Site-specific DNA cleavage by antisense oligonucleotides covalently linked to phenazine di-N-oxide

Enzyme-Activated Generation of Reactive Oxygen Species from Heterocyclic N-Oxides under Aerobic and Anaerobic Conditions and Its Relevance to Hypoxia-Selective Prodrugs

Enzymatic one-electron reduction of heterocyclic N-oxides can lead to the intracellular generation of reactive oxygen species via several different chemical pathways. These reactions may be relevant to hypoxia-selective anticancer drugs, antimicrobial agents, and unwanted toxicity of heterocylic nitrogen compounds.

Double-strand cleavage of DNA by a polyamide-phenazine-di-N-oxide conjugate

Phenazine and its derivatives have been widely applied as nucleic acid cleavage agents due to active oxygen activating the C-H bond of the substrate. However, diffusion of oxygen radicals limits their potential applications in the DNA-targeted metal-free drug. Introduction of groove binder moiety such as polyamide enhanced the regional stability of radical molecules and reduced cytotoxicity of the drugs. In this work, we described the design and synthesis of a polyamide-modified phenazine-di-N-oxide as a DNA double-strand cleavage agent. The gel assays showed the hybrid conjugates can effectively break DNA double strands in a non-random manner under physiological conditions. The probable binding mode to DNA was investigated by sufficient spectral experiments, revealing weak interaction between hybrid ligand and nucleic acid molecules. The results of our study have implications on the design of groove-binding hybrid molecules as new artificial nucleases and may provide a strategy for developing efficient and safe DNA cleavage reagents.

DNA strand cleaving properties and hypoxia-selective cytotoxicity of 7-chloro-2-thienylcarbonyl-3-trifluoromethylquinoxaline 1,4-dioxide

The heterocyclic N-oxide, 3-amino-1,2,4-benzotriazine 1,4-dioxide (tirapazamine, 1), shows promising antitumor activity in preclinical studies, but there is a continuing need to explore new compounds in this general structural category. In the work described here, we examined the properties of 7-chloro-2-thienylcarbonyl-3-trifluoromethylquinoxaline 1,4-dioxide (9h). We find that 9h causes redox-activated, hypoxia-selective DNA cleavage that mirrors the lead compound, tirapazamine, in both mechanism and potency. Furthermore, we find that 9h displays hypoxia-selective cytotoxicity against human cancer cell lines.

Synthesis and biological evaluation of new 2-arylcarbonyl-3-trifluoromethylquinoxaline 1,4-di-N-oxide derivatives and their reduced analogues

As a continuation of our research in the quinoxaline 1,4-di-N-oxide new series of 2-arylcarbonyl-3-trifluoromethylquinoxaline, 1,4-di-N-oxide derivatives have been synthesized and evaluated in a full panel of 60 human tumor cell lines. Selective reductions were carried out on two compounds which allowed us to determine the compound structures by comparison of the 1H NMR spectra. In general, all the di-N-oxidized compounds showed good cytotoxic parameters. The best activity was observed in derivatives with electron-withdrawing groups in position 6 or 7 on the quinoxaline ring and in the unsubstituted analogues, whereas loss of one or two oxygens reduced the cytotoxicity. The best five compounds were selected for evaluation for the in vivo hollow fiber assays. In vitro studies reveal that compound 5h efficiently generates reactive oxygen species via redox cycling in the presence of the NADPH/cytochrome P450 enzyme system, providing a plausible molecular mechanism for the observed aerobic cytotoxicity of these quinoxaline N-oxides.

DNA cleavage by UVA irradiation of NADH with dioxygen via radical chain processes

Efficient DNA cleaving-activity is observed by UVA irradiation of an O(2)-saturated aqueous solution of NADH (beta-nicotinamide adenine dinucleotide, reduced form). No DNA cleavage has been observed without NADH under otherwise the same experimental conditions. In the presence of NADH, energy transfer from the triplet excited state of NADH ((3)NADH*) to O(2) occurs to produce singlet oxygen ((1)O(2)) that is detected by the phosphorescence emission at 1270 nm. No quenching of (1)O(2) by NADH was observed as indicated by no change in the intensity of phosphorescence emission of (1)O(2) at 1270 nm in the presence of various concentrations of NADH. In addition to the energy transfer, photoinduced electron transfer from (3)NADH* to O(2) occurs to produce NADH(*+) and O(2)(*-), both of which was observed by ESR. The quantum yield of the photochemical oxidation of NADH with O(2) increases linearly with increasing concentration of NADH but decreases with increasing the light intensity absorbed by NADH. Such unusual dependence of the quantum yield on concentration of NADH and the light intensity absorbed by NADH indicates that the photochemical oxidation of NADH with O(2) proceeds via radical chain processes. The O(2)(*-) produced in the photoinduced electron transfer is in the protonation equilibrium with HO(2)(*), which acts as a chain carrier for the radical chain oxidation of NADH with O(2) to produce NAD(+) and H(2)O(2), leading to the DNA cleavage.

Generation of reactive oxygen species by a persulfide (BnSSH)

Hydropersulfides (RS(x)SH) have been implicated as important intermediates in the cell-killing action of the anticancer natural products leinamycin and varacin. It has been suggested that persulfides can mediate the conversion of molecular oxygen to reactive oxygen species (O2*-, H2O2, and HO*). Here, experiments with synthetic benzyl hydrodisulfide (BnSSH) provide direct evidence that persulfides readily decompose to produce reactive oxygen species under physiologically relevant conditions.

Chemical sequencing of restriction fragments 3'-end-labeled with [35S]dATPalphaS

Although the phosphorous radioisotope 32P is routinely used in Maxam-Gilbert sequencing, it presents disadvantages that adversely affect safety and ease of use, resolution, and DNA degradation rates. Here, we introduce a new protocol utilizing the alternative isotope 35S for 3'-end-labeling DNA restriction fragments. In our method, plasmid DNA is labeled with [35S]dATPalphaS and 7 Sequenase Version 2.0. We have shown that bands on Maxam-Gilbert sequencing gels are sharp with extremely low background. In addition, a single labeling reaction produces DNA sufficient for 80 sequencing lanes, and the labeled DNA can be utilized for prolonged periods of time without significant degradation. We have further demonstrated the utility of our 35S-end-labeling procedure by successfully mapping the sequence-specificity of DNA damage induced by photoexcited riboflavin. Overall, we have shown that 35S can be used as a safe and practical alternative to 32P in the 3'-end-labeling of DNA restriction fragments.

Sequence-recognition and cleavage of DNA by a netropsin-phenazine-di-N-oxide conjugate

We report the synthesis, DNA-binding and cleaving properties, and cytotoxic activities of R-128, a hybrid molecule in which a bis-pyrrolecarboxamide-amidine element related to the antibiotic netropsin is covalently tethered to a phenazine-di-N-oxide chromophore. The affinity and mode of interaction of the conjugate with DNA were investigated by a combination of absorption spectroscopy, circular dichroism, and electric linear dichroism. This hybrid molecule binds to AT-rich sequences of DNA via a bimodal process involving minor groove binding of the netropsin moiety and intercalation of the phenazine moiety. The bidentate mode of binding was evidenced by linear dichroism using calf thymus DNA and poly(dA-dT).(dA-dT). In contrast, the drug fails to bind to poly(dG-dC).poly(dG-dC), because of the obstructive effect of the guanine 2-amino group exposed in the minor groove of this polynucleotide. DNase I footprinting studies indicated that the conjugate interacts preferentially with AT-rich sequences, but the cleavage of DNA in the presence of a reducing agent can occur at different sequences not restricted to the AT sites. The main cleavage sites were detected with a periodicity of about 10 base pairs corresponding to approximately one turn of the double helix. This suggests that the cleavage may be dictated by the structure of the double helix rather than the primary nucleotide sequence. The conjugate which is moderately toxic to cancer cells complements the tool box of reagents which can be utilized to produce DNA strand scission. The DNA cleaving properties of R-128 entreat further exploration into the use of phenazine-di-N-oxides as tools for investigating DNA structure.

First electron spin resonance evidence for the production of semiquinone and oxygen free radicals from orellanine, a mushroom nephrotoxin

Orellanine is the tetrahydroxylated and di-N-oxidized bipyridine toxin from several Cortinarius mushrooms. The mechanism responsible for its lethal nephrotoxicity was unknown until now. Our present ESR spectroscopic study of the redox properties of the toxin is an original contribution to the knowledge of its toxicity. It was achieved in particular by comparison of the properties of orellanine to that of other bipyridine compounds. After a one-electron oxidation (e.g., photochemical oxidation upon visible light), a radical form of orellanine is observed at physiological pH under aerobic or anaerobic conditions. This radical, identified as ortho-semiquinone anion radical, can also be generated by oxidation with biological oxidizing agents or enzymatic systems. Production of superoxide and hydroxyl radicals is shown by the spin-trapping method using DMPO as a spin trap. Bioreducing agents like GSH and cysteine involve in vitro the semiquinone radical and orellanine in a redox cycling process resulting in the production of glutathionyl and oxygen free radicals. This process leads in vitro to a large oxygen consumption and to a dramatic depletion of glutathione level. The formation of an apparently stable ortho-semiquinone anion radical and of reactive oxygen radical species is observed for the first time with a mushroom toxin. It is due to the catechol-like functions borne by the di-N-oxidized bipyridine structure of the toxin and may at least partly explain the toxicity of orellanine.

Duplex and triplex directed DNA cleavage by oligonucleotide-Cu(II)/Co(III) metallodesferal conjugates

Cu(II) desferal conjugated to d(T)10 at 5'-end is shown to direct the cleavage of single stranded 19-mer target DNA d(TA1GCCCGGCG), with a base preference G > C >> A. In contrast, the corresponding Co(II)-desferal conjugate directed the cleavage specific to only G sites (G12, G16, G17 and G19). Triplex targetting on the duplex 5'-TCCTGATAAAGGAGGAGATGAAGAAAAAATGA-3': 3'-AGGACTATTTCCTCCTCTACTTCTTTTTTACT-5', using Cu(II) desferal conjugated to 5'-end of 3'-TTTCCTCCTCT-5' directed the cleavage at G5.