DNA Cleavage by the Photolysis of Cyclopentadienyl Metal Complexes: Mechanistic Studies and Sequence Selectivity of Strand Scission by CpW(CO)3CH3

Visible Light-Induced Radical Mediated DNA Damage

Light-responsive compounds have been used to manipulate biological systems with spatial and temporal control of the event of interest. Illumination of alkylcobalamins with green light (>500 nm) produces carbon-centered radicals, which have been demonstrated to effectively cause DNA damage. Molecules that cause DNA and RNA strand scission are useful for studying polynucleotide structure and the binding of small molecules and proteins to polynucleotides. Most molecules that cause DNA damage in a light-dependent manner require high energy, short wavelength ultraviolet light, which is readily absorbed by nucleotide bases causing damage to the polynucleotides. Therefore, using alkylcobalamins is advantageous for causing strand scission of polynucleotides, because they are activated by light wavelengths that are not absorbed by nucleotide bases. Green-light illumination of methylcobalamin effectively causes DNA strand scission based on gel mobility assays. This cleavage is due to the generation of carbon-centered radicals based on the results of a radical trapping study. In addition, synthesis of an alkylcobalamin with a DNA binding moiety, spermine, improves DNA cleavage efficacy by an order of magnitude in comparison with methylcobalamin.

Metal-mediated diradical tuning for DNA replication arrest via template strand scission

A series of M(PyED)·X (X = 2Cl-, SO42-) pyridine-metalloenediyne complexes [M = Cu(II), Fe(II), or Zn(II)] and their independently synthesized, cyclized analogs have been prepared to investigate their potential as radical-generating DNA-damaging agents. All complexes possess a 1:1 metal-to-ligand stoichiometry as determined by electronic absorption spectroscopy and X-ray diffraction. Solution structural analysis reveals a pπ Cl [Formula: see text] Cu(II) LMCT (22,026 cm-1) for Cu(PyED)·2Cl, indicating three nitrogens and a chloride in the psuedo-equatorial plane with the remaining pyridine nitrogen and solvent in axial positions. EPR spectra of the Cu(II) complexes exhibit an axially elongated octahedron. This spectroscopic evidence, together with density functional theory computed geometries, suggest six-coordinate structures for Cu(II) and Fe(II) complexes and a five-coordinate environment for Zn(II) analogs. Bergman cyclization via thermal activation of these constructs yields benzannulated product indicative of diradical generation in all complexes within 3 h at 37 °C. A significant metal dependence on the rate of the reaction is observed [Cu(II) > Fe(II) > Zn(II)], which is mirrored in in vitro DNA-damaging outcomes. Whereas in situ chelation of PyED leads to considerable degradation in the presence of all metals within 1 h under hyperthermia conditions, Cu(II) activation produces >50% compromised DNA within 5 min. Additionally, Cu(II) chelated PyED outcompetes DNA polymerase I to successfully inhibit template strand extension. Exposure of HeLa cells to Cu(PyBD)·SO4 (IC50 = 10 μM) results in a G2/M arrest compared with untreated samples, indicating significant DNA damage. These results demonstrate metal-controlled radical generation for degradation of biopolymers under physiologically relevant temperatures on short timescales.

Cellular and cell-free studies of catalytic DNA cleavage by ruthenium polypyridyl complexes containing redox-active intercalating ligands

The ruthenium(ii) polypyridyl complexes (RPCs), [(phen)2Ru(tatpp)]2+ (32+ ) and [(phen)2Ru(tatpp)Ru(phen)2]4+ (44+ ) are shown to cleave DNA in cell-free studies in the presence of a mild reducing agent, i.e. glutathione (GSH), in a manner that is enhanced upon lowering the [O2]. Reactive oxygen species (ROS) are involved in the cleavage process as hydroxy radical scavengers attenuate the cleavage activity. Cleavage experiments in the presence of superoxide dismutase (SOD) and catalase reveal a central role for H2O2 as the immediate precursor for hydroxy radicals. A mechanism is proposed which explains the inverse [O2] dependence and ROS data and involves redox cycling between three DNA-bound redox isomers of 32+ or 44+ . Cultured non-small cell lung cancer cells (H358) are sensitive to 32+ and 44+ with IC50 values of 13 and 15 μM, respectively, and xenograft H358 tumors in nude mice show substantial (∼80%) regression relative to untreated tumors when the mice are treated with enantiopure versions of 32+ and 44+ (Yadav et al. Mol Cancer Res, 2013, 12, 643). Fluorescence microscopy of H358 cells treated with 15 μM 44+ reveals enhanced intracellular ROS production in as little as 2 h post treatment. Detection of phosphorylated ATM via immunofluorescence within 2 h of treatment with 44+ reveals initiation of the DNA damage repair machinery due to the ROS insult and DNA double strand breaks (DSBs) in the nuclei of H358 cells and is confirmed using the γH2AX assay. The cell data for 32+ is less clear but DNA damage occurs. Notably, cells treated with [Ru(diphenylphen)3]2+ (IC50 1.7 μM) show no extra ROS production and no DNA damage by either the pATM or γH2AX even after 22 h. The enhanced DNA cleavage under low [O2] (4 μM) seen in cell-free cleavage assays of 32+ and 44+ is only partially reflected in the cytotoxicity of 32+ and 44+ in H358, HCC2998, HOP-62 and Hs766t under hypoxia (1.1% O2) relative to normoxia (18% O2). Cells treated with RPC 32+ show up to a two-fold enhancement in the IC50 under hypoxia whereas cells treated with RPC 44+ gave the same IC50 whether under hypoxia or normoxia.

Regression of lung cancer by hypoxia-sensitizing ruthenium polypyridyl complexes

The ruthenium (II) polypyridyl complexes (RPC), Δ-[(phen)2Ru(tatpp)]Cl2 (Δ-[3]Cl2) and ΔΔ-[(phen)2Ru(tatpp)Ru(phen)2]Cl4 (ΔΔ-[4]Cl4, are a new generation of metal-based antitumor agents. These RPCs bind DNA via intercalation of the tatpp ligand, which itself is redox-active and is easily reduced at biologically relevant potentials. We have previously shown that RPC 4(4+) cleaves DNA when reduced by glutathione to a radical species and that this DNA cleavage is potentiated under hypoxic conditions in vitro. Here, we show that 3(2+) also exhibits free radical-mediated DNA cleavage in vitro and that 3(2+) and 4(4+) both exhibit selective cytotoxicity toward cultured malignant cell lines and marked inhibition of tumor growth in vivo. The murine acute toxicity of RPCs 3(2+) and 4(4+) (maximum tolerable doses ~ 65 μmol/kg) is comparable with that for cisplatin (LD50 ~ 57 μmol/kg), but unlike cisplatin, RPCs are generally cleared from the body unchanged via renal excretion without appreciable metabolism or nephrotoxic side effects. RPCs 3(2+) and 4(4+) are shown to suppress growth of human non-small cell lung carcinoma (~83%), show potentiated cytotoxicity in vitro under hypoxic conditions, and induce apoptosis through both intrinsic and extrinsic pathways. The novel hypoxia-enhanced DNA cleavage activity and biologic activity suggest a promising new anticancer pharmacophore based on metal complexes with aromatic ligands that are easily reduced at biologically accessible potentials.

Efficient double-strand scission of plasmid DNA by quaternized-chitosan zinc complex

N-[(2-Hydroxy-3-trimethylammonium) propyl] chitosan chloride (HTACC) was prepared to construct a chitosan-based zinc complex (HTACC-Zn(II)) as a catalyst with good water solubility for rapid DNA cleavage. Results indicated that the observed rate constant (k(obs)) of plasmid DNA cleaved by HTACC-Zn(II) could be enhanced by 10(7)-fold compared with that of uncatalyzed DNA cleavage. The kinetic behavior of HTACC-Zn(II) for DNA cleavage is well fitted by Michaelis-Menten model. The results of gel electrophoresis suggested that HTACC-Zn(II) preferentially perform double-strand break of plasmid DNA.

A new trick (hydroxyl radical generation) for an old vitamin (B12)

Photolysis of hydroxocobalamin in the presence of plasmid DNA (pBR322) results in DNA cleavage. Temporal control of hydroxyl radical production and DNA strand scission by hydroxocobalamin was demonstrated using a 2-deoxyribose assay and a plasmid relaxation assay, respectively. The light-driven hydroxocobalamin-mediated catalytic formation of hydroxyl radicals was demonstrated using radical scavenging studies of DNA cleavage and via recycling of a hydroxocobalamin-resin conjugate several times without loss of efficacy.

Electronic structures and spin topologies of gamma-picoliniumyl radicals. A study of the homolysis of N-methyl-gamma-picolinium and of benzo-, dibenzo-, and naphthoannulated analogs

Radicals resulting from one-electron reduction of (N-methylpyridinium-4-yl) methyl esters have been reported to yield (N-methylpyridinium-4-yl) methyl radical, or N-methyl-gamma-picoliniumyl for short, by heterolytic cleavage of carboxylate. This new reaction could provide the foundation for a new structural class of bioreductively activated, hypoxia-selective antitumor agents. N-methyl-gamma-picoliniumyl radicals are likely to damage DNA by way of H-abstraction and it is of paramount significance to assess their H-abstraction capabilities. In this context, the benzylic C-H homolyses were studied of toluene (T), gamma-picoline (P, 4-methylpyridine), and N-methyl-gamma-picolinium (1c, 1,4-dimethylpyridinium). With a view to providing capacity for DNA intercalation the properties also were examined of the annulated derivatives 2c (1,4-dimethylquinolinium), 3c (9,10-dimethylacridinium), and 4c (1,4-dimethylbenzo[g]quinolinium). The benzylic C-H homolyses were studied with density functional theory (DFT), perturbation theory (up to MP4SDTQ), and configuration interaction methods (QCISD(T), CCSD(T)). Although there are many similarities between the results obtained here with DFT and CI theory, a number of significant differences occur and these are shown to be caused by methodological differences in the spin density distributions of the radicals. The quality of the wave functions is established by demonstration of internal consistencies and with reference to a number of observable quantities. The analysis of spin polarization emphasizes the need for a clear distinction between "electron delocalization" and "spin delocalization" in annulated radicals. Aside from their relevance for the rational design of new antitumor drugs, the conceptional insights presented here also will inform the understanding of ferromagnetic materials, of spin-based signaling processes, and of spin topologies in metalloenzymes.

DNA cleavage by photolysis of aryl sulfoxides

Aryl sulfoxides have been identified as a class of organic compounds capable of inducing DNA cleavage in the presence of UV light. Phenyl sulfoxide and methyl phenyl sulfoxide were both shown to cleave pBR322 DNA at concentrations of 180 and 360 microM, respectively. Radical trapping studies indicate carbon-centered radicals are the active cleavage species.

Preferential DNA cleavage under anaerobic conditions by a DNA-binding ruthenium dimer

In the absence of dioxygen, the cationic complex [(phen)2Ru(tatpp)Ru(phen)2]4+ (P4+) undergoes in situ reduction by glutathione (GSH) to form a species that induces DNA cleavage. Exposure to air strongly attenuates the cleavage activity, even in the presence of a large excess of reducing agent (e.g., 40 equiv of GSH per P4+), suggesting that the complex may be useful in targeting cells with a low-oxygen microenvironment (hypoxia) for destruction via DNA cleavage. The active species is identified as the doubly reduced, doubly protonated complex H2P4+, and a carbon-based radical species is implicated in the cleavage action. We postulate that the dioxygen concentration regulates the degree to which the carbon radical forms and thus regulates the DNA cleavage activity.