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European Journal of Medicinal Chemistry Jan 2017Distamycin, a natural polyamide containing three heterocycle rings with a polar end, has inspired several groups to prepare synthetic analogues, which proved to have...
Distamycin, a natural polyamide containing three heterocycle rings with a polar end, has inspired several groups to prepare synthetic analogues, which proved to have anti-trypanosomal and anti-tumoral activity. We describe the synthesis of bi and tri thiazoles amides that harbor different substitutions at their ends and the evaluation of their anti-Trypanosoma brucei activity. The most active compound 10b showed better biological activity (EC 310 nM and selectivity index 16) than the control drug nifurtimox (EC 15 μM and selectivity index 10). Studies on the mode of action show that the parasiticidal activity of 10b originates from disruption of lysosomal homeostasis, which is followed by release of redox active iron, an increase in oxidizing species and collapse of cell membrane integrity. In this respect, our study suggests that non-charged lipophylic distamycins destabilize cell membranes.
Topics: Africa; Antineoplastic Agents; Cell Membrane; Distamycins; Lysosomes; Oxidation-Reduction; Thiazoles; Trypanocidal Agents; Trypanosoma; Trypanosoma brucei brucei
PubMed: 27951486
DOI: 10.1016/j.ejmech.2016.12.002 -
Journal of Molecular Recognition : JMR May 2015Molecular dynamics simulations of the DNA 10-mer 5'-CCACGCGTGG-3' alone and complexed with the formamido-imidazole-pyrrole-imidazole (f-ImPyIm) polyamide minor groove...
Dynamic hydrogen bonding and DNA flexibility in minor groove binders: molecular dynamics simulation of the polyamide f-ImPyIm bound to the Mlu1 (MCB) sequence 5'-ACGCGT-3' in 2:1 motif.
Molecular dynamics simulations of the DNA 10-mer 5'-CCACGCGTGG-3' alone and complexed with the formamido-imidazole-pyrrole-imidazole (f-ImPyIm) polyamide minor groove binder in a 2:1 fashion were conducted for 50 ns using the pbsc0 parameters within the AMBER 12 software package. The change in DNA structure upon binding of f-ImPyIm was evaluated via minor groove width and depth, base pair parameters of Slide, Twist, Roll, Stretch, Stagger, Opening, Propeller, and x-displacement, dihedral angle distributions of ζ, ε, α, and γ determined using the Curves+ software program, and hydrogen bond formation. The dynamic hydrogen bonding between the f-ImPyIm and its cognate DNA sequence was compared to the static image used to predict sequence recognition by polyamide minor groove binders. Many of the predicted hydrogen bonds were present in less than 50% of the simulation; however, persistent hydrogen bonds between G5/15 and the formamido group of f-ImPyIm were observed. It was determined that the DNA is wider in the Complex than without the polyamide binder; however, there is flexibility in this particular sequence, even in the presence of the f-ImPyIm as evidenced by the range of minor groove widths the DNA exhibits and the dynamics of the hydrogen bonding that binds the two f-ImPyIm ions to the minor groove. The Complex consisting of the DNA and the 2 f-ImPyIm binders shows slight fraying of the 5' end of the 10-mer at the end of the simulation, but the portion of the oligomer responsible for recognition and binding is stable throughout the simulation. Several structural changes in the Complex indicate that minor groove binders may have a more active role in inhibiting transcription than just preventing binding of important transcription factors.
Topics: Bacterial Proteins; Base Pairing; Base Sequence; Binding Sites; Deoxyribonucleases, Type II Site-Specific; Distamycins; Hydrogen Bonding; Imidazoles; Molecular Dynamics Simulation; Oligodeoxyribonucleotides
PubMed: 25711379
DOI: 10.1002/jmr.2448 -
Biochemistry. Biokhimiia Oct 2018We studied the thermodynamics of melting of isolated rat liver nuclei with different degrees of chromatin condensation determined by the concentration of polyamines (PA)...
We studied the thermodynamics of melting of isolated rat liver nuclei with different degrees of chromatin condensation determined by the concentration of polyamines (PA) and the solution ionic strength, as well as the effect of the antibiotic distamycin A (DM) on melting. Differential scanning calorimetry (DSC) profiles of nuclear preparations contained three peaks that reflected melting of three main chromatin domains. The number of peaks did not depend on the degree of condensation; however, nuclei with more condensed chromatin had a higher total enthalpy. DM stabilized peaks II and III corresponding to the melting of relaxed and topologically strained DNA, respectively, but destabilized peak I corresponding to the melting of nucleosome core histones. At the saturating concentration (DM/DNA molar ratio = 0.1), DM increased T of peaks II and III by ~5°C and decreased T of peak I by ~2.5°C. Based on the dependence of ΔH on DM concentration, we established that at low DM/DNA ratio (≤0.03), when DM interacted predominantly with AT-rich DNA regions, the enthalpy of peak II decreased in parallel with the increase in the enthalpy of peak III, which indicated that DM induces structural transitions in the nuclear chromatin associated with the increase in torsional stress in DNA. An increase in free energy under saturation conditions was equal to the change in the free energy of DM interaction with DNA. However, the increase in the enthalpy of melting of the nuclei in the presence of DM was much greater than the enthalpy of titration of nuclei with DM. This indicates a significant increase in the strength of interaction between the two DNA strands apparently due, among other things, to changes in the torsional stress of DNA in the nuclei. Titration of the nuclei with increasing PA concentrations resulted in the decrease in the number of DM-binding sites and the non-monotonous dependence of the enthalpy and entropy contribution to the binding free energy on the PA content. We suggested that the observed differences in the thermodynamic parameters were due to the different width of the minor groove in the nuclear chromatin DNA, which depends on PA concentration.
Topics: Animals; Binding Sites; Calorimetry, Differential Scanning; Cell Nucleus; Chromatin; DNA; Distamycins; Female; Liver; Microscopy, Electron; Polyamines; Rats; Thermodynamics; Transition Temperature
PubMed: 30472960
DOI: 10.1134/S0006297918100085 -
ACS Chemical Biology Feb 2015The pyrrolamides constitute a small family of secondary metabolites that are known for their ability to bind noncovalently to the DNA minor groove with some sequence...
The pyrrolamides constitute a small family of secondary metabolites that are known for their ability to bind noncovalently to the DNA minor groove with some sequence specificity. To date, only a single pyrrolamide biosynthetic gene cluster has been reported, directing the synthesis of congocidine (netropsin) in Streptomyces ambofaciens. In this study, we improve our understanding of pyrrolamide biosynthesis through the identification and characterization of the gene cluster responsible for the production of distamycin in Streptomyces netropsis DSM40846. We discover that the strain produces two other pyrrolamides, the well-characterized congocidine and a congocidine/distamycin hybrid that we named disgocidine. S. netropsis DSM40846 genome analysis led to the identification of two distinct pyrrolamide-like biosynthetic gene clusters. We show here that these two clusters are reciprocally dependent for the production of the three pyrrolamide molecules. Furthermore, based on detailed functional analysis of these clusters, we propose a biosynthetic route to congocidine and distamycin and an updated model for pyrrolamide assembly. The synthesis of disgocidine, the distamycin/congocidine hybrid, appears to constitute the first example of "natural combinatorial biosynthesis" between two related biosynthetic pathways. Finally, we analyze the genomic context of the two biosynthetic gene clusters and suggest that the presently interdependent clusters result from the coevolution of two ancestral independent pyrrolamide gene clusters.
Topics: Anti-Bacterial Agents; Biological Evolution; Combinatorial Chemistry Techniques; Distamycins; Gene Expression Regulation, Bacterial; Molecular Structure; Multigene Family; Streptomyces
PubMed: 25415678
DOI: 10.1021/cb500652n -
Bioorganic & Medicinal Chemistry Jul 2015The alarming rise of extensively drug-resistant tuberculosis (XDR-TB) strains, compel the development of new molecules with novel modes of action to control this world...
The alarming rise of extensively drug-resistant tuberculosis (XDR-TB) strains, compel the development of new molecules with novel modes of action to control this world health emergency. Distamycin analogues containing N-terminal biaryl-motifs 2(1-5)(1-7) were synthesised using a solution-phase approach and evaluated for their anti-mycobacterial activity and DNA-sequence selectivity. Thiophene dimer motif-containing polyamide 2(2,6) exhibited 10-fold higher inhibitory activity against Mycobacterium tuberculosis compared to distamycin and library member 2(5,7) showed high binding affinity for the 5'-ACATAT-3' sequence.
Topics: Antitubercular Agents; Binding Sites; Combinatorial Chemistry Techniques; DNA Footprinting; DNA, Bacterial; Distamycins; Ligands; Microbial Sensitivity Tests; Models, Molecular; Mycobacterium tuberculosis; Nylons; Small Molecule Libraries; Structure-Activity Relationship; Thiophenes
PubMed: 25921267
DOI: 10.1016/j.bmc.2015.04.001 -
Journal of Clinical and Diagnostic... Jun 2017Fragile sites represent regions of chromatin that fail to compact during mitosis. Based on the prevalence and pattern of inheritance they are classified as rare fragile...
Fragile sites represent regions of chromatin that fail to compact during mitosis. Based on the prevalence and pattern of inheritance they are classified as rare fragile sites or common fragile sites. Rare fragile sites either occur spontaneously or can be induced by certain AT-specific binding chemicals namely distamycin, Hoechst 33258, Berenil and others. The most common of all rare autosomal fragile sites is fra(16)(q22) with a heterozygote frequency of ~5%. FRA16B results from an expansion of a 33 bp AT-rich Minisatellite repeat. These rare forms are usually heritable and segregate in a Mendelian fashion. The proband who was referred for secondary amenorrhoea, revealed 46,XX,fra(16)(q22.1)pat karyotype. Her father and younger sibling were also found to be carriers. This study aimed to delineate the genotypic and phenotypic features exhibited by these carriers and to evaluate FRA16B expression using AT-specific binding chemicals. The additives employed were Berenil, BrdU and Hoechst 33258. Berenil at a concentration of 150 µg/ml showed the highest expression of FRA16B. Although the recent breakthrough in molecular characterization of fragile sites plays a critical role in comprehending their association with various diseases, the physiological link between them and amenorrhoea is not clearly understood.
PubMed: 28764253
DOI: 10.7860/JCDR/2017/26545.10043 -
Pharmaceutical Biology Dec 2017Natural oligopeptide antibiotic distamycin A (Dst) biosynthesized by Streptomyces distallicus is traditionally used in medical practice as an anti-inflammatory and...
CONTEXT
Natural oligopeptide antibiotic distamycin A (Dst) biosynthesized by Streptomyces distallicus is traditionally used in medical practice as an anti-inflammatory and antitumour drug.
OBJECTIVE
Dst was investigated for its effect on the structural components of native chromatin directly within isolated rat liver nuclei in the presence of physiologically significant cations (magnesium or spermine and spermidine).
MATERIALS AND METHODS
Differential scanning calorimetry (DSC) was used to study the Dst action at molar ratio Dst/DNA = 0.1 and 0.15 mM Dst on the melting profile of nuclei suspension in different conditions.
RESULTS
Results showed that the thermodynamic parameters of control nuclei in the presence of polyamines or Mgwere different. The incubation of nuclei with Dst raised transition temperatures of relaxed (peak II) and topologically constrained DNA (peak III) by 6-8 °C and decreased by 2-4 °C that of core-histones (peak I). The total excess transition enthalpy (ΔH) in buffer with polyamines (24.7 kJ/mol DNA nucleotides) increased by1.5 times versus control but in buffer with Mg, the value of ΔH (35.8 kJ/mol DNA nucleotides) remained unchanged.
CONCLUSIONS
The association of Dst with chromatin in the nucleus weakens histone-DNA contacts and causes additional strengthening of interaction between two complementary DNA chains. Our results contribute towards validation of DSC to test drug ability to modulate chromatin structure in the physiological environment and to clarify the mechanism of these modulations.
Topics: Animals; Anti-Bacterial Agents; Calorimetry, Differential Scanning; Cell Nucleus; Chromatin; Chromatin Assembly and Disassembly; DNA; Distamycins; Female; Histones; Liver; Magnesium; Nucleic Acid Conformation; Protein Binding; Rats; Spermidine; Spermine; Temperature
PubMed: 27982735
DOI: 10.1080/13880209.2016.1258427 -
European Journal of Medicinal Chemistry Jun 2020We have designed and synthesized anthraquinone containing compounds which have oligopyrrole side chains of varying lengths. These compounds stabilized the G-quadruplex...
Specific stabilization of promoter G-Quadruplex DNA by 2,6-disubstituted amidoanthracene-9,10-dione based dimeric distamycin analogues and their selective cancer cell cytotoxicity.
We have designed and synthesized anthraquinone containing compounds which have oligopyrrole side chains of varying lengths. These compounds stabilized the G-quadruplex DNA formed in the promoter regions of c-MYC oncogenes selectively over the duplex DNA. These observations were recorded using UV-vis spectroscopic titrations, fluorescence measurements and circular dichroism (CD) spectral titrations. The potency of the compounds to stabilize the G4 DNA has been shown from the thermal denaturation experiments. The compound interacts with c-MYC G-quadruplex DNA through stacking mode as obtained from ethidium bromide displacement assay, cyclic voltammetric titration, and docking experiments. Molecular modeling studies suggested that the stacking of the anthraquinone moiety over the G-tetrad of the G4 structures are responsible for the stability of such quadruplex secondary structure. Furthermore, polymerase stop assay also supported the formation of stable G4 structures in the presence of the above-mentioned compounds. The compounds have shown selective cancer cell (HeLa and HEK293T) cytotoxicity over normal cells (NIH3T3 and HDFa) under in vitro conditions as determined from MTT based cell viability assay. Apoptosis was found to be the mechanistic pathway underlying the cancer cell cytotoxicity as obtained from Annexin V-FITC and PI dual staining assay which was further substantiated by nuclear morphological changes as observed by AO/EB dual staining assay. Cellular morphological changes, as well as nuclear condensation and fragmentation upon treatment with these compounds, were observed under bright field and confocal microscopy.
Topics: Anthracenes; Antineoplastic Agents; DNA; Dimerization; Distamycins; Drug Design; G-Quadruplexes; Models, Molecular; Promoter Regions, Genetic; Proto-Oncogene Proteins c-myc
PubMed: 32302880
DOI: 10.1016/j.ejmech.2020.112202 -
Bioorganic & Medicinal Chemistry Letters Sep 2015The design, synthesis, and DNA binding properties of azaHx-PI or p-anisyl-4-aza-benzimidazole-pyrrole-imidazole (5) are described. AzaHx,...
AzaHx, a novel fluorescent, DNA minor groove and G·C recognition element: Synthesis and DNA binding properties of a p-anisyl-4-aza-benzimidazole-pyrrole-imidazole (azaHx-PI) polyamide.
The design, synthesis, and DNA binding properties of azaHx-PI or p-anisyl-4-aza-benzimidazole-pyrrole-imidazole (5) are described. AzaHx, 2-(p-anisyl)-4-aza-benzimidazole-5-carboxamide, is a novel, fluorescent DNA recognition element, derived from Hoechst 33258 to recognize G·C base pairs. Supported by theoretical data, the results from DNase I footprinting, CD, ΔT(M), and SPR studies provided evidence that an azaHx/IP pairing, formed from antiparallel stacking of two azaHx-PI molecules in a side-by-side manner in the minor groove, selectively recognized a C-G doublet. AzaHx-PI was found to target 5'-ACGCGT-3', the Mlu1 Cell Cycle Box (MCB) promoter sequence with specificity and significant affinity (K(eq) 4.0±0.2×10(7) M(-1)).
Topics: Antigens, Neoplasm; Base Pairing; Benzimidazoles; Binding Sites; Chemistry Techniques, Synthetic; Circular Dichroism; DNA; DNA Topoisomerases, Type II; DNA-Binding Proteins; Deoxyribonuclease I; Drug Design; Fluorescent Dyes; Nylons; Promoter Regions, Genetic; Pyrroles
PubMed: 26122210
DOI: 10.1016/j.bmcl.2015.06.055 -
Journal of Computational Chemistry Apr 2020Alchemically derived free energies are artifacted when the perturbed moiety has a nonzero net charge. The source of the artifacts lies in the effective treatment of the...
Alchemically derived free energies are artifacted when the perturbed moiety has a nonzero net charge. The source of the artifacts lies in the effective treatment of the electrostatic interactions within and between the perturbed atoms and remaining (partial) charges in the simulated system. To treat the electrostatic interactions effectively, lattice-summation (LS) methods or cutoff schemes in combination with a reaction-field contribution are usually employed. Both methods render the charging component of the calculated free energies sensitive to essential parameters of the system like the cutoff radius or the box side lengths. Here, we discuss the results of three previously published studies of ligand binding. These studies presented estimates of binding free energies that were artifacted due to the charged nature of the ligands. We show that the size of the artifacts can be efficiently calculated and raw simulation data can be corrected. We compare the corrected results with experimental estimates and nonartifacted estimates from path-sampling methods. Although the employed correction scheme involves computationally demanding continuum-electrostatics calculations, we show that the correction estimate can be deduced from a small sample of configurations rather than from the entire ensemble. This observation makes the calculations of correction terms feasible for complex biological systems. To show the general applicability of the proposed procedure, we also present results where the correction scheme was used to correct independent free energies obtained from simulations employing a cutoff scheme or LS electrostatics. In this work, we give practical guidelines on how to apply the appropriate corrections easily.
Topics: Artifacts; Binding Sites; DNA; Distamycins; Ligands; Molecular Dynamics Simulation; Netropsin; Solvents; Static Electricity; Thermodynamics; Trypsin Inhibitors
PubMed: 31930547
DOI: 10.1002/jcc.26143