Conformational aspects of drug-DNA interactions: Studies on anthracycline antibiotics and psoralen derivatives

The interaction of anticancer agents, analogues of adriamycin and of photo-chemotherapeutic compounds of the psoralen structural type with DNA was investigated using spectroscopic, hydrodynamic and chiroptical techniques. The nucleic acid may undergo conformational changes from the B form to more compact structures as a result of the binding process to charged compounds. Different complex geometries adopted byvarious drugs were observed and discussed in terms of intercalation into the polynucleotide double helix and orientation of the ligand in the base-pair pocket. The binding of chemotherapeutic agents to functionally organized DNA was also studied. Lower binding affinities and modified spectral responsesareindicativeofdifferent drug-DNA complexation patternsinthiscase. The results of these studies allow a better understanding of drug-nucleic acid interactions at a molecular level.     

Oxidation of anthracycline antibiotics

The quantum-chemical estimation of the highest occupied molecular orbital energy for the aglycons of carminomycin, rubomycin, adriamycin and aclacinomycin A in the neutral and ionized states was performed with a semiempirical method. It was shown that the aglycon ionization amplified the electron donor properties of the antibiotics. On the basis of the difference in the absorption spectra of the neutral and ionized chromophores their ionization constants were determined spectrophotometrically. For comparison of the electron donor properties of the anthracyclines at the physiological pH value the reaction of their oxidation with potassium ferricyanide accompanied by decoloration of the solutions was studied. On the basis of the quantum-chemical and experimental data it was concluded that the electron donor properties amplified as follows: aclacinomycin A less than adriamycin-rubomycin less than carminomycin. At the same time their acute toxicity increased (a decrease in the LD50). Therefore, the toxicity of the anthracycline antibiotics could be also due to formation of the radicals with high reactivity on the monoelectronic oxidation.     

Advances in bioconversion of anthracycline antibiotics

During the last decade new anthracycline-type structures with potential usefulness in cancer treatment have been supplied both by new microbial strains and by bioconversions of precursor molecules employing cells or enzymes. We highlight recent advances in bioconversion of anthracycline structures with the main focus on late transformations such as are carried out by oxidoreductases.     

Interaction of anthracycline antibiotics with actin and heavy meromyosin.

For the purpose of elucidating the biochemical mechanism of anthracycline cardiomyopathy, the interaction with actin and heavy meromyosin (HMM) was studied. HMM and acto-HMM Mg²⁺-ATPase reactions were inhibited by daunorubicin and adriamycin; but not significantly by aclacinomycin A. The three antibiotics induced G-actin polymerization. Difference absorption spectra showed a direct interaction of adriamycin or aclacinomycin A with actin or HMM. Equilibrium dialysis and spectrofluorometric studies indicated that actin monomer possesses one binding site for adriamycin or aclacinomycin A with the same order of association constants (1.4 – 7.2 × 10⁴ M^?1). Adriamycin exhibited significantly higher affinity for HMM than aclacinomycin A.     

Interaction of anthracycline antibiotics with biopolymers: 7. Equilibrium binding studies on the interaction of iremycin and DNA

We report spectrophotometric equilibrium studies of both the self-association of the new antibiotic iremycin and of its binding to calf thymus DNA in solution (ionic strength 0.2 M; pH 6.0). Iremycin forms dimers in this solution with a dimerization constant K₄=(1.19 ± 0.10) × 10³ M⁻¹. This equilibrium is taken into account in the evaluation of the interaction of iremycin with DNA. The binding behaviour can be completely described by a single binding mechanism of monomeric iremycin to DNA with allowance both for neighbour exclusion and for cooperativity of interaction. The three intrinsic binding parameters for the homogeneous model were determined simultaneously by a least squares fit of the original titration data: equilibrium constant of cooperative binding K = (2.72 ± 0.66) × 10⁵ M⁻¹ cooperativity parameter σ=0.38±3.27 ± 0.32. The binding parameters of iremycin and adriamycin and their microbial activities are compared.     

Investigation of the interaction of superoxide ion with adriamycin and the possible origin of cardiotoxicity of the anthracycline anticancer antibiotics

Interaction of superoxide ion with adriamycin in an aprotic medium has been studied. It was shown that superoxide ion reacts irreversibly with adriamycin, giving a diamagnetic product (the dimer or oligomer of semiquinone) which can be reoxidized to adriamycin. This product was also obtained when adriamycin reacted with benzosemiquinone, ubisemiquinone, and the semiquinones of tocopherylquinone and vitamin K₁. It is suggested that the cardiotoxicity of adriamycin and other anthracycline anticancer antibiotics is caused by the high elcctron-attracting properties of these antibiotics, while the ability of natural quinones to reduce cardiotoxicity and to induce recovery of respiration in mitochondria is due to their interaction with the semiquinone states of the antibiotics.     

Interaction of anthracycline antibiotics with biopolymers: 9. Comparative study of the interaction kinetics of daunomycin,adriamycin and iremycin with DNA

The interaction kinetics of the three anthracycline antibiotics, daunomycin, adriamycin and iremycin, with calf thymus DNA has been investigated using the temperature-jump technique. Experimental data obtained at high binding ratio have been fitted by a kinetic theory which, for the binding of large ligands to a linear polymer chain, takes into account both nearest-neighbour ligand interaction and the overlap of potential binding sites. The kinetics of such cooperative binding according to a single-step mechanism can be described completely by two independent microscopic parameters, namely one rate constant and a kinetic cooperativity parameter. Both these parameters have been determined for the three anthracyclcine antibiotics, making use of the known equilibrium binding parameters. The association rate constant in the singly contiguous case turns out to be almost the same for all three antibiotics ($\text{7 × 10}{}^6\text{to 8 × 10}{}^6\text{1 mol}{}^{\mathrm{?1}}\text{s}{}^{\mathrm{?1}}$), while the corresponding dissociation rate constant ranges from 3.5 s^?1 for adriamycin to 10 s^?1 for daunomycin and about 35 s^?1 for iremycin. The different equilibrium binding constants thus correspond to different mean attachment times of the antibiotics at the polymer chain, which positively correlate with the inhibitory action of these drugs on in vitro DNA synthesis. Nearest-neighbour interaction in the case of adriamycin-DNA binding kinetics implies that adriamycin molecules dissociate from an isolated binding site nine times more frequently than from a site between two adjacent ligands.     

Conformational preference functions for predicting helices in membrane proteins

A suite of FORTRAN programs, PREF, is described for calculating preference functions from the data base of known protein structures and for comparing smoothed profiles of sequence-dependent preferences in proteins of unknown structure. Amino acid preferences for a secondary structure are considered as functions of a sequence environment. Sequence environment of amino acid residue in a protein is defined as an average over some physical, chemical, or statistical property of its primary structure neighbors. The frequency distribution of sequence environments in the data base of soluble protein structures is approximately normal for each amino acid type of known secondary conformation. An analytical expression for the dependence of preferences on sequence environment is obtained after each frequency distribution is replaced by corresponding Gaussian function. The preference for the α-helical conformation increases for each amino acid type with the increase of sequence environment of buried solvent-accessible surface areas. We show that a set of preference functions based on buried surface area is useful for predicting folding motifs in α-class proteins and in integral membrane proteins. The prediction accuracy for helical residues is 79% for 5 integral membrane proteins and 74% for 11 α-class soluble proteins. Most residues found in transmembrane segments of membrane proteins with known α-helical structure are predicted to be indeed in the helical conformation because of very high middle helix preferences. Both extramembrane and transmembrane helices in the photosynthetic reaction center M and L subunits are correctly predicted. We point out in the discussion that our method of conformational preference functions can identify what physical properties of the amino acids are important in the formation of particular secondary structure elements. © 1993 John Wiley & Sons, Inc.     

Release of iron from ferritin by cardiotoxic anthracycline antibiotics

The use of the extremely effective anthracycline antitumor drugs adriamycin and daunomycin is limited by a severe, dose-dependent cardiomyopathy. Anthracycline-induced toxicity has been proposed to involve iron-dependent oxidative damage to biological macromolecules yet little is known regarding the availability of physiologic iron. We now report that, in the presence of NADPH-cytochrome P-450 reductase, these drugs undergo redox cycling to generate superoxide which mediates a slow, reductive release of iron from ferritin, the major intracellular iron storage protein. Anaerobically, the semiquinone free radical forms of adriamycin and daunomycin catalyze a very rapid, extensive release of iron from ferritin. In contrast, diaziquone, an aziridinyl quinone antitumorigenic agent which is less cardiotoxic, is unable to release iron from ferritin. Thus, the present studies suggest that the cardiomyopathy observed with the anthracyclines, and perhaps their antineoplastic activity as well, may be related to their ability to delocalize tissue iron, thereby contributing to the formation of strong oxidants capable of damaging critical cellular constituents.     

Kinetics of dissociation of nogalamycin from DNA: comparison with other anthracycline antibiotics

Stopped-flow spectrometry and simple mixing techniques have been employed to investigate the detergent-induced dissociation of anthracycline antibiotics from natural and synthetic DNAs. Both daunomycin and nogalamycin dissociate more slowly from poly(dG-dC) than from poly(dA-dT) but the difference is much more marked for nogalamycin. With an equimolar mixture of poly(dG-dC) and poly(dA-dT), or with poly(dA-dC).poly(dG-dT), dissociation of nogalamycin occurs very slowly. In all cases the release of antibiotic from a synthetic polynucleotide is a one-step process following a single exponential. Dissociation of daunomycin, adriamycin and iremycin from calf thymus DNA is a more complex reaction which requires a two-exponential fit, in contrast to earlier reports, but differences between the behaviour of the three antibiotics are minor. Dissociation of nogalamycin from natural DNA requires a three-exponential fit, is in general far slower, and depends upon the base composition, the level of binding and the time allowed for the complex to equilibrate. It is concluded that sequence selectivity is minimal or lacking for daunomycin, whereas nogalamycin binding is sequence dependent and probably involves migration of the antibiotic between DNA binding sites. There is an inverse correlation between dissociation rate constants and antibacterial potency in simple tests.     

Kinetics of dissociation of nogalamycin from DNA: comparison with other anthracycline antibiotics

Stopped-flow spectrometry and simple mixing techniques have been employed to investigate the detergent-induced dissociation of anthracycline antibiotics from natural and synthetic DNAs. Both daunomycin and nogalamycin dissociate more slowly poly(dG-dC) than from poly(dA-dT), but the difference is much more marked for nogalamycin. With an equimolar mixture of poly(dG-dC) and poly(dA-dT), or with poly(dA-dC)·poly(dG-dT), dissociation of nogalamycin occurs very slowly. In all cases the release of antibiotic from a synthetic polynucleotide is a one-step process following a sinigle exponential. Dissociation of daunomycin, adrianmycin and iremycin from calf thymus DNA is a more complex reaction which requires a two-exponential fit, in contrast to earlier reports, but differences between the behaviour of the three antibotics are minor. Dissociation of nogalamycin from natural DNA requires a three-exponential fit, is in general far slower, and depends upon the base composition, the level of binding and the time allowed for the complex to equilibrate. It is concluded that sequence selectivity is minimal or lacking for daunomycin, whereas nogalamycin binding is sequence dependent and probably involves migration of the antibiotic between DNA binding sites. There is an inverse correlation between dissociation rate constants and antibacterial potency in simple tests.     

Effect of anthracycline antibiotics on the reconstituted mitochondrial tricarboxylate carrier

The effect of anthracycline antibiotics on the activity of the partially purified and reconstituted tricarboxylate carrier system of the rat liver mitochondria was studied. It was found that the citrate/citrate exchange activity is inhibited by Br-daunomycin and with less potency by doxorubicin, daunomycin, epirubicin and idarubicin. The inhibition of the citrate transport activity is concentration and time-dependent. Cardiolipin protects against the inhibition by Br-daunomycin and the reconstituted citrate transport activity depends upon the ratio of cardiolipin/Br-daunomycin.     

Rat macrophage activation after treatment with the bleomycin group of antitumour antibiotics in vivo

Summary We have previously reported that bleomycin and its derivative peplomycin enhance the release of cytokines by rat spleen cells during mitogen-stimulated cell culture in vitro, but liblomycin, another derivative of bleomycin, decreases cytokine release to below untreated control levels. Cytokine release correlated well with the inhibition of subcutaneous tumour growth after treatment with equivalent doses of the three analogues. In contrast, ascites tumour growth is completely inhibited by liblomycin and appears to be at least partly macrophage-mediated because the antitumour effect can be significantly inhibited by carageenan. This study shows that bleomycin and its analogues activate rat peritoneal macrophages and increase interleukin-6 release, O₂ ^– production, cell spreading, phagocytosis and random migration of macrophages, but only bleomycin enhances peritoneal macrophage invasion into a monolayer of rat lung endothelial cells in vitro. This study also shows that although liblomycin decreases spleen cell cytokine production and is less effective than bleomycin against subcutaneous tumour, as we have previously reported, the antitumour drug activates peritoneal macrophages and, compared to bleomycin, has a remarkable therapeutic effect on rat ascites tumour.     

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) is a new technology to study genome-wide long-range chromatin interactions bound by protein factors. Here we present ChIA-PET Tool, a software package for automatic processing of ChIA-PET sequence data, including linker filtering, mapping tags to reference genomes, identifying protein binding sites and chromatin interactions, and displaying the results on a graphical genome browser. ChIA-PET Tool is fast, accurate, comprehensive, user-friendly, and open source (available at http://chiapet.gis.a-star.edu.sg).     

Study of the structure of anthracycline antibiotics by ERIAD mass spectrometry

Fragmentation of antibiotics daunorubicin, carminomycin, doxorubicin and their semisynthetic analogues under conditions of the new mass spectrometry method ERIAD is discussed. Signals of protonated molecular ion (M + H)+ and ions of fragments are present in all the mass spectra. The results are compared with literary data obtained by means of other (EI and FAB MS) mass spectrometry methods.     

Productivity of cultures from secondary colonies of streptomycetes producing anthracycline antibiotics

At late stages of development of surface cultures streptomycetes producing anthracycline antibiotics were shown to form secondary colonies on PRIDHAM & GOTTLIEB 'S medium with xylose. Stable variants obtained from them possessed an increased biological activity (by a factor of 2–3 times) due to the accumulation of amounts of antibiotically active anthracyclines.