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Bioinformation 2013Sliding Box Docking is a program that manages simulations of ligand docking at different defined positions of a three-dimensional DNA structure. The procedure is similar...
UNLABELLED
Sliding Box Docking is a program that manages simulations of ligand docking at different defined positions of a three-dimensional DNA structure. The procedure is similar to inverse docking, which is a method that performs docking simulations of a single ligand in the active sites of different targets. Sliding Box Docking manages docking simulations of one ligand into a box that slides along the DNA helix axis in regular steps. For each box position a score is calculated using the separate Autodock Vina software, and the results are automatically plotted. The evaluation of ligand interaction at different DNA locations can highlight the specificity of ligands for different DNA- sequences. When assessing the affinity between ligans AT base pairs, results for docking simulations with a test set that included berenil, distamycin, hoechst 33258, and netropsin were as expected, agreeing well with affinities previously described in the literature.
AVAILABILITY
Binaries are freely available at https://sourceforge.net/projects/slidingboxdocki.
PubMed: 23976834
DOI: 10.6026/97320630009750 -
Journal of Inorganic Biochemistry Nov 2013The nuclease activity and the cytotoxicity toward human leukemia cancer cells of iron complexes, [Fe(HPClNOL)Cl2]NO3 (1), [Cl(HPClNOL)Fe(μ-O)Fe(HPClNOL)Cl]Cl2·2H2O...
The nuclease activity and the cytotoxicity toward human leukemia cancer cells of iron complexes, [Fe(HPClNOL)Cl2]NO3 (1), [Cl(HPClNOL)Fe(μ-O)Fe(HPClNOL)Cl]Cl2·2H2O (2), and [(SO4)(HPClNOL)Fe(μ-O)Fe(HPClNOL)(SO4)]·6H2O (3) (HPClNOL=1-(bis-pyridin-2-ylmethyl-amino)-3-chloropropan-2-ol), were investigated. Each complex was able to promote plasmid DNA cleavage and change the supercoiled form of the plasmid to circular and linear ones. Kinetic data revealed that (1), (2) and (3) increase the rate of DNA hydrolysis about 278, 192 and 339 million-fold, respectively. The activity of the complexes was inhibited by distamycin, indicating that they interact with the minor groove of the DNA. The cytotoxic activity of the complexes toward U937, HL-60, Jukart and THP-1 leukemia cancer cells was studied employing 3-(4,5-dimethythiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT), fluorescence and electronic transmission microscopies, flow cytometry and a cytochrome C release assay. Compound (2) has the highest activity toward cancer cells and is the least toxic for normal ones (i.e. peripheral blood mononuclear cells (PBMCs)). In contrast, compound (1) is the least active toward cancer cells but displays the highest toxicity toward normal cells. Transmission electronic microscopy indicates that cell death shows features typical of apoptotic cells, which was confirmed using the annexin V-FITC/PI (fluorescein isothiocyanate/propidium iodide) assay. Furthermore, our data demonstrate that at an early stage during the treatment with complex (2) mitochondria lose their transmembrane potential, resulting in cytochrome C release. A quantification of caspases 3, 9 (intrinsic apoptosis pathway) and caspase 8 (extrinsic apoptosis pathway) indicated that both the intrinsic (via mitochondria) and extrinsic (via death receptors) pathways are involved in the apoptotic stimuli.
Topics: Apoptosis; Caspases; Cell Line, Tumor; Cell Survival; Coordination Complexes; Cytochromes c; DNA; DNA, Superhelical; Deoxyribonucleases; Enzyme Activation; HL-60 Cells; Humans; Hydrogen-Ion Concentration; Hydrolysis; Iron Compounds; Jurkat Cells; Kinetics; Leukemia; Leukocytes, Mononuclear; Membrane Potential, Mitochondrial; Microscopy, Electron, Transmission; Mitochondria; Signal Transduction; U937 Cells
PubMed: 23933562
DOI: 10.1016/j.jinorgbio.2013.07.019 -
Nucleic Acids Research Oct 2013DNA lesions produced by aromatic isocyanates have an extra bulky group on the nucleotide bases, with the capability of forming stacking interaction within a DNA helix....
DNA lesions produced by aromatic isocyanates have an extra bulky group on the nucleotide bases, with the capability of forming stacking interaction within a DNA helix. In this work, we investigated the conformation of the 2'-deoxyadenosine and 2'-deoxycytidine derivatives tethering a phenyl or naphthyl group, introduced in a DNA duplex. The chemical modification experiments using KMnO4 and 1-cyclohexyl-3 -(2-morpholinoethyl) carbodiimide metho-p-toluenesulfonate have shown that the 2'-deoxycytidine lesions form the base pair with guanine while the 2'-deoxyadenosine lesions have less ability of forming the base pair with thymine in solution. Nevertheless, the kinetic analysis shows that these DNA lesions are compatible with DNA ligase and DNA polymerase reactions, as much as natural DNA bases. We suggest that the adduct lesions have a capability of adopting dual conformations, depending on the difference in their interaction energies between stacking of the attached aromatic group and base pairing through hydrogen bonds. It is also presented that the attached aromatic groups change their orientation by interacting with the minor groove binding netropsin, distamycin and synthetic polyamide. The nucleotide derivatives would be useful for enhancing the phenotypic diversity of DNA molecules and for exploring new non-natural nucleotides.
Topics: DNA Adducts; DNA Ligases; DNA Replication; DNA-Directed DNA Polymerase; Deoxyadenosines; Deoxycytidine; Distamycins; Guanine; Netropsin; Nucleic Acid Conformation; Thymine
PubMed: 23873956
DOI: 10.1093/nar/gkt608 -
Biochemistry. Biokhimiia Feb 2013In vitro phosphorylation of histones H1 and H3 by cAMP-dependent protein kinase A and endogenous phosphokinases in the presence of [γ-³²P]ATP was studied in isolated...
Influence of chromatin structure, antibiotics, and endogenous histone methylation on phosphorylation of histones H1 and H3 in the presence of protein kinase A in rat liver nuclei in vitro.
In vitro phosphorylation of histones H1 and H3 by cAMP-dependent protein kinase A and endogenous phosphokinases in the presence of [γ-³²P]ATP was studied in isolated rat liver nuclei with different variants of chromatin structural organization: condensed (diameter of fibrils 100-200 nm; N-1) and partly decondensed (diameter of fibrils ~30 nm; N-2). In the N-1 state histone, H1 is phosphorylated approximately twice as much than histone H3. Upon the decondensation of the chromatin in the N-2 state, 1.5-fold decrease of total phosphorylation of H1 is observed, while that of H3 does not change, although the endogenous phosphorylation of both histones is reduced by half. Changes in histone phosphorylation in the presence of low or high concentrations of distamycin and chromomycin differ for H1 and H3 in N-1 and N-2. It was found that distamycin (DM) stimulates the phosphorylation of tightly bound H1 fraction, which is not extractable by polyglutamic acid (PG), especially in N-1. Chromomycin (CM) increases the phosphorylation of both histones in PG extracts and in the nuclear pellets, particularly in N-2. At the same time, in N-1 one can detect phosphorylation of a tightly bound fraction of histones H1 whose N-termini are located on AT-rich sites that become inaccessible for protein kinase in the process of chromatin decondensation in N-2. At the same time, in N-2 the accessibility for protein kinase A of tightly bound H1 fractions, whose N-termini are located on GC-rich sites, increases dramatically. High concentrations of both CM and DM in N-1 and N-2 stimulated phosphorylation of the non-extractable by PG fraction of H1 whose N-termini are located on sites where AT ≈ GC. CM at high concentration stimulated 4-7 times the phosphorylation of a small fraction of H3, which is extracted by PG from both types of nuclei. We detected an effect of endogenous methylation of histones H1 and H3 in the nuclei on their subsequent phosphorylation depending on the chromatin structure, histone-chromatin binding strength, and concentration of DM.
Topics: Animals; Anti-Bacterial Agents; Cell Nucleus; Chromatin; Cyclic AMP-Dependent Protein Kinases; Histones; Liver; Methylation; Phosphorylation; Rats
PubMed: 23581988
DOI: 10.1134/S0006297913020065 -
Bioorganic & Medicinal Chemistry Jun 2013The proximicins A-C are naturally occurring cytotoxic γ-peptides that contain the unique 4-amino-furan-carboxylic acid. In contrast to the structurally related...
The proximicins A-C are naturally occurring cytotoxic γ-peptides that contain the unique 4-amino-furan-carboxylic acid. In contrast to the structurally related cytotoxic natural DNA binder netropsin and distamycin, both exhibiting as core building block N-methyl-4-amino-pyrrol-carboxylic acid, no DNA binding was observed for the procimicins. X-ray analysis of crystals of a protected 4-amino-furan-2-carboxylic acid dipeptide revealed a stretched conformation. In contrast, for netropsin and distamycin, sickle-shaped crystal conformations were observed. DFT-calculations elegantly confirm these conformational arrangements. The most stable conformers of the proximicins are linear whereas sickle-shaped conformations are less stable, having higher Gibbs energies. For netropsin, distamycin and the netropsin-proximicin-hybrid a sickle shaped conformation appears energetically favored. The reported results are consistent with the observations that the proximicins A-C do not bind to the DNA and have a different mode of action concerning their cytotoxic activity with respect to netropsin and distamycin.
Topics: Anti-Bacterial Agents; Crystallography, X-Ray; Models, Molecular; Netropsin; Peptides; Protein Conformation; Quantum Theory
PubMed: 23548628
DOI: 10.1016/j.bmc.2013.02.051 -
Pharmacology & Therapeutics Jul 2013Minor groove binders are small molecules that form strong complexes with the minor groove of DNA. There are several structural types of which distamycin and netropsin... (Review)
Review
Minor groove binders are small molecules that form strong complexes with the minor groove of DNA. There are several structural types of which distamycin and netropsin analogues, oligoamides built from heterocyclic and aromatic amino acids, and bis-amidines separated by aromatic and heterocyclic rings are of particular pharmaceutical interest. These molecules have helical topology that approximately matches the curvature of DNA in the minor groove. Depending upon the precise structure of the minor groove binder, selectivity can be obtained with respect to the DNA base sequence to which the compound binds. Minor groove binders have found substantial applications in anti-cancer therapy but their significance in anti-infective therapy has also been significant and is growing. For example, compounds of the bis-amidine class have been notable contributors to antiparasitic therapy for many years with examples such as berenil and pentamidine being well-known. A recent growth area has been inreased sophistication in the oligoamide class. High sequence selectivity is now possible and compounds with distinct antibacterial, antifungal, antiviral, and antiparasitic activity have all been identified. Importantly, the structures of the most active compounds attacking the various infective organisms differ significantly but not necessarily predictively. This poses interesting questions of mechanism of action with many different targets involved in DNA processing being candidates. Access of compounds to specific cell types also plays a role and in some cases, can be decisive. Prospects for a range of selective therapeutic agents from this class of compounds are higher now than for some considerable time.
Topics: Animals; Anti-Bacterial Agents; Antiparasitic Agents; Bacterial Infections; DNA; Humans; Parasitic Diseases
PubMed: 23507040
DOI: 10.1016/j.pharmthera.2013.03.002 -
PloS One 2013The condensed structure of chromatin limits access of cellular machinery towards template DNA. This in turn represses essential processes like transcription,...
The condensed structure of chromatin limits access of cellular machinery towards template DNA. This in turn represses essential processes like transcription, replication, repair and recombination. The repression is alleviated by a variety of energy dependent processes, collectively known as "chromatin remodeling". In a eukaryotic cell, a fine balance between condensed and de-condensed states of chromatin helps to maintain an optimum level of gene expression. DNA binding small molecules have the potential to perturb such equilibrium. We present herein the study of an oligopeptide antibiotic distamycin, which binds to the minor groove of B-DNA. Chromatin mobility assays and circular dichroism spectroscopy have been employed to study the effect of distamycin on chromatosomes, isolated from the liver of Sprague-Dawley rats. Our results show that distamycin is capable of remodeling both chromatosomes and reconstituted nucleosomes, and the remodeling takes place in an ATP-independent manner. Binding of distamycin to the linker and nucleosomal DNA culminates in eviction of the linker histone and the formation of a population of off-centered nucleosomes. This hints at a possible corkscrew type motion of the DNA with respect to the histone octamer. Our results indicate that distamycin in spite of remodeling chromatin, inhibits transcription from both DNA and chromatin templates. Therefore, the DNA that is made accessible due to remodeling is either structurally incompetent for transcription, or bound distamycin poses a roadblock for the transcription machinery to advance.
Topics: Adenosine Triphosphate; Animals; Chromatin; Chromatin Assembly and Disassembly; Circular Dichroism; DNA; Distamycins; Histones; Male; Nucleic Acid Conformation; Protein Binding; Rats; Rats, Sprague-Dawley; Transcription, Genetic
PubMed: 23460895
DOI: 10.1371/journal.pone.0057693 -
Journal of Molecular Biology May 2013Members of the ETS family of transcription factors regulate a functionally diverse array of genes. All ETS proteins share a structurally conserved but sequence-divergent...
Probing the electrostatics and pharmacological modulation of sequence-specific binding by the DNA-binding domain of the ETS family transcription factor PU.1: a binding affinity and kinetics investigation.
Members of the ETS family of transcription factors regulate a functionally diverse array of genes. All ETS proteins share a structurally conserved but sequence-divergent DNA-binding domain, known as the ETS domain. Although the structure and thermodynamics of the ETS-DNA complexes are well known, little is known about the kinetics of sequence recognition, a facet that offers potential insight into its molecular mechanism. We have characterized DNA binding by the ETS domain of PU.1 by biosensor-surface plasmon resonance (SPR). SPR analysis revealed a striking kinetic profile for DNA binding by the PU.1 ETS domain. At low salt concentrations, it binds high-affinity cognate DNA with a very slow association rate constant (≤10(5)M(-)(1)s(-)(1)), compensated by a correspondingly small dissociation rate constant. The kinetics are strongly salt dependent but mutually balance to produce a relatively weak dependence in the equilibrium constant. This profile contrasts sharply with reported data for other ETS domains (e.g., Ets-1, TEL) for which high-affinity binding is driven by rapid association (>10(7)M(-)(1)s(-)(1)). We interpret this difference in terms of the hydration properties of ETS-DNA binding and propose that at least two mechanisms of sequence recognition are employed by this family of DNA-binding domain. Additionally, we use SPR to demonstrate the potential for pharmacological inhibition of sequence-specific ETS-DNA binding, using the minor groove-binding distamycin as a model compound. Our work establishes SPR as a valuable technique for extending our understanding of the molecular mechanisms of ETS-DNA interactions as well as developing potential small-molecule agents for biotechnological and therapeutic purposes.
Topics: Animals; Base Sequence; Binding Sites; Binding, Competitive; Biosensing Techniques; DNA; DNA-Binding Proteins; Distamycins; Mice; Models, Molecular; Protein Structure, Tertiary; Proto-Oncogene Proteins; Static Electricity; Surface Plasmon Resonance; Trans-Activators
PubMed: 23416556
DOI: 10.1016/j.jmb.2013.02.010 -
Chembiochem : a European Journal of... Oct 2012Recently, the versatility of N-methylpyrrole (Py)-N-methylimidazole (Im) polyamide conjugates, which have been developed from the DNA-binding antibiotics distamycin A... (Review)
Review
Recently, the versatility of N-methylpyrrole (Py)-N-methylimidazole (Im) polyamide conjugates, which have been developed from the DNA-binding antibiotics distamycin A and netropsin, has been shown. These synthetic small molecules can permeate cells to bind with duplex DNA in a sequence-specific manner, and hence can influence gene expression in vivo. Accordingly, several reports demonstrating the sequence specificity and biological activity of Py-Im polyamides have accumulated. However, the benefits of Py-Im polyamides, in particular those conjugated with fluorophores, has been overlooked. Moreover, clear directions for the employment of these attractive artificial small molecules have not yet been shown. Here, we present a detailed overview of the current and prospective applications of Py-Im polyamide-fluorophore conjugates, including sequence-specific recognition with fluorescence emission properties, and their potential roles in biological imaging.
Topics: Animals; DNA; DNA Probes; Fluorescent Dyes; Humans; Imidazoles; Models, Molecular; Nylons; Optical Imaging; Pyrroles
PubMed: 23023993
DOI: 10.1002/cbic.201200451 -
Journal of Photochemistry and... Oct 2012Most of the clinically used anticancer drugs exert their antitumor effect by damaging the replication machinery of DNA either by covalent or non-covalent binding.... (Review)
Review
Most of the clinically used anticancer drugs exert their antitumor effect by damaging the replication machinery of DNA either by covalent or non-covalent binding. Intercalation and groove fitting are the major modes of non-covalent interaction. Small crescent shaped molecules have been claimed to bind with DNA via minor grooves. A plethora of hybrid molecules based on distamycin or netropsin have been synthesised with the objectives of improved selectivity and specificity with no/reduced unwanted side effects. This review critically and objectively describes the previously known hybrid DNA minor groove binding agents based on five membered, distamycin or netropsin. Moreover, the future use of six-membered benzamides has also been highlighted. Special emphasis has been put on developing structure-activity relationships of DNA minor groove binding agents.
Topics: Animals; Antineoplastic Agents; DNA; Humans; Nucleic Acid Conformation; Organic Chemicals
PubMed: 22857824
DOI: 10.1016/j.jphotobiol.2012.07.003