Ferrocene-conjugated copper(II) dipyridophenazine complex as a multifunctional model nuclease showing DNA cleavage in red light

The copper(II) complex [Cu(L)(dppz)](ClO₄)₂ (1) having a tripodal ligand ferrocenylmethylbis(2-pyridylmethylamine) (L) with a pendant ferrocenyl unit and a planar NN-donor dipyrido-[3,2-a:2′,3′-c]-phenazine (dppz) base is prepared and its DNA binding and cleavage properties studied. The complex is redox active showing cyclic voltammetric responses at 0.52 and –0.01 V vs. SCE due to Fe(III)/Fe(II) and Cu(II)/Cu(I) couples, respectively. The complex that binds to the major groove of DNA shows dual chemical nuclease activity involving both the metal centres. The complex displays efficient photo-induced DNA cleavage activity in visible laser light of 458 and 568 nm wavelengths forming cleavage active hydroxyl radicals. Significant DNA cleavage is also observed in red light of 647 nm within the photodynamic therapy (PDT) window.     

A new Os,Rh bimetallic with O2 independent DNA cleavage and DNA photobinding with red therapeutic light excitation

Many Ru and Os systems display photoactive (3)MLCT states. Systems activated by therapeutic window light in the absence of O(2) remain elusive. [(bpy)(2)Os(dpp)RhCl(2)(phen)](3+) photobinds and photocleaves DNA under red light in an oxygen independent manner, due to molecular design involving one Os chromophore coupled to a photoactive cis-Rh(III)Cl(2) moiety.     

Studies on the DNA binding and cleavage activity of a synthesized polyamide containing dipeptide Ser-His

The DNA binding and cleavage activity of a synthetic polyamide containing dipeptide Ser-His has been investigated by spectroscopic techniques, such as electronic absorbance and circular dichroism (CD) spectropolarimetry, as well as gel electrophoresis. The results show that the molecule has a strong interaction with DNA and can improve DNA-cleavage ability about 100 fold as compared with single dipeptide Ser-His.     

Novel pyrazole fused heterocyclic ligands: Synthesis,characterization, DNA binding/cleavage activity and anti-BVDV activity

A series of novel pyrazole fused heterocyclic derivatives were synthesized via a two-step procedure or a one-pot two step method,and their catalytic DNA cleavage abilities and anti-BVDV activities were also evaluated.The results obtained indicated that compounds 3b-3c could catalyze the cleavage of supercoiled DNA(pUC 19 plasmid DNA) to nicked DNA under physiological conditions with high yields via a hydroiytic mechanism.The studies on anti-viral activities against bovine viral diarrhea virus(BVDV) demonstrated that some of the pyrazole derivatives showed pronounced anti-BVDV activity with interesting EC_(50) values and no significant cytotoxicity.Among them,compound 31 showed the highest antiviral activity(EC_(50) = 0.12 μmoI/L) and was 10 fold more than that of the positive control ribavirin(EC_(50)= 1.3 μmol/L),which provided a potential candidate for the development of anti-BVDV agents.     

Homopolymeric pyrrolidine-amide oligonucleotide mimics: Fmoc-synthesis and DNA/RNA binding properties

By chemically modifying or replacing the backbone of oligonucleotides it is possible to modulate the DNA and RNA recognition properties and fine-tune the physiochemical properties of oligomers. This is important because it challenges our understanding of natural nucleic acid structural and recognition properties and can lead to nucleic acid mimics with a wide range of applications in nucleic acid targeting, analysis or diagnostics. In this paper we describe the solid phase synthesis of pyrrolidine-amide oligonucleotide mimics (POMs) using Fmoc-peptide chemistry. This required the synthesis of adeninyl, cytosinyl, thyminyl and guaninyl pyrrolidine monomers, with Fmoc- and standard acyl-protecting groups on the exocyclic amino groups and nucleobases respectively. These monomers were used to synthesise several thyminyl and adeninyl POM pentamers, with modest coupling efficiency. The pentamers were purified by RP-HPLC, characterised by mass spectrometry and their DNA and RNA binding properties were investigated using UV thermal denaturation/renaturation experiments. This revealed that all the pentamers exhibit strong affinity for complementary nucleic acids. The further evaluation of longer mixed-sequence POMs is described in a second accompanying paper (R. J. Worthington et al., Org. Biomol. Chem., 2006, DOI: 10.1039/b613386j).     

Synthesis and antimicrobial activity of some netropsin analogues

Nine novel lexitropsins were synthesized by linking two netropsin-like moieties through three different dicarboxylic acids; 9,10-dihydro-2,7-phenanthrenedicarboxylic acid; [(3-[[(carboxymethyl)amino]carbonyl]benzoyl)amino]acetic acid and indole-2,5-dicarboxylic acid. The netropsin residues were modified by the use of N-isopentylpyrrole, 5-methylthiophene or 5-isopropylthiazole heterocyclic building blocks in place of the usual N-methylpyrrole. The compounds were tested against five gram-positive bacteria: Staphylococcus aureus, Streptomyces faecalis, methicillin resistant Staphylococcus aureus, Enterobacter cloacae, Mycobacterium fortuitum, three gram-negative bacteria: Klebsiella aerogenes, Proteus vulgaris, Escherichia coli and three fungi: Aspergillus niger, Candida albicans and Aspergillus nidulans. Some of the compounds showed significant inhibitory effects on the growth of the microorganisms.     

DNA-bleomycin interaction: Nucleotide sequence-specific binding and cleavage of DNA by bleomycin

Biosynthetic intermediates and synthetic analogues of bleomycin (BLM) have been investigated for their metal binding, dioxygen activation, and DNA cleavage. Molecular O₂ was activated by the Fe(II) complex of a synthetic model ligand. Nucleotide sequence specificities in DNA cleavage by the BLM-Fe(II) and deglyco-BLM-Fe(II) complexes were almost identical. It has been shown that (1) the β-aminoalanine-pyrimidine-β-hydroxyhistidine portion of BLM is essential for the metal binding and dioxygen activation and (2) the bithiazole moiety contributes to the specific binding to guanine base of DNA.     

Metal-assisted red light-induced efficient DNA cleavage by dipyridoquinoxaline-copper(II) complex

Complete cleavage of double stranded pUC19 DNA by the complex [Cu(dpq)2(H2O)](ClO4)2 (dpq, dipyridoquinoxaline) has been observed on irradiation at 694 nm from a pulsed ruby laser, assisted by the metal d-band transition as well as the quinoxaline triplet states in the absence of any external additives.     

Mixed-ligand copper(II)-phenolate complexes: effect of coligand on enhanced DNA and protein binding, DNA cleavage, and anticancer activity

The copper(II) complex [Cu(tdp)(ClO4)].0.5H2O (1), where H(tdp) is the tetradentate ligand 2-[(2-(2-hydroxyethylamino)ethylimino)methyl]phenol, and the mixed ligand complexes [Cu(tdp)(diimine)]+ (2-5), where diimine is 2,2'-bipyridine (bpy) (2), 1,10-phenanthroline (phen) (3), 3,4,7,8-tetramethyl-1,10-phenanthroline (tmp) (4), and dipyrido-[3,2-d:2',3'-f]-quinoxaline (dpq) (5), have been isolated and characterized by analytical and spectral methods. Complexes 1 and [Cu(tdp)(phen)]ClO4 (3) have been structurally characterized, and their coordination geometries around copper(II) are described as distorted octahedral. The equatorially coordinated ethanolic oxygen in 1 is displaced to an axial position upon incorporating the strongly chelating phen, as in 3. The solution structures of all the complexes have been assessed to be square-based using electronic absorption and electron paramagnetic resonance (EPR) spectroscopy. The interaction of the complexes with calf thymus DNA (CT DNA) has been explored by using absorption, emission, and circular dichroic spectral and viscometric studies, and modes of DNA binding for the complexes have been proposed. Absorption spectral (Kb = 0.071 +/- 0.005 (2), 0.90 +/- 0.03 (3), 7.0 +/- 0.2 (4), 9.0 +/- 0.1 x 10(5) M(-1) (5)), emission spectral (Kapp = 4.6 (1), 7.8 (2), 10.0 (3), 12.5 (4), 25.0 x 10(5) M(-1) (5)), and viscosity measurements reveal that 5 interacts with DNA more strongly than the other complexes through partial intercalation of the extended planar ring of the coordinated dpq with the DNA base stack. Interestingly, only complex 4 causes a B to A conformational change upon binding DNA. All the complexes hydrolytically cleave pBR322 supercoiled DNA in 10% DMF/5 mM Tris-HCl/50 mM NaCl buffer at pH 7.1 in the absence of an activating agent, and the cleavage efficiency varies in the order 5 > 3 > 2 > 4 > 1 with 5 displaying the highest Kcat value (5.47 +/- 0.10 h(-1)). The same order of cleavage is observed for the oxidative cleavage of DNA in the presence of ascorbic acid as a reducing agent. Interestingly, of all the complexes, only 5 displays efficient photonuclease activity through double-strand DNA breaks upon irradiation with 365 nm light through a mechanistic pathway involving hydroxyl radicals. The protein binding ability of 1-5 has been also monitored by using the plasma protein bovine serum albumin (BSA), and 4 exhibits a protein binding higher than that of the other complexes. Further, the anticancer activity of the complexes on human cervical epidermoid carcinoma cell line (ME180) has been examined. Interestingly, the observed IC50 values reveal that complex 4, which effects conformational change on DNA and binds to BSA more strongly, exhibits a cytotoxicity higher than the other complexes. It also exhibits approximately 100 and 6 times more potency than cisplatin and mitomycin C for 24 and 48 h incubation times, respectively, suggesting that 4 can be explored further as a potential anticancer drug. Complexes 4 and 5 mediate the arrest of S and G2/M phases in the cell cycle progression at 24 h harvesting time, which progress into apoptosis.     

A designer bleomycin with significantly improved DNA cleavage activity

The bleomycins (BLMs) are used clinically in combination with a number of other agents for the treatment of several types of tumors, and the BLM, etoposide, and cisplatin treatment regimen cures 90-95% of metastatic testicular cancer patients. BLM-induced pneumonitis is the most feared, dose-limiting side effect of BLM in chemotherapy, which can progress into lung fibrosis and affect up to 46% of the total patient population. There have been continued efforts to develop new BLM analogues in the search for anticancer drugs with better clinical efficacy and lower lung toxicity. We have previously cloned and characterized the biosynthetic gene clusters for BLMs from Streptomyces verticillus ATCC15003, tallysomycins from Streptoalloteichus hindustanus E465-94 ATCC31158, and zorbamycin (ZBM) from Streptomyces flavoviridis SB9001. Comparative analysis of the three biosynthetic machineries provided the molecular basis for the formulation of hypotheses to engineer novel analogues. We now report engineered production of three new analogues, 6'-hydroxy-ZBM, BLM Z, and 6'-deoxy-BLM Z and the evaluation of their DNA cleavage activities as a measurement for their potential anticancer activity. Our findings unveiled: (i) the disaccharide moiety plays an important role in the DNA cleavage activity of BLMs and ZBMs, (ii) the ZBM disaccharide significantly enhances the potency of BLM, and (iii) 6'-deoxy-BLM Z represents the most potent BLM analogue known to date. The fact that 6'-deoxy-BLM Z can be produced in reasonable quantities by microbial fermentation should greatly facilitate follow-up mechanistic and preclinical studies to potentially advance this analogue into a clinical drug.     

Synthesis,magnetic properties,DNA binding and cleavage activity of a new oxalato bridged copper(II) complex

A novel oxalato‐bridged copper(II) complex has been prepared and structurally characterized: [Cu(bpa)(μ‐C₂O₄)].H₂O (bpa = bis(2‐pyridylmethyl) amine). In the complex, the copper ion is linked in an unusual μ_1,2,3‐C₂O₄^2? bridging mode, generating one‐dimensional zigzag chain disposition. Variable‐temperature magnetic susceptibility studies (2–300 K) reveal a weak ferromagnetic coupling, J = 0.63 cm^?1, between the copper ions. The interaction of the complex with CT‐DNA has been studied using UV–visible absorption and emission spectral methods, and the binding constant of the complex with CT‐DNA is K_app = 9 × 10⁴ m ^?1, which indicates that the interaction of the complex with DNA is a moderate intercalative mode. Furthermore, the complex cleaves supercoiled plasmid DNA efficiently in the presence of hydrogen peroxide. The mechanistic investigations suggest that the hydroxyl radical and singlet oxygen are involved in the DNA degradation. Copyright © 2012 John Wiley & Sons, Ltd.     

Structural, spectroscopic, and magnetic properties of a diphenolate-bridged FeNi complex showing excellent phosphodiester cleavage activity

To mimic the phosphate ester hydrolysis behavior of purple acid phosphatases the heterobimetallic complex [(BNPP)Fe^IIIL(μ-BNPP)Ni^II(H₂O)](ClO₄) (1) has been synthesized from the precursor complexes [Fe^III(LH₂)(H₂O)₂](ClO₄)₃·3H₂O and [Fe^III(LH₂)(H₂O)Cl](ClO₄)₂·2H₂O. In these compounds, L²⁻ is the anion of the tetraiminodiphenol macrocyclic ligand (H₂L), while LH₂ is the zwitterionic form in which the phenolic protons are shifted to the two metal-uncoordinated imine nitrogens, and BNPP is bis(4-nitrophenyl)phosphate. The X-ray crystal structure of compound 1 has been determined. The structure of 1 comprises of two edge-shared distorted octahedrons whose metal centers are bridged by two equatorial phenolate oxygens and two axially disposed oxygens of a BNPP ligand. The internuclear Fe?Ni distance is 3.083 Å. The high-spin iron(III) and nickel(II) in 1 are antiferromagnetically coupled (J = −7.1 cm⁻¹; H = −2JS₁·S₂) with S = 3/2 spin ground state. The phosphodiesterase activity of 1 has been studied in 70:30 H₂O-(CH₃)₂SO medium with NaBNPP as the substrate. The reaction rates have been measured by varying pH (3-10), temperature (25-50 °C), and with different concentrations of the substrate and complex at a fixed pH and temperature. Treatment of the rate data, obtained at pH 6.0 and at 35 °C, by the Michaelis-Menten approach have provided the following parameters: K_M = 3.6 × 10⁻⁴ M, V_max = 1.83 × 10⁻⁷ M s⁻¹, k_cat = 9.15 × 10⁻³ s⁻¹. As compared to the uncatalyzed hydrolysis rate of BNPP, the k_cat value is 8.3 × 10⁸ times higher, showing that 1 behaves as an excellent model for phosphate ester hydrolysis.     

A novel pyrrolidinyl PNA showing high sequence specificity and preferential binding to DNA over RNA

A novel conformationally constrained pyrrolidinyl peptide nucleic acid (PNA) carrying an D-aminopyrrolidine carboxylic acid (D-Apc) spacer was synthesized, and its interactions with complementary oligo- and polynucleotides were studied by UV and CD spectroscopy. The decathymine PNA formed very stable PNA-DNA complexes with poly(dA) and (dA)(10) by a sequence-specific A-T pairing. The interaction with poly(rA) gave the corresponding PNA-RNA complex with much lower stability.     

Mixed-sequence pyrrolidine-amide oligonucleotide mimics: Boc(Z) synthesis and DNA/RNA binding properties

Pyrrolidine-amide oligonucleotide mimics (POMs) exhibit promising properties for potential applications, including in vivo DNA and RNA targeting, diagnostics and bioanalysis. Before POMs can be evaluated in these applications it is first necessary to synthesise and establish the properties of fully modified oligomers, with biologically relevant mixed sequences. Accordingly, Boc-Z-protected thyminyl, adeninyl and cytosinyl POM monomers were prepared and used in the first successful solid phase synthesis of a mixed sequence POM, Lys-TCACAACTT-NH2. UV thermal denaturation studies revealed that the POM oligomer is capable of hybridising with sequence selectivity to both complementary parallel and antiparallel RNA and DNA strands. Whilst the duplex melting temperatures (Tm) were higher than the corresponding duplexes formed with isosequential PNA, DNA and RNA oligomers the rates of association/dissociation of the mixed sequence POM with DNA/RNA targets were noticeably slower.     

Synthesis, DNA binding, photo-induced DNA cleavage and cytotoxicity studies of europium(III) complexes

Two Eu(III) complexes, [Eu(acac)(3)(dpq)] (1) and [Eu(acac)(3)(dppz)] CH(3)OH (2) {viz. acetylacetonate (acac), dipyrido[3,2-d:20,30-f]quinoxaline (dpq), dipyrido[3,2-a:20,30-c] phenazine (dppz)}, have been synthesized and their DNA binding, photo-induced DNA cleavage activity and cell cytotoxicity are studied. The complexes display significant binding propensity to the calf thymus DNA in the order: 2(dppz) >1(dpq). Cleavage experiments using pBR322 supercoiled DNA suggest major groove binding for 2 and minor groove binding for 1. The mechanistic aspects on natural light (natural light in room during the day) and UV-A (365 nm) irradiation are via a mechanistic pathway involving formation of singlet oxygen and hydroxyl radical as the reactive species. The photo-induced DNA cleavage activity of 2 is also stronger than 1. The cytotoxicity of 1 and 2 against HeLa (cervical) cancer cells show that the IC(50) value of 19.11 ± 3.56 μM and 17.95 ± 5.47 μM, respectively.     

459—The effect of netropsin on the electrochemical oxidation of DNA at a graphite electrode

The interaction of netropsin with calf thymus, Bacillus cereus and Micrococcus luteus DNAs and with the RNA of phage f2 was studied by means of differential pulse voltammetry at a paraffin-wax-impregnated spectroscopic graphite electrode. It was found that the oxidation voltammetric peaks of double-helical calf thymus and Bacillus cereus DNAs were lowered when netropsin was added to the DNA solution. The peak corresponding to electro-oxidation of adenine residues was lowered more than that corresponding to electro-oxidation of guanine residues. Under the same experimental conditions the oxidation peaks of double-helical Micrococcus luteus DNA, double-helical RNA and thermally denatured samples of all DNAs used were almost uninfluenced by the addition of netropsin. The results observed were explained by (i) decreased flexibility of the segments to which netropsin was bound, and (ii) the specific binding of netropsin to the segments of double-helical DNA rich in adenine thymine pairs.