Ivana Stolić

Effect of 3,4-ethylenedioxy-extension of thiophene core on the DNA/RNA binding properties and biological activity of bisbenzimidazole amidines

Novel bisbenzimidazoles (4-6), characterized by 3,4-ethylenedioxy-extension of thiophene core, revealed pronounced affinity and strong thermal stabilization effect toward ds-DNA. They interact within ds-DNA grooves as dimmers or even oligomers and agglomerate along ds-RNA. Compounds 4-6 have shown moderate to strong antiproliferative effect toward panel of eight carcinoma cell lines. Compound 5 displayed the best inhibitory potential and in equitoxic concentration (IC(50)=1 x 10(-6)M) induced accumulation of cells in G2/M phase after 48 h of incubation. Fluorescence microscopy showed that 5 entered into live HeLa cells within 30 min, but did not accumulate in nuclei even after 2.5h. Compound 5 inhibited the growth of Trypanosome cruzi epimastigotes (IC(50)=4.3 x 10(-6)M).

Synthesis, DNA/RNA affinity and antitumour activity of new aromatic diamidines linked by 3,4-ethylenedioxythiophene.

A series of novel 2,5-bis(amidinophenyl)-3,4-ethylenedioxythiophenes (5-10 and 15) has been synthesized. Compounds 5-10 bind to the DNA minor groove as the dominant binding site and strongly stabilize the double helix of ct-DNA. Surprisingly, the same compounds also thermally stabilize ds-RNA, whereby most of them form stacked dimers along the RNA double helix. The only exception is compound 15 which, due to its structural features, showed no interaction with DNA or RNA. Compounds 5-10 have shown a moderate to strong cytotoxic effect (GI50=1.5-9.0 μM) on a panel of seven tumour cell lines. The diimidazoline derivative 9, due to its highest inhibitory potential on the growth of all tested tumour cell lines, was investigated in more detail by testing its ability to enter into cells and influence the cell cycle. Compound 9 (5 μM) was internalized successfully in cell cytoplasm during a 30-min incubation period, followed by nuclear localization upon 90-min incubation. Significant arrest in HeLa cells in the G2/M phase, shown by cell cycle analysis at an equitoxic (50 μM) concentration, suggests interaction of a studied compound with cellular DNA as the main mode of biological action.

Synthesis and structure–activity relationship of amidine derivatives of 3, 4-ethylenedioxythiophene as novel antibacterial agents

Current antibacterial chemotherapeutics are facing an alarming increase in bacterial resistance pressuring the search for novel agents that would expand the available therapeutic arsenal against resistant bacterial pathogens. In line with these efforts, a series of 9 amidine derivatives of 3,4-ethylenedioxythiophene were synthesized and, together with 18 previously synthesized analogs, evaluated for their relative DNA binding affinity, in vitro antibacterial activities and preliminary in vitro safety profile. Encouraging antibacterial activity of several subclasses of tested amidine derivatives against Gram-positive (including resistant MRSA, MRSE, VRE strains) and Gram-negative bacterial strains was observed. The bis-phenyl derivatives were the most antibacterially active, while compound 19 from bis-benzimidazole class exhibited the widest spectrum of activity (with MIC of 4, 2, 0.5 and ≤0.25 μg/ml against laboratory strains of Staphyloccocus aureus, Streptococcus pneumoniae, Streptococcus pyogenes, Moraxella catarrhalis, respectively and 4-32 μg/ml against clinical isolates of sensitive and resistant S. aureus, Staphylococcus epidermidis and Enterococcus faecium) and also demonstrated the strongest DNA binding affinity (ΔTm of 15.4 °C). Asymmetrically designed compounds and carboxamide-amidines were, in general, less active. Molecular docking indicated that the shape of the 3,4-ethylenedioxythiophene derivatives and their ability to form multiple electrostatic and hydrogen bonds with DNA, corresponds to the binding modes of other minor-groove binders. Herein reported results encourage further investigation of this class of compounds as novel antibacterial DNA binding agents.

An Aromatic Diamidine That Targets Kinetoplast DNA, Impairs the Cell Cycle in Trypanosoma cruzi, and Diminishes Trypomastigote Release from Infected Mammalian Host Cells.

ABSTRACT Trypanosoma cruzi is the etiological agent of Chagas disease, affecting approximately 10 million people in the Americas and with some 40 million people at risk. The objective of this study was to evaluate the anti-T. cruzi activity of three new diamidines that have a 3,4-ethylenedioxy extension of the thiophene core, designated MB17, MB19, and MB38. All three diamidines exhibited dose-dependent inhibition of epimastigote replication. The mechanisms of action of these diamidines were investigated. Unlike MB17 and MB19, MB38 exhibited a significant increase in the number of annexin-propidium iodide double-labeled cells compared to levels in control parasites. As MB17 had shown a lower 50% inhibitory concentration (IC50) against epimastigote growth, the mechanism of action of this drug was studied in more detail. MB17 triggered a decrease in the intracellular ATP levels. As a consequence, MB17 affected the genomic DNA and kinetoplast DNA (kDNA) and impaired the parasite cell cycle. Moreover, MB17 caused DNA fragmentation, with a more severe effect on kDNA than on nuclear DNA, resulting in dyskinetoplastic cells. MB17 was tested for toxicity and effectiveness for the treatment of infected CHO-K1 cells, exhibiting a 50% cytotoxic concentration (CC50) of 13.47 ± 0.37 μM and an IC50 of 0.14 ± 0.12 μM against trypomastigote release. MB17 also diminished the infection index by 60% at 0.5 μM. In conclusion, despite belonging to the same family, these diamidines have different efficiencies. To summarize, MB17 was the most potent of these diamidines against epimastigotes, producing DNA damage preferentially in kDNA, impairing the parasite cell cycle, and decreasing the infection index and trypomastigote release from infected mammalian host cells, with a high selectivity index (SI) (<90). These data suggest that MB17 could be an interesting lead compound against T. cruzi.

Axial chirality of N,N′-disubstituted 3,4-ethylenedioxythiophene-2,5-dicarboxamides

A series of N,N’-disubstituted 3,4-ethylenedioxythiophene-2,5-dicarboxamides was synthesised by amide bond formation between 3,4-ethylenedioxythiophene-2,5-dicarbonyl chloride and corresponding primary amines, where the size and the nature of the substituent were varied. The crystal structures of prepared compounds were determined by X-ray structure analysis. Mechanism and reaction rates of interconversion between conformational isomers were obtained by DFT calculations. All studied compounds reveal axial chirality with molecular symmetry C2. Amide bond isomerisation and twisting of the dioxane ring in studied compounds results in the formation of series of conformers of which the s-trans/s-trans conformer is energetically most favourable.

Fragmentation of diamide derivatives of 3,4-ethylenedioxythiophene

The sequential product ion (MS(n)) fragmentation of four symmetric diamide derivatives of 3,4-ethylenedioxythiophene were characterized using ion trap mass spectrometry with electrospray ionization and their fragmentation patterns were studied. The experimental data consists of mass spectra obtained by tandem mass spectrometry, and calculations were obtained by the M06-2X/6-31 G (d,p) method. Investigated compounds represent building blocks in synthesis of compounds used in different areas of chemistry and industry such as in medicinal chemistry, as potential anticancer and anticonvulsant agents, in organic chemistry as linkers for solid-phase synthesis, and in the synthesis of a variety of materials in polymer chemistry. We present herein the investigation of the fragmentation pathway of protonated diamide derivatives of 3,4-ethylenedioxythiophene that involves the identification of fragments, influence of proton transfer on direction of fragmentation and mechanisms of reactions by which the fragmentation process occurs. Data obtained from product ion spectra of these protonated compounds and density functional theory (DFT) calculations indicate that the fragmentation process takes place via four main reactions: amido-iminol proton transfer, reverse cycloaddition, cleavage of the amide bond, and isocyanic acid elimination. The 3,4-ethylenedioxythiophene-2,5-dicarboxamide was observed as an intermediate in the fragmentation of its alkyl derivatives. To our knowledge, this work brings the first correct description of the mechanism of elimination of isocyanic acid.

2-(4-Amino­phen­yl)-3,4,5,6-tetra­hydro­pyrimidin-1-ium chloride

In the title compound, C10H14N3 +·Cl−, the tetrahydropyridinium ring of the cation, which adopts a slightly distorted envelope conformation, is disordered over two orientations with an occupancy ratio of 0.653 (5):0.347 (5). The amidinium fragment of the major conformer is twisted relative to the benzene ring by 22.5 (6)° and the two C—N bond lengths of this fragment are similar [1.3228 (16) and 1.319 (2) Å]. In the crystal, the chloride anions are involved in three N—H⋯Cl hydrogen bonds, which link the components into a two-dimensional hydrogen-bonded network parallel to (010).

Bis[2-(4-amino-phen-yl)-4,5-dihydro-1H-imidazol-3-ium] dichloride monohydrate.

The asymmetric unit of the title compound, 2C9H12N3 +·2Cl−·H2O, comprises two molecules, two chloride anions and one molecule of crystal water. In the imidazolinium ring, the protonation contributes to delocalization of the positive charge over the two C—N bonds. Both chloride anions are acceptors of four hydrogen bonds in a flattened tetrahedron environment. The donors are NH2 groups, the NH groups of the imidazolinium rings and the water molecule. These hydrogen bonds and N—H⋯O(H2O) hydrogen bonds form a three-dimensional network.

Synthesis, anti-bacterial and anti-protozoal activities of amidinobenzimidazole derivatives and their interactions with DNA and RNA

Abstract Amidinobenzimidazole derivatives connected to 1-aryl-substituted 1,2,3-triazole through phenoxymethylene linkers 7a–7e, 8a–8e, and 9a–9e were designed and synthesised with the aim of evaluating their anti-bacterial and anti-trypanosomal activities and DNA/RNA binding affinity. Results from anti-bacterial evaluations of antibiotic-resistant pathogenic bacteria revealed that both o-chlorophenyl-1,2,3-triazole and N-isopropylamidine moieties in 8c led to strong inhibitory activity against resistant Gram-positive bacteria, particularly the MRSA strain. Furthermore, the non-substituted amidine and phenyl ring in 7a induced a marked anti-bacterial effect, with potency against ESBL-producing Gram-negative E. coli better than those of the antibiotics ceftazidime and ciprofloxacin. UV–Vis and CD spectroscopy, as well as thermal denaturation assays, indicated that compounds 7a and 8c showed also binding affinities towards ctDNA. Anti-trypanosomal evaluations showed that the p-methoxyphenyl-1,2,3-triazole moiety in 7b and 9b enhanced inhibitory activity against T. brucei, with 8b being more potent than nifurtimox, and having minimal toxicity towards mammalian cells. Graphical Abstract

QSAR Analysis of Antitumor Activities of 3, 4-Ethylenedioxythiphene Derivatives

QSAR analysis was performed for the antitumor activity of 27 derivatives of 3,4-ethylenedioxythiophene against six carcinoma cell lines. The best models were obtained with surface area (SAG) in combination with lipohilicity (log P) as descriptors. Results have shown that molecules with smaller solvent accessible surface area and higher lipophilicy should have higher biological activity against carcinoma cell.