the dppz ligand with respect to the local DNA helix axis, prohibition of the ethidium binding, the light switch effect and binding stoichiometry, increase in the viscosity upon binding to DNA, increase in the melting temperature are in agreement with classical intercalation of dppz ligand of the [Ru(phen)₂dppz]²⁺ complex, in which both phenanthroline ligand anchored to the DNA phosphate groups by electrostatic interaction. [Ru(phen)(py)₂ dppz]²⁺ and [Ru(phen)(py) Cl dppz]⁺ complexes had one of the phenanthroline ligand replaced by either two pyridine ligands or one pyridine plus a chlorine ion. They exhibited similar protection from water molecules, interaction with DNA bases, and occupying site that is common with ethidium. The dppz ligand of these two Ru(II) complex were greatly tilted relative to the DNA helix axis, suggesting that the dppz ligand resides inside the DNA and is not perpendicular relative to the DNA helix axis. These observation suggest that anchoring the [Ru(phen)₂dppz]²⁺complex by both phenanthroline is essential for the dppz ligand to be classically intercalated between DNA base-pairs.     

pH effects on optical and DNA binding properties of a thiophene-containing ruthenium(II) complex

A new ruthenium(II) complex, [Ru(bpy)₂(Htip)]Cl₂ {where bpy = 2,2′-bipyridine and Htip = 2-(thiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline}, has been synthesized and characterized by ¹H NMR spectroscopy, elemental analysis, and mass spectrometry. The pH effects on UV-Vis absorption and emission spectra of the complex have been studied, and the ground- and excited-state acidity ionization constant values have been derived. The calf thymus (ct) DNA binding properties of the complex have been investigated with UV-Vis absorption and luminescence titrations, steady-state emission quenching by [Fe(CN)₆]⁴⁻, DNA competitive binding with ethidium bromide, DNA melting experiments, and viscosity measurements. The molecular structures and electronic properties of [Ru(bpy)₂(Htip)]²⁺ and deprotonated form [Ru(bpy)₂(tip)]⁺ have also been investigated by means of density functional theory calculations in an effort to understand the DNA binding properties. The results suggest that the complex undergo three-step successive protonation/deprotonation reactions with one of which occurring over physiological pH region, and act as a ct-DNA intercalator with an intrinsic DNA binding constant value on 10⁵ M⁻¹ order of magnitude that is insensitive to pH.     

Synthesis, double stranded DNA-binding and photocleavage studies of a functionalized ruthenium(II) complex with 7,7′-methylenedioxyphenyldipyrido[3,2-a:2′,3′-c]-phenazine

A new Ru(II) complex [Ru(phen)₂(mdpz)]²⁺ (phen = 1,10-phenanthroline, mdpz = 7,7′-methylenedioxyphenyl-dipyrido-[3,2-a:2′,3′-c]phenazine) has been synthesized and characterized in detail by elemental analysis, mass spectrometry and ¹H NMR spectroscopy. The interaction of the complex with calf thymus DNA was investigated by spectroscopic and viscosity measurements. The results suggest that the complex binds to DNA via an intercalative mode and serves as a molecular “light switch” for DNA. Moreover, the complex has been found to promote the photocleavage of plasmid DNA pBR322 under irradiation at 365 nm. The mechanism studies reveal that singlet oxygen (¹O₂) plays a significant role in the photocleavage.     

Ruthenium(II) mixed-ligand complexes containing 2-(6-methyl-3-chromonyl)imidazo[4,5-f][1,10]-phenanthroline: Synthesis, DNA-binding and photocleavage studies

Two novel Ru(II) complexes [Ru(bpy)₂(MCMIP)]²⁺ (1) and [Ru(phen)₂(MCMIP)]²⁺ (2) (bpy = 2,2′-bipyridine; phen = 1,10-phenanthroline; MCMIP = 2-(6-methyl-3-chromonyl)imidazo[4,5-f][1,10]-phenanthroline) have been synthesized and characterized by elemental analysis, mass spectra and ¹H NMR. The DNA-binding properties of the complexes were investigated by absorption, emission, melting temperature and viscosity measurements. Experimental results indicate that the two complexes can intercalate into DNA base pairs. Upon irradiation at 365 nm, two Ru(II) complexes were found to promote the cleavage of plasmid pBR 322 DNA from supercoiled form I to nicked form II, and the mechanisms for DNA cleavage by the complexes were also investigated.     

Effect of ligand congeniality on energy transfer reaction between photo-excited tris(bipyridine)ruthenium(II) and chromate(III) complexes in aqueous solutions

Energy-transfer rate-constants from photo-excited [Ru(N–N)₃]²⁺ (N–N = 2,2′-bipyridine (bpy), 4,4′-dimethyl-2,2′-bipyridine (4dmb), 5,5′-dimethyl-2,2′-bipyridine (5dmb)) to [Cr(O–O)₃]³⁻ (O–O²⁻ = ox²⁻ ((COO⁻)₂), mal²⁻ (CH₂(COO⁻)₂)) and [Cr(CN)₆]³⁻ in encounter complexes were evaluated in aqueous solutions containing alkali metal ion. The rate constant depends on the molecular size of the ruthenium(II) complex: 1.8 × 10⁸ s⁻¹ for [Ru(bpy)₃]²⁺ (molecular radius, r = 5.8 Å), 1.4 × 10⁸ s⁻¹ for [Ru(5dmb)₃]²⁺ (r = 6.1 Å) and 0.96 × 10⁸ s⁻¹ for [Ru(4dmb)₃]²⁺ (r = 6.7 Å) in the system of [Ru(N–N)₃]²⁺–[Cr(ox)₃]³⁻ in aqueous solution. However, the rate constant is much more sensitive to the chromate(III) complex than to ruthenium(II) complex; 1.8 × 10⁸ s⁻¹ and 0.43 × 10⁸ s⁻¹ for [Cr(ox)₃]³⁻ (r = 4.0 Å) and [Cr(mal)₃]³⁻ (r = 4.2 Å) in the [Ru(bpy)₃]²⁺–[Cr(O–O)₃]³⁻ systems, respectively. We conclude that the congeniality between the donor’s and acceptor’s ligands in encounter complex plays an important role in energy transfer in aqueous solution.     

Study on nucleic acid (CT-DNA and yeast tRNA) binding behaviors and cytotoxic properties of a heterodinuclear Ru(II)-Co(III) polypyridyl complex

A heterodinuclear (Ru(II), Co(III)) metal polypyridyl complex [(phen)₂Ru(bpibH₂)Co(phen)₂]⁵⁺ {phen = 1,10-phenanthroline, bpibH₂ = 1,4-bis([1,10]phebanthroline-[5,6-d]imidazol-2-yl)-benzene} has been designed and synthesized. The comparative study on the interactions of the Ru(II)-Co(III) complex with calf thymus DNA (CT-DNA) and yeast tRNA has been investigated by UV-visible spectroscopy, fluorescence spectroscopy, viscosity, as well as equilibrium dialysis and circular dichroism (CD). The antitumor activities of the complex have been evaluated by MTT {3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide} method and Giemsa staining experiment. These results indicate that the structures of nucleic acids have significant effects on the binding behaviors of metal complexes. Furthermore, the complex demonstrates different antitumor activity against selected tumor cell lines in vitro, and can make the cell apoptosis.     

Tris-ruthenium(II)/copper(II) multimetallic porphyrin: Synthesis, characterization, DNA binding and supercoiled DNA photocleavage studies

The porphyrin, meso-5-(pentafluorophenyl)-10, 15, 20-tris(4-pyridyl)porphyrin has been used to synthesize two new metalloporphyrin complexes. Insertion of copper(II) into the porphyrin center gives the copper(II) porphyrin. Coordination of three [Ru(bipy)₂Cl]⁺ moieties (where bipy = 2,2′-bipyridine) to the pyridyl nitrogens of the copper(II) porphyrin gives the target complex. Electronic transitions associated with the copper(II) porphyrin and the triruthenium copper(II) porphyrin include an intense Soret band and a less intense Q-band in the visible region of the spectrum. An intense π-π∗ transition in the UV region associated with the bipyridyl groups and a metal to ligand charge transfer (MLCT) band appearing as a shoulder to the Soret band are observed for the ruthenated copper(II) porphyrin. Electrochemical properties associated with the multimetallic complex include a redox couple in the cathodic region with E_1/2 = −0.86 V versus Ag/AgCl attributed to the porphyrin and a redox couple in the anodic region E_1/2 = 0.88 V versus Ag/AgCl due to the Ru^III/II couple. DNA titrations indicate the triruthenium copper(II) porphyrin interacts with DNA potentially through a groove binding mechanism. Irradiation of aqueous solutions of the target complex and supercoiled DNA at a 10:1 base pair to complex ratio with visible light above 400 nm indicates that the complex causes nicking of the DNA helix.     

Cyclodextrins improve the antimicrobial activity of the chloride salt of Ruthenium(II) chloro-phenanthroline-trithiacyclononane

The complex [Ru([9]aneS₃)phenCl]Cl (phen = 1,10-phenanthroline) and its synthetic precursor [Ru([9]aneS₃)dmsoCl₂] were immobilized in permethylated β-cyclodextrin (TRIMEB). A new crystalline structure of the precursor, obtained from a batch ethanol solution at low temperature (4°C), is fully described from single-crystal X-ray diffraction data. [Ru([9]aneS₃)phenCl]Cl was also encapsulated in native β-cyclodextrin for comparison with the TRIMEB compound. All three compounds were obtained with a 1:1 host:guest stoichiometry and were studied by powder X-ray diffraction (including synchrotron radiation data), thermogravimetric analysis (TGA), ¹³C{¹H} CP/MAS NMR and FTIR spectroscopies. The bacterial growth inhibitory action of the complex [Ru([9]aneS₃)phenCl]Cl and its two cyclodextrin compounds was tested on Gram-negative (Salmonella, Escherichia) and Gram-positive strains (Bacillus, Listeria, Enterococcus and Staphilococcus) and results show a positive effect of cyclodextrin immobilization on the antimicrobial properties. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

DNA-binding and photocleavage studies of mixed polypyridyl ruthenium(II) complexes with calf thymus DNA

New mixed polypyridyl {NMIP = 2′-(2″-nitro-3″,4″-methylenedioxyphenyl)imidazo-[4′,5′-f][1,10]-phenanthroline, dmb = 4,4′-dimethyl-2,2′-bipyridine, bpy = 2,2′-bipyridine} ruthenium(II) complexes [Ru(dmb)₂(NMIP)]²⁺ (1) and [Ru(bpy)₂(NMIP)]²⁺ (2) have been synthesized and characterized. The binding of these complexes to calf thymus DNA (CT-DNA) has been investigated with spectroscopic methods, viscosity and electrophoresis measurements. The experimental results indicate that both complexes could bind to DNA via partial intercalation from the minor/major groove. In addition, both complexes have been found to promote the single-stranded cleavage of plasmid pBR 322 DNA upon irradiation. Under comparable experimental conditions compared with [Ru(phen)₂(NMIP)]²⁺, during the course of the dialysis at intervals of time, the CD signals of both complexes started from none, increased to the maximum magnitude, then no longer changed, and the activity of effective DNA cleavage dependence upon concentration degree lies in the following order: [Ru(phen)₂NMIP]²⁺ > complex 2 > complex 1.     

DNA-binding and photocleavage studies of [Ru(phen)2(NMIP)]

A novel ligand 2′-(2″-nitro-3″,4″-methylenedioxyphenyl)imidazo[4′,5′-f][1,10]-phenanthroline (NMIP) and its complex [Ru(phen)₂(NMIP)]²⁺ have been synthesized and characterized by mass spectroscopy, ¹H NMR and cyclic voltammetry. Binding of the complex with calf thymus DNA (CT DNA) has been investigated by spectroscopic methods, viscosity and electrophoresis measurements. The experimental results indicate that [Ru(phen)₂(NMIP)]²⁺ binds to DNA via partial intercalative mode and the individual enantiomers of it bind to DNA in different rates. [Ru(phen)₂(NMIP)]²⁺ has also been found to promote cleavage of plasmid pBR 322 DNA from the supercoiled Form I to the open circular Form II upon irradiation.     

Topoisomerase II inhibition activity of new square planar Ni(II) complexes containing N-substituted thiosemicarbazones: Synthesis, spectroscopy, X-ray crystallography and electrochemical characterization

New Ni(II) thiosemicarbazone complexes containing triphenylphosphine namely [Ni(Sal-mtsc)(PPh₃)](2) and [Ni(Nap-mtsc)(PPh₃)] (3) (where Sal-mtsc = salicylaldehyde-N(4)-methylthiosemicarbazone and Nap-mtsc = 2-hydroxy-1-naphthaldehyde-N(4)-methylthiosemicarbazone) have been synthesised and characterized by elemental analysis, IR, electronic and ¹H NMR spectroscopy. The crystal structures of the complexes have been determined by single crystal X-ray diffraction technique. In all the complexes the thiosemicarbazone ligand coordinated to nickel through ONS mode. The electrochemical behavior of the complexes has been investigated by using cyclic voltammetry in acetonitrile. The new complexes were subjected to test their DNA topoisomerase II inhibition efficiency. The complex [Ni(Nap-mtsc)(PPh₃)] (3) showed 95% inhibition. The observed inhibition activity was found to be more potent than the activity of conventional standard Nalidixic acid.     

Synthesis, DNA-binding and photocleavage studies of ruthenium complexes [Ru(bpy)2(mitatp)] and [Ru(bpy)2(nitatp)]

Two new ruthenium complexes [Ru(bpy)₂(mitatp)](ClO₄)₂1 and [Ru(bpy)₂(nitatp)](ClO₄)₂2 (bpy = 2,2′-bipyridine, mitatp = 5-methoxy-isatino[1,2-b]-1,4,8,9-tetraazatriphenylene, nitatp = 5-nitro-isatino[1,2-b]-1,4,8,9-tetraazatriphenylene) have been synthesized and characterized by elemental analysis, ¹H NMR, mass spectrometry and cyclic voltammetry. Spectroscopic and viscosity measurements proved that the two Ru(II) complexes intercalate DNA with larger binding constants than that of [Ru(bpy)₂(dppz)]²⁺ (dppz = dipyrido[3,2-a:2′,3′-c]phenazine) and possess the excited lifetime of microsecond scale upon binding to DNA. Both complexes can efficiently photocleave pBR322 DNA in vitro under irradiation. Singlet oxygen (¹O₂) was proved to contribute to the DNA photocleavage process, the ¹O₂ quantum yields was determined to be 0.43 and 0.36 for 1 and 2, respectively. Moreover, a photoinduced electron transfer mechanism was also found to be involved in the DNA cleavage process.     

Studies on synthesis, characterization, and G-quadruplex binding of Ru(II) complexes containing two dppz ligands

In this work, the interaction between the guanine-rich single-strand oligomer AG₃(T₂AG₃)₃ quadruplex and two Ru(II) complexes, [Ru(L¹)(dppz)₂](PF₆)₄ (1) and [Ru(L²)(dppz)₂](PF₆)₄ (2) (L¹ = 5,5′-di(1-(trimethylammonio)methyl)-2,2′-dipyridyl cation, L² = 5,5′-di(1-(triethylammonio)methyl)-2,2′-dipyridyl cation, dppz = dipyrido[3,2-a:2′,3′-c] phenazine), has been studied by UV-Visible, fluorescence, DNA melting, and circular dichroism in K⁺ buffer. The two complexes after binding to G-quadruplex have shown different DNA stability and fluorescence enhancement. The results show that both complexes can induce the stabilization of quadruplex DNA. ΔT_m values of complexes 1 and 2 at [Ru]/[DNA] ratio of 1:1 were 9.4 and 7.0, respectively. Binding stoichiometry along with the quadruplex was investigated through a luminescence-based Job plot. The major inflection points for complexes 1 and 2 were 0.49 and 0.46, respectively. The data were consistent with the binding mode at a [quadruplex]/[complex] ratio of 1:1. In addition, the conformation of G-quadruplex was not changed by the complexes at the high ionic strength of K⁺ buffer.