DNA-binding and DNA-cleaving properties of a synthetic model AGAGLU related to the antitumour drugs AMSA and bleomycin

We have previously described two synthetic models gathering a simplified model of the complexing part of Bleomycin (Blm) and the intercalating moiety of m-AMSA. These molecules, namely AGGA and AGAMGA, do not seem able to cleave DNA as Blm does. The present work is devoted to the study of a new derivative, AGAGLU, which includes in its structure a judiciously chosen connector between the two parts of the molecule. This compound, the chelating and DNA-binding properties of which are described here, has been shown to induce single-strand breakage of duplex DNA in a high level.     

The sensitivities of SV40-transformed human fibroblasts to monofunctional and DNA-crosslinking alkylating agents.

4 repair-deficient (Mer-) and 2 repair-proficient (Mer+) lines of SV40-transformed human fibroblasts were assayed for colony-forming ability after treatment with MNNG, methyl methanesulfonate (MMS), 1,3-bis-(2-chloroethyl)-1-nitrosourea (BCNU), and 1-(2-chloroethyl)-3-(2-hydroxyethyl)-1-nitrosourea (HECNU). The sensitivities to MMS, BCNU and HECNU of these SV40-transformed lines were similar to those of comparably treated human tumor cells observed previously. However, unlike human tumor lines, whose post-MNNG survival is strongly dependent upon Mer phenotype, SV40-transformed lines showed a lack of dependence of post-MNNG colony-forming ability on Mer phenotype. No differences in glutathione levels that might explain these differences were detected. The amounts of SV40-specific DNA and RNA among the lines were found to vary widely, but no correlation with Mer phenotype was found.     

Molecular modelling, synthesis and antitumour activity of carbocyclic analogues of netropsin and distamycin--new carriers of alkylating elements

A series of netropsin and distamycin analogues was synthesised and investigated by molecular modelling. The lowest-energy conformations of four carbocyclic lexitropsins, potential carriers of alkylating elements, were obtained using the HyperChem 4.0 program, and compared with the DNA-lexitropsin crystal structures from the Brookhaven National Laboratory Protein Data Bank. A method for synthesis of carbocyclic lexitropsins was elaborated, with the use of a nitro group or azobenzene as precursors for the aromatic amino group. The influence of methoxy group in ortho position with respect to amide groups on the activity of the new compounds was investigated. All of the compounds tested showed high antitumour activity in the standard cell line of mammalian tumour MCF-7.     

A complex pattern of sensitivity to simple monofunctional alkylating agents exists amongst the rad mutants of Saccharomyces cerevisiae

Summary The radiation-sensitive rad mutants of the yeast Saccharomyces cerevisiae exhibit a complex pattern of sensitivity to simple monofunctional alkylating agents. The RAD1, RAD2, RAD4 and RAD14 genes of the RAD3 epistasis group are implicated in the repair of ethylations to DNA. The RAD3, RAD10 and RAD16 genes of this group are not involved. The RAD4 and RAD14 genes have a particular role in repair following exposure to those ethylating agents that preferentially alkylate oxygen, but not to those that preferentially ethylate nitrogen. The RAD1 and RAD2 genes are involved in the repair of damage induced by all the ethylating agents used except EMS. The mutants in this group that are sensitive to ENU were not sensitive to MNU, suggesting that nucleotide excision operates on ethylations but not on methylations.In the RAD6 group, the RAD6 and RAD18 genes are involved in DNA repair after exposure to all the alkylating agents tested, whereas RAD8 appears to have a role in the repair of O-alkylations but not N-alkylations. RAD9 operates in the repair of methylations and ethylations, but does not influence events after exposure to EMS. In the RAD52 group, the mutants tested were sensitive to ENU and DES. Thus some members of all three epistasis groups are involved in the repair of alkylations to DNA.Abbreviations DES diethylsulphate - EMS ethylmethanesulphonate - ENNG N-ethyl-N-nitro-N-nitrosoguanidine - ENU N-ethylnitrosourea - MNU N-methylnitrosourea - DMSO dimethylsulphoxide - MMS methylmethanesulphonate     

The influence of linker chain length on the sequence specificity of DNA damage by n-bromoalkylphenanthridinium bromides in plasmid DNA and in intact human cells

The sequence specificity of DNA damage of n-bromoalkylphenanthridinium bromides, with linker chain lengths (n) of 4,6,8 and 10 methylene groups, was investigated in the plasmid pUC8 and in intact human cells. A linear amplification assay was used to elucidate the DNA sequence specificity of the alkylating agents. In this assay Taq DNA polymerase extends from an oligonucleotide primer up to the damage site and the products run on a DNA sequencing gel to reveal the precise sites of DNA damage. For both the plasmid and cellular experiments, the compound that caused the most damage to DNA was the n = 6 compound, followed by (in decreasing order) the n = 4, n = 8, and n = 10 compounds. There were significant differences in the sequence specificity of DNA damage between n-bromoalkylphenanthridinium bromides of different linker chain length: (1) the main sites of damage were at guanines for the n = 4,6 and 8 compounds but at guanines and adenines for the n = 10 compound; (2) a consensus sequence of 5′-c(a/t)Ggg-3′ was obtained for the n = 4,6 and 8 compounds but 5′-c(a/c)(G/A)(g/a)-3′ for the n = 10 compound; (3) runs of consecutive Gs were the major site of damage for the n = 4,6 and 8 compounds, but consecutive Gs or consecutive As for the n = 10 compound; (4) for damage at single isolated guanines, the most damaged sequences were at 5′-Ga-3′ for the n = 4 compound but at 5′-Gt-3′ for the n = 6,8 and 10 compounds. The tandemly repeated alpha RI DNA sequence was the DNA target in intact human K562 cells. In intact human cells, the compounds produced damage with similar DNA sequence selectivity to that found in plasmid DNA. The n = 4 and 6 compounds possess marginal anti-tumour activity and these compounds produced the most damage in intact human cells. The n = 8 and 10 compounds do not demonstrate significant anti-tumour activity and these compounds resulted in the least damage in cells.     

Spectroscopic properties and chromophore conformations of the photomorphogenic receptor: Phytochrome

Fluorescence lifetimes of ‘large’ (mol. wt. 120 000) and ‘small’ (mol. wt. 60 000) phytochromes isolated from oat and rye seedlings grown in the dark have been measured at 199 K and 298 K. Phytochrome model compounds have also been studied by phase modulation fluorometrically at 77 K for comparison with lifetime data for phytochrome. It was found that the fluorescence lifetime of ‘large’ phytochrome was significantly shorter than that of ‘small’ phytochrome and its chromophore models. The phytochrome chromophore of P_r form has been analyzed by fluorescence polarization, CD, and molecular orbital methods. The fluorescence excitation polarization of ‘small’ phytochrome and the chromophore model in buffer/glycerol mixture (3 : 1, v/v) at 77 K is very high (0.4) at the main absorption band and is negative (−0.1) and close to 0 in the near ultraviolet band, respectively. Analyses of the spectroscopic data suggest that the chromophore conformation of P_r and P_fr forms of phytochrome are essentially identical. The induced ellipticity of ‘large’ rye phytochrome in the blue and near ultraviolet regions was found to be significantly higher than that of ‘small’ phytochrome, indicating that the binding interaction between the phytochrome chromophore and apoprotein is much tighter in the former than in the latter. In addition, the excitation energy transfer does occur from Trp residue(s) to the chromophore in ‘large’ phytochrome but not in ‘small’ P_r. This illustrates one feature of the role played by the large molecular weight apoprotein in the binding site interactions and primary photoprocesses of P_r. Finally, a plausible model for the primary photoprocesses and the mechanism of phytochrome interactions triggered by the P_r → P_fr phototransformation have been proposed on the basis of the above results.     

Ataxia telangiectasia mutated- and Rad3-related kinase drives both the early and the late DNA-damage response to the monofunctional antitumour alkylator S23906

Numerous anticancer agents and environmental mutagens target DNA. Although all such compounds interfere with the progression of the replication fork and inhibit DNA synthesis, there are marked differences in the DNA-damage response pathways they trigger, and the relative impact of the proximal or the distal signal transducers on cell survival is mainly lesion-specific. Accordingly, checkpoint kinase inhibitors in current clinical development show synergistic activity with some DNA-targeting agents, but not with others. In the present study, we characterize the DNA-damage response to the antitumour acronycine derivative S23906, which forms monofunctional adducts with guanine residues in the minor groove of DNA. S23906 exposure is accompanied by specific recruitment of RPA (replication protein A) at replication sites and rapid Chk1 activation. In contrast, neither MRN (Mre11-Rad50-Nbs1) nor ATM (ataxia-telangiectasia mutated), contributes to the initial response to S23906. Interestingly, genetic attenuation of ATR (ATM- and Ras3-related) activity inhibits not only the early phosphorylation of histone H2AX and Chk1, but also interferes with the late phosphorylation of Chk2. Moreover, loss of ATR function or pharmacological inhibition of the checkpoint kinases by AZD7762 is accompanied by abrogation of the S-phase arrest and increased sensitivity towards S23906. These findings identify ATR as a central co-ordinator of the DNA-damage response to S23906, and provide a mechanistic rationale for combinations of S23906 and similar agents with checkpoint abrogators.     

Spectroscopic properties and chromophore conformations of the photomorphogenic receptor: phytochrome.

Fluorescence lifetimes of 'large (mol. wt. 120,000) and 'small' (mol. wt. 60,000) phytochromes isolated from oat and rye seedlings grown in the dark have been measured at 199 K and 298 K. Phytochrome model compounds have also been studied by phase modulation fluorometrically at 77 K for comparison with lifetime data for phytochrome. It was found that the fluorescence lifetime of 'large' phytochrome was significantly shorter than that of 'small' phytochrome and its chromophore models. The phytochrome chromophore of Pr form has been analyzed by fluorescence polarization, CD, and molecular orbital methods. The fluorescence excitation polarization of 'small' phytochrome and the chromophore model in buffer/glycerol mixture (3 : 1, v/v) at 77 K is very hight (0.4) at the main absorption band and is negative (--0.1) and close to 0 in the near ultraviolet band, respectively. Analyses of the spectroscopic data suggest that the chromophore conformation of Pr and Pfr forms of phytochrome are essentially identical. The induced ellipticity of 'large' rye phytochrome in the blue and near ultraviolet regions was found to be significantly higher than that of 'small' phytochrome, indicating that the binding interaction between the phytochrome chromophore and apoprotein is much tighter in the former than in the latter. In addition, the excitation energy transfer does occur from Trp residue(s) to the chromophore in 'large' phytochrome but not in 'small' Pr. This illustrates one feature of the role played by the large molecular weight apoprotein in the binding site interactions and primary photoprocesses of Pr. Finally, a plausible model for the primary photoprocesses and the mechanism of phytochrome interactions triggered by the Pr leads to Pfr phototransformation have been proposed on the basis of the above results.     

The AidB component of the Escherichia coli adaptive response to alkylating agents is a flavin-containing, DNA-binding protein

Upon exposure to alkylating agents, Escherichia coli increases expression of aidB along with three genes (ada, alkA, and alkB) that encode DNA repair proteins. In order to begin to identify the role of AidB in the cell, the protein was purified to homogeneity, shown to possess stoichiometric amounts of flavin adenine dinucleotide (FAD), and confirmed to have low levels of isovaleryl-coenzyme A (CoA) dehydrogenase activity. A homology model of an AidB homodimer was constructed based on the structure of a four-domain acyl-CoA oxidase. The predicted structure revealed a positively charged groove connecting the two active sites and a second canyon of positive charges in the C-terminal domain, both of which could potentially bind DNA. Three approaches were used to confirm that AidB binds to double-stranded DNA. On the basis of its ability to bind DNA and its possession of a redox-active flavin, AidB is predicted to catalyze the direct repair of alkylated DNA.     

Spectral properties and chromophore rotation of phytochrome bound to substituted Sepharose

Brushite purified phytochrome from Avena sativa L. cv. Sol II was bound to phenyl Sepharose, octyl Sepharose, CNBr-activated Sepharose and to anti-phytochrome immunoglobulins immobilized on Sepharose. The spectral properties of phytochrome bound to anti-phytochrome immunoglobulins and to phenyl Sepharose were similar to phytochrome in solution. Phytochrome bound to CNBr-activated Sepharose or to octyl Sepharose showed reduced P_fr formation after red irradiation. The reversal to P_r with far-red light was only partial but a further increase at 667 nm took place slowly in the dark. A peak at 657 nm was seen in the difference spectrum between CNBr-activated Sepharose-bound phytochrome kept in darkness and the identical sample immediately after a far-red irradiation.
The change in linear dichroism at 660 nm and 730 nm, induced by plane polarized red or far-red light, was measured. It was computed that the long-wavelength transition moment of phytochrome had an average rotation angle of 31.5° or 180°–31.5°. The substrate used for immobilization had a limited effect on the rotation angle. Phytochrome immobilized on CNBr-activated Sepharose gave an angle of 27.8° and phytochrome immobilized on phenyl Sepharose gave an angle of 32.6°.     

Cyclic assemblies formed by metal ions, pyrimidines and isogeometrical heterocycles: DNA binding properties and antitumour activity

In this contribution, we discuss the use of simple pyrimidine derivatives and geometrically related heterocycles in combination with protected metal ions to build cyclic polynuclear coordination assemblies. The resulting assemblies range from conformationally rigid triangles to corrugated octagons with positively charged cavities and surfaces that can interact with anionic species in a supramolecular fashion. Special attention has been focussed to the supramolecular interaction of these systems towards mononucleotides and DNA as a possible novel interaction of DNA binding metallo-drugs. The results show that these systems efficiently interact with both mononucleotides and ds-DNA. The molecular recognition of ds-DNA leads to significant conformational changes, however, this interaction gives only rise to moderate cytotoxic effects towards tumour cell lines.     

The preparation and properties of ficin chemically attached to carboxymethylcellulose

1. Purified ficin has been coupled to four CM-celluloses by reaction with their acid azide derivatives. Insoluble products containing 1.8-4.7mg. of ficin/100mg. of product and retaining 8.0-12.0% of the free enzyme's esterase activity have been obtained. 2. The amount of bound ficin in these preparations is dependent on the degree of carboxymethyl substitution of the CM-cellulose to which the ficin is attached. 3. A shift of the alkaline limb of the pH-activity curve of ficin when chemically attached to CM-cellulose has been shown. 4. Only a small loss has been observed in the enzymic activity of these products when stored at 2 degrees for 4 months. They are more resistant than free enzyme to heat denaturation. 5. Columns of CM-cellulose-ficin have been packed. The degree of hydrolysis of perfused substrate has been measured for different flow rates through the column. 6. The properties of these derivatives have been discussed.     

Structure, antimicrobial activity and DNA-binding properties of the cobalt(II)-sparfloxacin complex

The neutral mononuclear cobalt(II) complex with sparfloxacin has been prepared and characterized with physicochemical, spectroscopic and electrochemical techniques, and molecular mechanics calculations. The interaction of the complex with calf-thymus DNA has been investigated with UV spectroscopy, cyclic voltammetry, and competitive studies with ethidium bromide. The antimicrobial activity of the complex has been tested against three microorganisms.     

Stability of an organometallic ruthenium-ubiquitin adduct in the presence of glutathione: relevance to antitumour activity

The interactions of the ruthenium(II) complex Ru(η⁶-p-cymene)(pta)Cl₂ (RAPTA-C), an effective anticancer and antimetastatic agent, with biological nucleophiles are important with respect to its mechanism of action, for example, the reaction with glutathione (GSH) potentially plays an important role in detoxification. RAPTA-C reacts rapidly with glutathione forming a series of adducts including Ru(η⁶-p-cymene)(pta)(GS), Ru(η⁶-p-cymene)(GS) and bis-GSH conjugates, which were characterised by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). In addition, the ability of glutathione to cleave ruthenium-ubiquitin bonds was assayed and it was shown that GSH is capable of removing the Ru moiety from the protein, although no ternary adducts were identified.     

Immobilized enzymes: the catalytic properties of lactate dehydrogenase convalently attached to glass beads

Chick LDH (H₄ and M₄) has been covalently attached to aryl and alkyl amine glass using sodium nitrite and glutaraldehyde respectively. These immobilized enzymes remain active for months at 0°C and exhibit Km values similar to those of the soluble enzyme; however, they have pH-rate profiles that are independent of pH and show decreased substrate inhibition. Disaggregation followed by reassociation indicate the enzymes are bound by all four subunits and the resulting activity restored to the native, aryl amine and glutaraldehyde bound enzyme are 33, 25 and 90% respectively. At a pH of 3.2 and 25°, the soluble and aryl amine glass LDH's are rapidly denatured while the glutaraldehyde bound enzyme shows no loss of activity for at least 35 days.     

Intrachain reactions of a pair of reactive groups attached to polymer ends. V. Formation of disulfide linkages in the air-oxidation of sulfhydryl groups attached to ends of polysarcosine chain

Polysarcosine having sulfhydryl groups attached to both ends was synthesized by the NCA method and its air-oxidation was investigated in aqueous solution with cupric-ion or ferric-ion catalysts. Air-oxidation was also conducted for a polysarcosine having one terminal sulfhydryl group. The product of the air-oxidation was fractionated by gel chromatography. The product analysis of the fully oxidized monofunctional polymer showed that the sulfhydryl groups were converted into disulfide bonds exclusively. There was no evidence for the interchange between two disulfide linkages or between a disulfide linkage and a sulfhydryl group during the air-oxidation. The analysis of the products from the bifunctional polysarcosine showed that they were composed of a series of cyclic “monomer,” “dimer,” “trimer,” and higher “oligomers.” The cyclic structure was characterized by the larger elution volume in the gel chromatogram than that for a linear homologue having the same molecular weight. The weight fraction of each cyclic oligomer was determined by gel chromatography. The fraction of cyclic monomer F₁ decreased monotonously with increasing the chain length. Smaller values of F₁ were observed with cupric-ion catalyst than with ferric-ion catalyst. The dependence of F₁ on the polymer concentration was much smaller than that expected from a simple competition mechanism between intra- and intermolecular reactions. These results indicate that the choice between intra- and intermolecular reactions is governed by the mode of the coordination of sulfhydryl groups to transition metal ions.     

Synthesis and antitumor activity of duocarmycin derivatives: modification at C-8 position of A-ring pyrrole compounds bearing the simplified DNA-binding groups

A series of the 8-O-substituted A-ring pyrrole derivatives of duocarmycin bearing the simplified DNA-binding moieties such as cinnamoyl or heteroarylacryloyl groups were synthesized, and evaluated for in vitro anticellular activity against HeLa S3 cells and in vivo antitumor activity against murine sarcoma 180 in mice. In addition, the stability of the 8-O-substituted analogues in aqueous solution and the conversion to their active form (cyclopropane compound) from the 8-O-substituted analogues in mice or human serum were examined. The 8-O-substituted A-ring pyrrole derivatives bearing the simplified DNA-binding moieties showed remarkably potent in vivo antitumor activity and low peripheral blood toxicity compared with the 8-O-substituted A-ring pyrrole derivatives having the trimethoxyindole skeleton in segment-B (Seg-B), which were equal to 8-O-[(N-methylpiperazinyl)carbonyl] derivatives of 4'-methoxycinnamates and 4'-methoxy-beta-heteroarylacrylates. Moreover, among 8-O-substituted analogues, several compounds can be chemically or enzymatically converted to their active form in human serum. This result indicated that new 8-O-substituted derivatives were different prodrugs from KW-2189 and 8-O-substituted analogues being the same type of prodrug as KW-2189.     

Inactivation of the T7 coliphage by monofunctional alkylating agents. Action of phage adsorption and injection of its DNA.

Alkylation by ethyl or methyl methanesulfonate to an extent that inactivates more than 99.5% of T7 coliphages has no effect on phage adsorption on Escherichia coli B cells, but decreases the amount of phage DNA injected into the host cells. Depurination interferes with the injection of the phage DNA. Failure to inject the whole phage genome thus appears to be a cause of the immediate as well as of the delayed inactivation of the T7 coliphage treated by monofunctional alkylating agents; the hypothesis that it is the only cause of inactivation, although not very likely, cannot be excluded at the present time.