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1.
Microbiol Spectr ; 12(4): e0407223, 2024 Apr 02.
Article in English | MEDLINE | ID: mdl-38376353

ABSTRACT

We previously identified the bisbenzimide Hoechst 33342 (H42) as a potent multi-stage inhibitor of the prototypic poxvirus, the vaccinia virus (VACV), and several parapoxviruses. A recent report showed that novel bisbenzimide compounds similar in structure to H42 could prevent human cytomegalovirus replication. Here, we assessed whether these compounds could also serve as poxvirus inhibitors. Using virological assays, we show that these bisbenzimide compounds inhibit VACV spread, plaque formation, and the production of infectious progeny VACV with relatively low cell toxicity. Further analysis of the VACV lifecycle indicated that the effective bisbenzimide compounds had little impact on VACV early gene expression but inhibited VACV late gene expression and truncated the formation of VACV replication sites. Additionally, we found that bisbenzimide compounds, including H42, can inhibit both monkeypox and a VACV mutant resistant to the widely used anti-poxvirus drug TPOXX (Tecovirimat). Therefore, the tested bisbenzimide compounds were inhibitors of both prototypic and pandemic potential poxviruses and could be developed for use in situations where anti-poxvirus drug resistance may occur. Additionally, these data suggest that bisbenzimide compounds may serve as broad-activity antiviral compounds, targeting diverse DNA viruses such as poxviruses and betaherpesviruses.IMPORTANCEThe 2022 mpox (monkeypox) outbreak served as a stark reminder that due to the cessation of smallpox vaccination over 40 years ago, most of the human population remains susceptible to poxvirus infection. With only two antivirals approved for the treatment of smallpox infection in humans, the need for additional anti-poxvirus compounds is evident. Having shown that the bisbenzimide H33342 is a potent inhibitor of poxvirus gene expression and DNA replication, here we extend these findings to include a set of novel bisbenzimide compounds that show anti-viral activity against mpox and a drug-resistant prototype poxvirus mutant. These results suggest that further development of bisbenzimides for the treatment of pandemic potential poxviruses is warranted.


Subject(s)
Poxviridae , Smallpox , Humans , Bisbenzimidazole/metabolism , Pandemics , Vaccinia virus/genetics
2.
Commun Biol ; 3(1): 525, 2020 09 22.
Article in English | MEDLINE | ID: mdl-32963293

ABSTRACT

Understanding the dynamic interactions of ligands to DNA is important in DNA-based nanotechnologies. By structurally tracking the dissociation of Hoechst 33258-bound DNA (d(CGCAAATTTGCG)2) complex (H-DNA) with T-jump 2D-IR spectroscopy, the ligand is found to strongly disturb the stability of the three C:G base pairs adjacent to A:T the binding site, with the broken base pairs being more than triple at 100 ns. The strong stabilization effect of the ligand on DNA duplex makes this observation quite striking, which dramatically increases the melting temperature and dissociation time. MD simulations demonstrate an important role of hydration water and counter cations in maintaining the separation of terminal base pairs. The hydrogen bonds between the ligand and thymine carbonyls are crucial in stabilizing H-DNA, whose breaking signal appearing prior to the complete dissociation. Thermodynamic analysis informs us that H-DNA association is a concerted process, where H cooperates with DNA single strands in forming H-DNA.


Subject(s)
Bisbenzimidazole/metabolism , DNA/metabolism , Binding Sites , DNA Breaks/drug effects , Hydrogen Bonding , Nucleic Acid Denaturation , Spectroscopy, Fourier Transform Infrared , Thermodynamics
3.
Biophys Chem ; 256: 106270, 2020 01.
Article in English | MEDLINE | ID: mdl-31706136

ABSTRACT

DNA strands can be designed to assemble into stable three-dimensional structures, based on Watson-Crick base pairing rules. The simplest of these is the DNA tetrahedron that is composed of four oligonucleotides. We have re-designed the sequence of a DNA tetrahedron so that it contains a single (AATT) binding site for the minor groove binding ligand Hoechst 33258. We examined the stability of this structure by placing fluorescent groups within each of its edges and have shown that all the edges melt at the same temperature in the absence of the ligand. The minor groove ligand still binds to its recognition sequence within the tetrahedron and increases the melting temperature of the folded complex. This ligand-induced stabilisation is propagated into the adjacent helical arms and the tetrahedron melts as a single entity in a cooperative fashion.


Subject(s)
DNA/chemistry , Ligands , Base Sequence , Binding Sites , Bisbenzimidazole/chemistry , Bisbenzimidazole/metabolism , Nucleic Acid Conformation , Phase Transition/radiation effects , Spectrometry, Fluorescence , Transition Temperature , Ultraviolet Rays
4.
Biochim Biophys Acta Gen Subj ; 1863(10): 1524-1535, 2019 10.
Article in English | MEDLINE | ID: mdl-31145964

ABSTRACT

BACKGROUND: Topoisomerase is a well known target to develop effective antibacterial agents. In pursuance of searching novel antibacterial agents, we have established a novel bisbenzimidazole (PPEF) as potent E. coli topoisomerase IA poison inhibitor. METHODS: In order to gain insights into the mechanism of action of PPEF and understanding protein-ligand interactions, we have produced wild type EcTopo 67 N-terminal domain (catalytic domain) and its six mutant proteins at acidic triad (D111, D113, E115). The DDE motif is replaced by alanine (A) to create three single mutants: D111A, D113A, E115A and three double mutants: D111A-D113A, D113A-E115A and D111A-E115A. RESULTS: Calorimetric study of PPEF with single mutants showed 10 fold lower affinity than that of wild type EcTopo 67 (7.32 × 106 M-1for wild type, 0.89 × 106 M-1for D111A) and 100 fold lower binding with double mutant D113A-E115A (0.02 × 106 M-1) was observed. The mutated proteins showed different CD signature as compared to wild type protein. CD and fluorescence titrations were done to study the interaction between EcTopo 67 and ligands. Molecular docking study validated that PPEF has decreased binding affinity towards mutated enzymes as compared to wild type. CONCLUSION: The overall study reveals that PPEF binds to D113 and E115 of acidic triad of EcTopo 67. Point mutations decrease binding affinity of PPEF towards DDE motif of topoisomerase. GENERAL SIGNIFICANCE: This study concludes PPEF as poison inhibitor of E. coli Topoisomerase IA, which binds to acidic triad of topoisomerase IA, responsible for its function. PPEF can be considered as therapeutic agent against bacteria.


Subject(s)
Anti-Bacterial Agents/pharmacology , Bisbenzimidazole/pharmacology , Catalytic Domain/drug effects , DNA Topoisomerases, Type I/drug effects , Escherichia coli/enzymology , Bisbenzimidazole/metabolism , Cloning, Molecular , DNA Topoisomerases, Type I/genetics , DNA Topoisomerases, Type I/metabolism , Mutagenesis, Site-Directed , Thermodynamics
5.
Spectrochim Acta A Mol Biomol Spectrosc ; 192: 384-392, 2018 Mar 05.
Article in English | MEDLINE | ID: mdl-29195192

ABSTRACT

DNA is a major target for a number of anticancer substances. Interaction studies between small molecules and DNA are essential for rational drug designing to influence main biological processes and also introducing new probes for the assay of DNA. Tschimgine (TMG) is a monoterpene derivative with anticancer properties. In the present study we tried to elucidate the interaction of TMG with calf thymus DNA (CT-DNA) using different spectroscopic methods. UV-visible absorption spectrophotometry, fluorescence and circular dichroism (CD) spectroscopies as well as molecular docking study revealed formation of complex between TMG and CT-DNA. Binding constant (Kb) between TMG and DNA was 2.27×104M-1, that is comparable to groove binding agents. The fluorescence spectroscopic data revealed that the quenching mechanism of fluorescence of TMG by CT-DNA is static quenching. Thermodynamic parameters (ΔH<0 and ΔS<0) at different temperatures indicated that van der Waals forces and hydrogen bonds were involved in the binding process of TMG with CT-DNA. Competitive binding assay with methylene blue (MB) and Hoechst 33258 using fluorescence spectroscopy displayed that TMG possibly binds to the minor groove of CT-DNA. These observations were further confirmed by CD spectral analysis, viscosity measurements and molecular docking.


Subject(s)
Bridged Bicyclo Compounds/metabolism , DNA/metabolism , Hydroxybenzoates/metabolism , Molecular Docking Simulation , Monoterpenes/metabolism , Animals , Binding, Competitive , Bisbenzimidazole/chemistry , Bisbenzimidazole/metabolism , Bridged Bicyclo Compounds/chemistry , Cattle , Circular Dichroism , Hydrogen-Ion Concentration , Hydroxybenzoates/chemistry , Methylene Blue/chemistry , Methylene Blue/metabolism , Monoterpenes/chemistry , Osmolar Concentration , Spectrometry, Fluorescence , Spectrophotometry, Ultraviolet , Thermodynamics , Viscosity
6.
Cold Spring Harb Protoc ; 2017(5)2017 05 01.
Article in English | MEDLINE | ID: mdl-28461657

ABSTRACT

Measuring the concentration of DNA using fluorometry is more sensitive than spectrophotometry, allowing the detection of nanogram quantities of DNA. In this assay, DNA preparations of known and unknown concentrations are incubated with the fluorochrome Hoechst 33258. Absorption values for the unknown sample are compared with those observed for a known dilution series, and the concentration of the unknown sample is estimated by interpolation. The assay can only be used to measure the concentration of DNAs whose sizes exceed ∼1 kb, as Hoechst 33258 binds poorly to smaller DNAs.


Subject(s)
Bisbenzimidazole , DNA/analysis , Fluorescent Dyes , Fluorometry/methods , Bisbenzimidazole/metabolism , DNA/metabolism , Indicators and Reagents , Solutions
7.
Nucleosides Nucleotides Nucleic Acids ; 36(2): 83-106, 2017 Feb.
Article in English | MEDLINE | ID: mdl-27835056

ABSTRACT

The interaction of copper(II)-ibuprofenato complex with calf thymus DNA (ct-DNA) has been explored following, UV-visible spectrophotometry, fluorescence measurement, dynamic viscosity measurements, and circular dichroism spectroscopy. In spectrophotometric studies of ct-DNA it was found that [Cu(ibp)2]2 can form a complex with double-helical DNA. The association constant of [Cu(ibp)2]2 with DNA from UV-Vis study was found to be 6.19 × 104 L mol-1. The values of Kf from fluorescence measurement clearly underscore the high affinity of [Cu(ibp)2]2 to DNA. The experimental results showed that the conformational changes in DNA helix induced by [Cu(ibp)2]2 are the reason for the fluorescence quenching of the DNA-Hoechst system. In addition, the fluorescence emission spectra of intercalated methylene blue (MB) with increasing concentrations of [Cu(ibp)2]2 represented a significant increase of MB intensity as to release MB from MB-DNA system. The results of circular dichroism (CD) suggested that copper(II)-ibuprofenato complex can change the conformation of DNA. In addition, the results of viscosity measurements suggest that copper(II)-ibuprofenato complex may bind with non-classical intercalative mode. From spectroscopic and hydrodynamic studies, it has been found that [Cu(ibp)2]2 interacts with DNA by partial intercalation mode which contains intercalation and groove properties.


Subject(s)
DNA/metabolism , Organometallic Compounds/chemistry , Organometallic Compounds/metabolism , Binding Sites , Binding, Competitive , Bisbenzimidazole/chemistry , Bisbenzimidazole/metabolism , Circular Dichroism , DNA/chemistry , Fluorescence , Intercalating Agents/chemistry , Methylene Blue/chemistry , Methylene Blue/metabolism , Molecular Docking Simulation , Nucleic Acid Conformation , Spectrophotometry, Ultraviolet , Spectroscopy, Fourier Transform Infrared , Thermodynamics , Viscosity
8.
Oxid Med Cell Longev ; 2016: 6849758, 2016.
Article in English | MEDLINE | ID: mdl-27891207

ABSTRACT

This study demonstrated that glycyrrhizate (GAS) could protect HEPG2 cells against damage and apoptosis induced by H2O2 (1600 µM, 4 h). Cell viability assay revealed that GAS was noncytotoxity at concentration 125 µg/mL, and GAS (5 µg/mL, 25 µg/mL, and 125 µg/mL) protected HepG2 cells against H2O2-induced cytotoxicity. H2O2 induced the HepG2 cells apoptosis, obvious morphologic changes were observed after Hochest 33258 staining, and more apoptotic cells were counted in flow cytometry assay compared to that of the natural group. Pretreatment GAS (5 µg/mL, 25 µg/mL, and 125 µg/mL) prior to H2O2 reverses the morphologic changes and reduced the apoptotic cells in HepG2 cells. GAS reduced the release of MDA, increased the activities of superoxide dismutase, and diminished the release of ALT and AST during oxidative stress in HepG2 cells. After Elisa kit detecting, GAS inhibited the caspase activity induced by H2O2, GAS decreased the level of caspase-3 and caspase-9 from mitochondria in dose-dependent manner. Western blot results showed that pretreatment GAS upregulated the expression of Bcl-2 and decreased the expression of Bax. These results reveal that GAS has the cytoprotection in HepG2 cells during ROS exposure by inhibiting the caspase activity in the mitochondria and influencing apoptogenic factors of the expression of Bax and Bcl-2.


Subject(s)
Apoptosis/drug effects , Glycyrrhizic Acid/pharmacology , Hydrogen Peroxide/toxicity , Alanine Transaminase/metabolism , Aspartate Aminotransferases/metabolism , Bisbenzimidazole/metabolism , Caspases/metabolism , Enzyme Activation/drug effects , Hep G2 Cells , Humans , Lipid Peroxidation/drug effects , Malondialdehyde/metabolism , Staining and Labeling , Superoxide Dismutase/metabolism , bcl-2-Associated X Protein/metabolism
9.
Cell Biochem Funct ; 34(6): 455-62, 2016 Aug.
Article in English | MEDLINE | ID: mdl-27558076

ABSTRACT

OBJECTIVE: Studies indicate that bupivacaine-induced neurotoxicity results from apoptosis. Gangliosides have been shown to promote neuronal repair and recovery of neurological function after spinal cord injury. Previously, we confirmed that in vivo administration of the ganglioside GM-1 attenuated bupivacaine-induced neurotoxicity in various animal models; however, the underlying mechanism remains unclear. METHODS: Cells of the neuroblastoma line N2a (Neuro2a cells) were divided into three experimental groups: control, bupivacaine-treated, and bupivacaine-treated with GM-1 pretreatment. Cell viability and apoptosis were assessed through CCK-8 assays, Hoechst staining, and flow cytometry analysis of Annexin-V/propidium iodide double labeling. Real-time polymerase chain reaction and western blotting assessed the expression of caspase-3, caspase-8, and caspase-9. RESULTS: Bupivacaine-induced apoptosis worsened with increasing dose and exposure time. Bupivacaine induced increased expression of caspase-3 and caspase-9, but not caspase-8, indicating that the mitochondrial pathway but not the death receptor apoptosis pathway was activated. GM-1 pretreatment inhibited bupivacaine-induced apoptosis and the expression of caspase-3 and caspase-9 in a dose-dependent manner. CONCLUSION: Bupivacaine induced neurotoxicity by activating apoptosis via the mitochondrial pathway, and this was inhibited by GM-1 pretreatment.


Subject(s)
Bupivacaine/toxicity , G(M1) Ganglioside/pharmacology , Neuroblastoma/pathology , Neurotoxins/toxicity , Animals , Apoptosis/drug effects , Bisbenzimidazole/metabolism , Blotting, Western , Cell Line, Tumor , Cell Survival/drug effects , Flow Cytometry , Mice , Neuroprotection/drug effects , RNA, Messenger/genetics , RNA, Messenger/metabolism , Real-Time Polymerase Chain Reaction
10.
Mol Pharmacol ; 88(4): 768-78, 2015 Oct.
Article in English | MEDLINE | ID: mdl-26240287

ABSTRACT

Radiotherapy, a therapeutic modality of cancer treatment, nonselectively damages normal tissues as well as tumor tissues. The search is ongoing for therapeutic agents that selectively reduce radiation-induced normal tissue injury without reducing tumoricidal effect, thereby increasing the therapeutic ratio of radiation therapy. Our laboratory established 5-(4-methylpiperazin-1-yl)-2-[2'-(3,4-dimethoxyphenyl)-5'benzimidazolyl] benzimidazole (DMA) as noncytotoxic radioprotector in mammalian cells. DMA showed an excellent radioprotection in mice at single nontoxic oral dose by a dose-reduction factor of 1.28. An oxygen radical absorbing capacity assay confirmed its free-radical quenching ability. Single bolus dose and 28-days of repeated administration of DMA in mice for toxicity studies determined an LD50 of >2000 mg/kg body weight (bw) and 225 mg/kg bw, respectively, suggesting DMA is safe. Histopathology, biochemical parameters, and relative organ weight analysis revealed insignificant changes in the DMA-treated animals. The pharmacokinetic study of DMA at oral and intravenous doses showed its C(max) = 1 hour, bioavailability of 8.84%, elimination half-life of 4 hours, and an enterohepatic recirculation. Biodistribution study in mice with Ehrlich ascites tumors showed that (99m)Tc-DMA achieved its highest concentration in 1 hour and was retained up to 4 hours in the lungs, liver, kidneys, and spleen, and in a low concentration in the tumor, a solicited property of any radioprotector to protect normal cells over cancerous cells. We observed that the single-dose treatment of tumor-bearing mice with DMA 2 hours before 8 Gy total body irradiation showed an impressive rescue of radiation-induced morbidity in terms of weight loss and mortality without a change in tumor response.


Subject(s)
Benzimidazoles/pharmacokinetics , Benzimidazoles/toxicity , Piperazines/pharmacokinetics , Piperazines/toxicity , Radiation-Protective Agents/pharmacokinetics , Radiation-Protective Agents/toxicity , Animals , Benzimidazoles/metabolism , Bisbenzimidazole/metabolism , Bisbenzimidazole/pharmacokinetics , Bisbenzimidazole/toxicity , Carcinoma, Ehrlich Tumor/drug therapy , Carcinoma, Ehrlich Tumor/metabolism , Carcinoma, Ehrlich Tumor/radiotherapy , Dose-Response Relationship, Radiation , Drug Evaluation, Preclinical/methods , Female , HEK293 Cells , Humans , Male , Mice , Mice, Inbred BALB C , Piperazines/metabolism , Radiation-Protective Agents/metabolism , Survival Rate/trends , Tissue Distribution/drug effects , Tissue Distribution/physiology
11.
Biochimie ; 108: 94-100, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25446655

ABSTRACT

In this study, a monomeric (MB) and a dimeric (DB) bisbenzimidazoles were identified as novel proteasome inhibitors of the trypsin-like activity located on ß2c sites of the constitutive 20S proteasome (IC50 values at 2-4 µM range). Remarkably, they were further shown to be 100- and 200-fold more potent inhibitors of the immunoproteasome trypsin-like activity (ß2i sites, IC50=24 nM) than of the homologous constitutive activity. Molecular models of inhibitor/enzyme complexes in the two types of trypsin-like sites and corresponding computed binding energy values corroborated kinetic data. Different binding modes were suggested for MB and DB to the ß2c and ß2i trypsic sites. Each pointed to better contacts of the ligand inside the ß2i active site than for ß2c site. MB and DB represent the first selective inhibitors of the immunoproteasome trypsin-like activity described to date and can be considered as prototypes for inhibiting this activity.


Subject(s)
Bisbenzimidazole/pharmacology , Catalytic Domain , Proteasome Endopeptidase Complex/chemistry , Proteasome Endopeptidase Complex/metabolism , Proteasome Inhibitors/pharmacology , Trypsin/chemistry , Animals , Bisbenzimidazole/metabolism , Calpain/antagonists & inhibitors , Cathepsin B/metabolism , HeLa Cells , Humans , Isoenzymes/antagonists & inhibitors , Isoenzymes/chemistry , Isoenzymes/immunology , Isoenzymes/metabolism , Mice , Molecular Docking Simulation , Proteasome Endopeptidase Complex/immunology , Proteasome Inhibitors/metabolism
12.
J Fluoresc ; 24(6): 1791-801, 2014 Nov.
Article in English | MEDLINE | ID: mdl-25312832

ABSTRACT

DNA-bound Hoechst 33258 is readily excited with UV light and emits blue fluorescence, however, upon exposure to UV, the dye undergoes photobleaching as well as photoconversion to a blue-excited green-emitting form. We demonstrate that the UV-generated green-emitting form of Hoechst 33258 exhibits spectral properties very similar to the form of the dye that can be obtained by subjecting it to an acidic environment (pH 0.5-3.0). We also demonstrate that exposure of Hoechst 33258 to UV light (or hydrogen peroxide) leads to generation of the protonated (1+, 2+, 3+ and possibly the 4+) forms of the dye. Photoconversion of Hoechst 33258 has recently been exploited in single molecule localisation microscopy, thus understanding photophysics of this process can facilitate further development of high resolution optical imaging.


Subject(s)
Bisbenzimidazole/chemistry , DNA/chemistry , Fluorescent Dyes/chemistry , Ultraviolet Rays , Bisbenzimidazole/metabolism , Bisbenzimidazole/radiation effects , Cells, Cultured , DNA/metabolism , DNA/radiation effects , Fibroblasts/cytology , Fibroblasts/drug effects , Fibroblasts/metabolism , Fluorescent Dyes/metabolism , Fluorescent Dyes/radiation effects , Humans , Hydrogen Peroxide/pharmacology , Hydrogen-Ion Concentration , Microscopy, Fluorescence , Oxidants/pharmacology , Protons , Spectrometry, Mass, Electrospray Ionization
13.
J Biomed Nanotechnol ; 10(7): 1320-35, 2014 Jul.
Article in English | MEDLINE | ID: mdl-24804553

ABSTRACT

The successful integration of a biomedical device is governed by the surface properties of the material and also depends on the interaction with the physiological fluid involving adsorption of proteins on the surface. Pre-adsorbed proteins act as pilots for cell adhesion and subsequently govern cellular activity. In this regard, nanograined materials are excellent vehicles to obtain an unambiguous understanding of protein adsorption, which regulate cell adhesion and cellular activity. Toward this end, we have used the concept of phase reversion-induced nanograined structure to understand grain structure-induced self-assembly of a model protein, bovine serum albumin. Furthermore, in the context of bio-mechanical interlocking between implant and bone, and osseointegration of the implant, grain boundaries were electrochemically grooved and studied for osteoblast functions. Experiments indicated that the significant differences in cell attachment, proliferation, and expression level of prominent proteins (actin, vinculin, and fibronectin) is related to synergistic effects of grain structure, pre-adsorbed protein, and grooving of grain boundaries such that the osteoblasts functions and cellular activity is promoted on the nanostructured surface in relation to the coarse-grained counterpart.


Subject(s)
Electrochemical Techniques , Nanostructures/chemistry , Osteoblasts/cytology , Osteoblasts/metabolism , Prostheses and Implants , Serum Albumin, Bovine/chemistry , Stainless Steel/chemistry , Adsorption , Animals , Bisbenzimidazole/metabolism , Cattle , Cell Adhesion , Cell Count , Cell Line , Cell Nucleus/metabolism , Cell Shape , Cell Survival , Fibronectins/metabolism , Immunohistochemistry , Mice , Microscopy, Fluorescence , Nanostructures/ultrastructure , Osteoblasts/ultrastructure , Particle Size , Vinculin/metabolism , Wettability
14.
Mol Biosyst ; 10(2): 338-47, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24322393

ABSTRACT

The interaction of methyldopa [(S)-2-amino-3-(3,4-dihydroxyphenyl)-2-methyl propanoic acid] (MDP), antihypertensive drug, with calf thymus DNA (ct-DNA) was investigated by spectroscopic and viscometric techniques. According to the results arising from the fluorescence spectra, viscosity measurements and molecular modeling studies; we concluded that MDP is a minor groove binder of ct-DNA and preferentially binds to AT rich regions. Ethidium bromide (EB) displacement studies revealed that MDP did not have any effect on EB bound DNA which is indicative of groove binding. This was substantiated by displacement studies with Hoechst 33258, a known minor groove binder. In addition, the thermodynamic and docking parameters showed that hydrophobic interaction via drug aromatic rings inside the DNA minor groove plays a major role in this binding.


Subject(s)
Antihypertensive Agents/metabolism , DNA/metabolism , Methyldopa/metabolism , AT Rich Sequence , Animals , Antihypertensive Agents/pharmacology , Binding Sites , Bisbenzimidazole/metabolism , Cattle , Circular Dichroism , Ethidium/metabolism , Methyldopa/chemistry , Methyldopa/pharmacology , Models, Molecular , Molecular Docking Simulation , Spectrometry, Fluorescence , Thermodynamics
15.
Bioorg Med Chem Lett ; 23(20): 5689-93, 2013 Oct 15.
Article in English | MEDLINE | ID: mdl-24012122

ABSTRACT

Synthesis of a novel class of compounds and their biophysical studies with TAR-RNA are presented. The synthesis of these compounds was achieved by conjugating neomycin, an aminoglycoside, with benzimidazoles modeled from a B-DNA minor groove binder, Hoechst 33258. The neomycin-benzimidazole conjugates have varying linkers that connect the benzimidazole and neomycin units. The linkers of varying length (5-23 atoms) in these conjugates contain one to three triazole units. The UV thermal denaturation experiments showed that the conjugates resulted in greater stabilization of the TAR-RNA than either neomycin or benzimidazole used in the synthesis of conjugates. These results were corroborated by the FID displacement and tat-TAR inhibition assays. The binding of ligands to the TAR-RNA is affected by the length and composition of the linker. Our results show that increasing the number of triazole groups and the linker length in these compounds have diminishing effect on the binding to TAR-RNA. Compounds that have shorter linker length and fewer triazole units in the linker displayed increased affinity towards the TAR RNA.


Subject(s)
Benzimidazoles/chemistry , Neomycin/chemistry , RNA, Viral/metabolism , Bisbenzimidazole/chemistry , Bisbenzimidazole/metabolism , Circular Dichroism , HIV Long Terminal Repeat , HIV-1/genetics , Humans , Ligands , RNA, Viral/chemistry , tat Gene Products, Human Immunodeficiency Virus/antagonists & inhibitors , tat Gene Products, Human Immunodeficiency Virus/metabolism
16.
Mol Biosyst ; 9(10): 2541-53, 2013 Oct.
Article in English | MEDLINE | ID: mdl-23921527

ABSTRACT

Recently synthesis of programmable DNA ligands which can regulate transcription factors have increased the interest of researchers on the functional ability of DNA interacting compounds. A series of DNA interacting compounds are being designed which can differentiate between GC and AT rich DNA. In this study, we have studied the specificity of a few novel bisbenzimidazoles having different bi/tri-substituted phenyl rings, with DNA duplexes using spectroscopic methods. This study entails an integrative approach where we combine biophysical methods and molecular dynamics simulation studies to establish suitable scaffolds to target A/T DNA. We have designed a few analogues of Hoechst 33342 viz.; dimethoxy (DMA), trimethoxy (TMA), dichloro (DCA) and difluoro (DFA) functionalities and performed molecular docking of newly designed analogues with biologically relevant AT and GC rich DNA sequences. The docking studies, along with molecular dynamics (MD) simulations of d(ATATATATATATATAT)2, d(GA4T4C)2, d(GT4A4C)2 and GC rich sequence: d(GCGCGCGCGCGCGCGC)2 complexed with DMA, TMA and DFA, showed that these molecules have higher binding affinity towards AT rich DNA. None of these compounds exhibited an affinity to GC rich DNA rather we observed that these compounds destabilize GC rich DNA. The binding was characterized by strong stabilization of the polynucleotides against thermal strand separation in thermal melting experiments. New insights into the molecules binding to DNA have emerged from these studies. All the DNA binding ligands stabilized d(GA4T4C)2 and d(GT4A4C)2 more out of the five oligomers used for the study, suggesting that these ligands bind 'A4T4' and 'T4A4' strongly as compared to 'ATAT' base pairs.


Subject(s)
Bisbenzimidazole/chemistry , DNA/chemistry , Models, Molecular , Nucleic Acid Conformation , Base Sequence , Biophysics , Bisbenzimidazole/metabolism , Circular Dichroism , DNA/metabolism , Ligands , Molecular Docking Simulation , Molecular Dynamics Simulation , Oligodeoxyribonucleotides/chemistry , Thermodynamics
17.
Microb Drug Resist ; 19(6): 469-76, 2013 Dec.
Article in English | MEDLINE | ID: mdl-23909485

ABSTRACT

Resistance to ciprofloxacin in Escherichia coli is increasing parallel to increased use of fluoroquinolones both in The Netherlands and in other European countries. The objective was to investigate the contribution of active efflux and expression of outer membrane proteins (OMPs) in a collection of clinical E. coli isolates collected at a clinical microbiology department in a Dutch hospital. Forty-seven E. coli isolates a wide range of ciprofloxacin minimum inhibitory concentrations and known mutations in the quinolone resistance determining region were included. A fluorometric determination of bisbenzimide efflux was used two different efflux pump inhibitors and compared to quantitative reverse transcription-polymerase chain reaction (qRT-PCR) for the expression levels of acrA, acrB, tolC, yhiV, and mdfA efflux pump genes and the OMPs ompF and ompX. Six isolates (12.7%) showed increased efflux. Although in 35 isolates (76%), overexpression of ≥1 efflux pump genes using qRT-PCR was present. Only the combined overexpression of acrAB-TolC and mdfA correlated with the phenotypic efflux assay using glucose/carbonyl cyanide m-chlorophenylhydrazone with glucose. Thus, efflux was involved in ciprofloxacin resistance in a limited number of E. coli isolates collected at a clinical microbiology department in a Dutch hospital complementing other resistance mechanisms.


Subject(s)
Anti-Bacterial Agents/pharmacology , Drug Resistance, Multiple, Bacterial/genetics , Escherichia coli/genetics , Fluoroquinolones/pharmacology , Gene Expression Regulation, Bacterial , Genes, MDR , Bacterial Outer Membrane Proteins/genetics , Bacterial Outer Membrane Proteins/metabolism , Biological Transport , Bisbenzimidazole/metabolism , Carbonyl Cyanide m-Chlorophenyl Hydrazone/pharmacology , Escherichia coli/drug effects , Escherichia coli/isolation & purification , Escherichia coli/metabolism , Escherichia coli Infections/drug therapy , Escherichia coli Infections/microbiology , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Fluorescent Dyes/metabolism , Glucose/metabolism , Humans , Hydrolases/genetics , Hydrolases/metabolism , Membrane Transport Proteins/genetics , Membrane Transport Proteins/metabolism , Microbial Sensitivity Tests , Porins/genetics , Porins/metabolism
18.
J Phys Chem B ; 117(19): 5820-30, 2013 May 16.
Article in English | MEDLINE | ID: mdl-23607615

ABSTRACT

Hoechst 33258 binds with high affinity into the minor groove of AT-rich sequences of double-helical DNA. Despite extensive studies of this and analogous DNA binding molecules, there still remains uncertainty concerning the interactions when multiple ligand molecules are accommodated within close distance. Albeit not of direct concern for most biomedical applications, which are at low drug concentrations, interaction studies for higher drug binding are important as they can give fundamental insight into binding mechanisms and specificity, including drug self-stacking interactions that can provide base-sequence specificity. Using circular dichroism (CD), isothermal titration calorimetry (ITC), and proton nuclear magnetic resonance ((1)H NMR), we examine the binding of Hoechst 33258 to three oligonucleotide duplexes containing AT regions of different lengths: [d(CGCGAATTCGCG)]2 (A2T2), [d(CGCAAATTTGCG)]2 (A3T3), and [d(CGAAAATTTTCG)]2 (A4T4). We find similar binding geometries in the minor groove for all oligonucleotides when the ligand-to-duplex ratio is less than 1:1. At higher ratios, a second ligand can be accommodated in the minor groove of A4T4 but not A2T2 or A3T3. We conclude that the binding of the second Hoechst to A4T4 is not cooperative and that the molecules are sitting with a small separation apart, one after the other, and not in a sandwich structure as previously proposed.


Subject(s)
Bisbenzimidazole/metabolism , DNA/chemistry , DNA/metabolism , Nucleic Acid Conformation , Base Sequence , DNA/genetics , Kinetics , Models, Molecular , Thermodynamics
19.
Mol Neurobiol ; 48(1): 205-16, 2013 Aug.
Article in English | MEDLINE | ID: mdl-23546740

ABSTRACT

The functions of chloride channels in preconditioning-induced cell protection remain unclear. In this report, we show that the volume-activated chloride channels play a key role in hydrogen peroxide (H2O2) preconditioning-induced cell protection in pheochromocytoma PC12 cells. The preconditioning with 100 µM H2O2 for 90 min protected the cells from injury induced by long period exposure to 300 µM H2O2. The protective effect was attenuated by pretreatment with the chloride channel blockers, 5-nitro-2-3-phenylpropylamino benzoic acid (NPPB) and tamoxifen. H2O2 preconditioning directly activated a chloride current, which was moderately outward-rectified and sensitive to the chloride channel blockers and hypertonicity-induced cell shrinkage. H2O2 preconditioning functionally up-regulated the activities of volume-activated chloride channels and enhanced the regulatory volume decrease when exposure to extracellular hypotonic challenges. In addition, acute application of H2O2 showed distinctive actions on cell volume and membrane permeability in H2O2 preconditioned cells. In H2O2 preconditioned cells, acute application of 300 µM H2O2 first promptly induced a decrease of cell volume and enhancement of cell membrane permeability, and then, cell volume was maintained at a relatively stable level and the facilitation of membrane permeability was reduced. Conversely, in control cells, 300 µM H2O2 induced a slow but persistent apoptotic volume decrease (AVD) and facilitation of membrane permeability. H2O2 preconditioning also significantly up-regulated the expression of ClC-3 protein, the molecular candidate of the volume-activated chloride channel. These results suggest that H2O2 preconditioning can enhance the expression and functional activities of volume-activated chloride channels, thereby modulate cell volume and cell membrane permeability, which may contribute to neuroprotection against oxidant-induced injury.


Subject(s)
Cell Membrane Permeability/drug effects , Cell Size/drug effects , Chloride Channels/metabolism , Hydrogen Peroxide/pharmacology , Ion Channel Gating/drug effects , Oxidants/toxicity , Animals , Apoptosis/drug effects , Bisbenzimidazole/metabolism , Chloride Channels/antagonists & inhibitors , Coloring Agents/metabolism , Cytoprotection/drug effects , DNA/metabolism , Hypotonic Solutions/pharmacology , Nitrobenzoates/pharmacology , PC12 Cells , Rats , Stress, Physiological/drug effects , Up-Regulation/drug effects
20.
Mol Med Rep ; 7(5): 1585-90, 2013 May.
Article in English | MEDLINE | ID: mdl-23467814

ABSTRACT

In the present study, the antitumor effects of the nor­Oleanane type triterpene saponin, Bigelovii A, isolated from Salicornia bigelovii Torr, were examined. Bigelovii A was demonstrated to inhibit HL­60 human acute promyelocytic leukaemia cell growth with an IC50 value of 2.15 µg/ml. In addition, Bigelovii A promoted apoptosis in HL­60 cells, as shown by apoptotic morphological changes and the hypodiploid cell assay. Apoptotic induction by Bigelovii A was associated with the downregulation of Bcl­2, the upregulation of Bax and the activation of caspase­3, as demonstrated by RT­PCR and western blot analysis. In addition, a lactate dehydrogenase release test indicated that Bigelovii A may exhibit cytotoxic activity by the induction of cell membrane impairment. This study is the first to identify that Bigelovii A exhibits potential antitumor activity and induces marked apoptosis and membrane permeabilisation in HL­60 cells. Bigelovii A may be a novel candidate for future cancer therapy.


Subject(s)
Apoptosis/drug effects , Leukemia, Promyelocytic, Acute/drug therapy , Leukemia, Promyelocytic, Acute/pathology , Saponins/pharmacology , Saponins/therapeutic use , Triterpenes/pharmacology , Triterpenes/therapeutic use , Bisbenzimidazole/metabolism , Blotting, Western , Caspase 3/metabolism , Cell Count , Cell Shape/drug effects , Drug Screening Assays, Antitumor , Enzyme Activation/drug effects , Gene Expression Regulation, Leukemic/drug effects , HL-60 Cells , Humans , L-Lactate Dehydrogenase/metabolism , Leukemia, Promyelocytic, Acute/enzymology , Leukemia, Promyelocytic, Acute/genetics , Saponins/chemistry , Signal Transduction/drug effects , Triterpenes/chemistry , bcl-2-Associated X Protein/genetics , bcl-2-Associated X Protein/metabolism
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