Photoinduced in situ generation of DNA-targeting ligands: DNA-binding and DNA-photodamaging properties of benzo[c]quinolizinium ions

The photoreactions of selected styrylpyridine derivatives to the corresponding benzo[c]quinolizinium ions are described. It is shown that these reactions are more efficient in aqueous solution (97-44%) than in organic solvents (78-20% in MeCN). The quinolizinium derivatives bind to DNA by intercalation with binding constants of 6-11 × 104 M-1, as shown by photometric and fluorimetric titrations as well as by CD- and LD-spectroscopic analyses. These ligand-DNA complexes can also be established in situ upon irradiation of the styrylpyridines and formation of the intercalator directly in the presence of DNA. In addition to the DNA-binding properties, the tested benzo[c]quinolizinium derivatives also operate as photosensitizers, which induce DNA damage at relative low concentrations and short irradiation times, even under anaerobic conditions. Investigations of the mechanism of the DNA damage revealed the involvement of intermediate hydroxyl radicals and C-centered radicals. Under aerobic conditions, singlet oxygen only contributes to marginal extent to the DNA damage.

Ruthenium(II)-Dithiocarbazates as Anticancer Agents: Synthesis, Solution Behavior, and Mitochondria-Targeted Apoptotic Cell Death

The reaction of the Ru(PPh₃ )₃ Cl₂ with HL^1-3 -OH (-OH stands for the oxime hydroxyl group; HL¹ -OH=diacetylmonoxime-S-benzyldithiocarbazonate; HL² -OH=diacetylmonoxime-S-(4-methyl)benzyldithiocarbazonate; and HL³ -OH=diacetylmonoxime-S-(4-chloro)benzyl-dithiocarbazonate) gives three new ruthenium complexes [Ru^II (L^1-3 -H)(PPh₃ )₂ Cl] (1-3) (-H stands for imine hydrogen) coordinated with dithiocarbazate imine as the final products. All ruthenium(II) complexes (1-3) have been characterized by elemental (CHNS) analyses, IR, UV-vis, NMR (¹ H, ¹³ C, and ³¹ P) spectroscopy, HR-ESI-MS spectrometry and also, the structure of 1-2 was further confirmed by single crystal X-ray crystallography. The solution/aqueous stability, hydrophobicity, DNA interactions, and cell viability studies of 1-3 against HeLa, HT-29, and NIH-3T3 cell lines were performed. Cell viability results suggested 3 being the most cytotoxic of the series with IC₅₀ 6.9±0.2 μM against HeLa cells. Further, an apoptotic mechanism of cell death was confirmed by cell cycle analysis and Annexin V-FITC/PI double staining techniques. In this regard, the live cell confocal microscopy results revealed that compounds primarily target the mitochondria against HeLa, and HT-29 cell lines. Moreover, these ruthenium complexes elevate the ROS level by inducing mitochondria targeting apoptotic cell death.

Ligands for Abasic Site-containing DNA and their Use as Fluorescent Probes

Apurinic and apyrimidinic sites, also referred to as abasic or AP sites, are residues of duplex DNA in which one DNA base is removed from a Watson-Crick base pair. They are formed during the enzymatic repair of DNA and offer binding sites for a variety of guest molecules. Specifically, the AP site may bind an appropriate ligand as a substitute for the missing nucleic base, thus stabilizing the abasic site-containing DNA (AP-DNA). Notably, ligands that bind selectively to abasic sites may be employed for analytical and therapeutical purposes. As a result, there is a search for structural features that establish a strong and selective association of a given ligand with the abasic position in DNA. Against this background, this review provides an overview of the different classes of ligands for abasic site-containing DNA (AP-DNA). This review covers covalently binding substrates, namely amine and oxyamine derivatives, as well as ligands that bind to AP-DNA by noncovalent association, as represented by small heterocyclic aromatic compounds, metal-organic complexes, macrocyclic cyclophanes, and intercalator-nucleobase conjugates. As the systematic development of fluorescent probes for AP-DNA has been somewhat neglected so far, this review article contains a survey of the available reports on the fluorimetric response of the ligand upon binding to the AP-DNA. Based on these data, this compilation shall present a perspective for future developments of fluorescent probes for AP-DNA.

Copper-Catalyzed Oxidative C-H Annulation of Quinolines with Dichloroethane toward Benzoquinoliziniums Using an In Situ Activation Strategy

Described herein is a copper-catalyzed oxidative C-H annulation of quinolines with 1,2-chloroethane (DCE), providing a concise synthetic approach to benzoquinoliziniums. In this protocol, DCE not only serves as a solvent and an in situ activation agent of quinoline C2-H but also works as vinyl equivalents to constitute the six-membered azonia ring. Furthermore, the resultant benzoquinolizinium library exhibits good properties of binding to DNA and low cytotoxicity.

Fluorogenic Protein Labeling by Generation of Fluorescent Quinoliziniums Using [Cp*RhCl2]2

Fluorogenic labeling has received considerable attention as a result of the high demand in chemical biology and synthetic biology applications. Herein, we develop a new strategy for fluorescent turn-on ligation targeting alkyne- and quinoline-linked peptides and proteins (λ_em of 515 nm and up to Φ_F of 0.20) using the [Cp*RhCl₂]₂ catalyst. The good conversion, high flexibility, broad utility, ease of use, and mild reaction conditions are great advantages to extend the rhodium-mediated turn-on fluorogenic bioconjugation for further applications.

RhodiumIII-Catalyzed Remote Difunctionalization of Arenes Assisted by a Relay Directing Group

Rhodium-catalyzed diverse tandem twofold C-H bond activation reactions of para olefin-tethered arenes have been realized, with unsaturated reagents such as internal alkynes, dioxazolones, and isocyanates being the coupling partner as...

Towards an understanding of the biological activity of naphthylisoquinoline alkaloids: DNA-binding properties of dioncophyllines A, B, and C

Dioncophylline A and B bind to duplex DNA in a half-intercalation binding mode and to abasic site-containing DNA by insertion.

Synthesis of new quinolizinium-based fluorescent compounds and studies on their applications in photocatalysis

Quinoliziniums, cationic aromatic heterocycles bearing a quaternary bridgehead nitrogen, have been widely used as fluorescent dyes, DNA intercalators, ionic liquids etc. A library of new quinolizinium compounds was synthesized from quinolines and internal alkyne substrates in up to 65% isolated yields. Systematic studies of their photophysical properties were conducted. The quinoliziniums have been used in three visible-light-induced photocatalysis reactions with good yields.

Synthesis, DNA-binding and antiproliferative properties of diarylquinolizinium derivatives

A series of ten 2,7- and 2,8-diarylquinolizinium derivatives was synthesized and their DNA-binding and cytotoxic properties were investigated. Except for one nitro-substituted derivative all tested diarylquinolizinium ions bind to DNA with sufficient affinity (2 × 10⁴ M^-1-2 × 10⁵ M^-1). It was shown with photometric, fluorimetric and polarimetric titrations as well as with flow-LD analysis that the ligands bind mainly by intercalation to duplex DNA, however, depending on the ligand-DNA ratio, groove binding and backbone association were also observed with some derivatives. The biological activity was further investigated with tests of cytotoxicity and antiproliferative properties towards non-tumor cells and selected cancer cells, along with cell cycle analysis and an annexin-V assay. Notably, substrates that carry donor-functionalities in the 4-position of the phenyl substituents revealed a strong, and in some cases selective, antiproliferative activity as quantified by the growth inhibition, GI₅₀, at very low micromolar and even submicromolar level both in leukemia and solid tumors.

Novel indole-thiazole and indole-thiazolidinone derivatives as DNA groove binders

In this study, we report the synthesis of eight novel indole-thiazole and indole-thiazolidinone derivatives, as well as their ability to interact with DNA, analysed through the UV-vis absorption, fluorescence, circular dichroism (CD), viscosity techniques and molecular docking. The ctDNA interaction analysis demonstrated different spectroscopic effects and the affinity constants (Kb) calculated by the UV-vis absorption method were between 2.08 × 10⁵ and 6.99 × 10⁶ M^-1, whereas in the fluorescence suppression constants (Ksv) ranged between 0.38 and 0.77 × 10⁴ M^-1 and 0.60-7.59 × 10⁴ M^-1 using Ethidium Bromide (EB) and 4',6-Diamidino-2-phenylindole (DAPI) as fluorescent probes, respectively. Most derivatives did not alter significantly the secondary structure of the ctDNA according to the CD results. None of the compounds was able to change the relative viscosity of the ctDNA. These results prove that compounds interact with ctDNA via groove binding, which was confirmed by A-T rich oligonucleotide sequence assay with compound JF-252, suggesting the importance of both the phenyl ring coupled to C-4 thiazole ring and the bromo-unsubstituted indole nucleus.

In vitro activity, ultrastructural studies and in silico pharmacokinetic properties of indol-3-yl-thiosemicarbazones derivatives and analogues against juvenile and adult worms of S. mansoni

The present work aimed to carry out in vitro biological assays of indol-3-yl derivatives thiosemicarbazones (2a-e) and 4-thiazolidinones (3a-d) against juvenile and adult worms of S. mansoni, as well as the in silico determination of pharmacokinetic parameters for the prediction of the oral bioavailability of these derivatives. All compounds were initially screened at a concentration of 200 μM against S. mansoni adult worms and the results evidenced the good activity of compounds 2b, 2d and 3b, which caused 100% mortality after 24, 48 and 72 h, respectively. Subsequent studies with these same compounds revealed that compound 2b was able to reduce the viability of the parasites by 85% and 83% at concentrations of 200 and 100 μM, respectively. In relation to the juvenile worms, all compounds (2b, 2d and 3b) were able to cause mortality, but compound 2b demonstrated better activity causing 100% mortality in 48 h. Additionally, it was possible to observe reduction in the viability of juvenile worms of 85%, 81% and 64% at concentrations of 200, 100 and 50 μM, respectively. Several ultrastructural damages were observed when adult and juvenile S. mansoni worms were exposed to compound 2b (200 μM) that was characterized by extensive destruction by the integument, which may justify the mortality rate of cultured parasites. In the DNA interaction assay, fragmentation of the genetic material of adult worms when treated with compound 2b (200 μM) was evidenced, indicating the apoptosis process as mechanism of parasite death. Regarding pharmacokinetic properties, all derivatives are according to the required parameters, predicting good oral bioavailability for the studied compounds. The results presented in this study reveal the good activity of compound 2b in both adult and juvenile worms of S. mansoni, pointing this compound as promising in the development of further studies on schistosomicidal activity.

Structural flexibility versus rigidity of the aromatic unit of DNA ligands: binding of aza- and azoniastilbene derivatives to duplex and quadruplex DNA

The known azastilbene (E)-1,2-di(quinolin-3-yl)ethane (2a) and the novel azoniastilbene derivatives (E)-2-(2-(naphthalen-2-yl)vinyl)quinolizinium (2b) and (E)-3,3'-(ethane-1,2-diyl)bis(1-methylquinolinin-1-ium) (2c) were synthesized. Their interactions with duplex and quadruplex DNA (G4-DNA) were studied by photometric, fluorimetric, polarimetric and flow-LD analysis, and by thermal DNA denaturation studies, as well as by ¹H-NMR spectroscopy. The main goal of this study was a comparison of these conformationally flexible compounds with the known G4-DNA-binding diazoniadibenzo[b,k]chrysenes, that have a comparable π-system extent, but a rigid structure. We have observed that the aza- and azoniastilbene derivatives 2a-c, i.e. compounds with almost the same spatial dimensions and steric demand, bind to DNA with an affinity and selectivity that depends significantly on the number of positive charges. Whereas the charge neutral derivative 2a binds unspecifically to the DNA backbone of duplex DNA, the ionic compounds 2b and 2c are typical DNA intercalators. Notably, the bis-quinolinium derivative 2c binds to G4-DNA with moderate affinity (K_b = 4.8 × 10⁵ M^-1) and also stabilizes the G4-DNA towards thermal denaturation (ΔT_m = 11 °C at ligand-DNA ratio = 5.0). Strikingly, the corresponding rigid counterpart, 4a,12a-diazonia-8,16-dimethyldibenzo[b,k]chrysene, stabilizes the G4-DNA to an even greater extent under identical conditions (ΔT_m = 27 °C). These results indicate that the increased flexibility of a G4-DNA ligand does not necessarily lead to stronger interactions with the G4-DNA as compared with rigid ligands that have essentially the same size and π system extent.

Rh-Catalyzed tandem C-C/C-N bond formation of quinoxalines with alkynes leading to heterocyclic ammonium salts

An efficient Rh-catalyzed oxidative C-H activation/annulation of 2-arylquinoxalines with internal alkynes is described using Cu(OAc)2·H2O and AgBF4 to afford a diverse variety of substituted quarternary ammonium salts at room temperature. The mechanism of the protocol is established on the basis of isolation of the 5-membered rhodacycle intermediate and kinetic isotope studies. The mild reaction conditions, substrate scope and functional group diversity are the salient practical features.

Dibenzopyridoimidazocinnolinium cations: a new family of light-up fluorescent DNA probes

A new family of weakly fluorescent azonia cations with DNA-binding ability by intercalation whose fluorescence intensity increases significantly upon DNA addition is reported. A live-cell staining cells analysis showed the capacity of these new compounds for active uptake and accumulation by living cells.

8-Styryl-substituted coralyne derivatives as DNA binding fluorescent probes

8-Styryl-substituted coralyne derivatives bind to duplex and quadruplex DNA and may be used for fluorimetric staining of nucleoli in cells.

Six new 8-styryl-substituted coralyne derivatives 4a–f were synthesized from coralyne (2) by a base catalysed Knoevenagel type reaction. It was shown by photometric and fluorimetric titrations of double stranded and quadruplex DNA to 4b–d as well as by fluorimetric DNA denaturation experiments that these ligands bind to DNA with different binding modes at varying ligand-DNA ratios (LDR). Specifically, the addition of DNA caused initially a hypochromic effect in absorbance and, at a particular LDR, the development of a new red shifted absorption band with a hyperchromic effect. Furthermore, 4b–d induced a significant and selective stabilization of quadruplex DNA towards unfolding (ΔT_m = 31.6–32.9 °C at LDR = 5), which is even more pronounced as compared to the parent compound coralyne (2). Most notably, the addition of DNA to the dimethylamino-substituted derivative 4b leads to a new, strongly red-shifted emission band at 695 nm. Hence, this derivative is a fluorescent probe that changes its fluorescence colour from green to red in the presence of DNA and even allows the fluorimetric analysis of living cells by staining of the nucleoli.

Control of the DNA-Binding and Antiproliferative Properties of Hydroxybenzo[b]quinolizinium Derivatives with pH and Light

The interactions of 8-hydroxybenzo[b]quinolizinium and 9-hydroxybenzo[b]quinolizinium with DNA are investigated in detail. Specifically, spectrophotometric and spectrofluorimetric titrations, thermal DNA-denaturation experiments as well as CD- and LD-spectroscopic analysis show that a pH shift by just one or two orders of magnitude has a significant impact on the interactions of the acidic ligands with the nucleic acid. Both ligands bind with high affinity to DNA at pH 6 (K_b ≈10⁵  m^-1 ). At pH 7 or 8, however, the binding interactions are much weaker because of the formation of the corresponding charge-neutral conjugate bases, the affinity to DNA of which is reduced because of the resulting lack of a positive charge. Notably, the variation of DNA affinity occurs in a range that corresponds to the fluctuations of pH values under physiological conditions, so that these ligands may be employed to target DNA in tissue with particular pH values, especially, cancer cells. The antiproliferative activity of the title compounds under different conditions is also investigated. In the absence of irradiation, both compounds show only a modest cytotoxicity toward cancer cells. However, upon irradiation, even at low UV-A doses, a significant reduction of cell viability of tumor cell lines is induced by the ligands.

Synthesis, DNA Binding, and Antiproliferative Activity of Novel Acridine-Thiosemicarbazone Derivatives

In this work, the acridine nucleus was used as a lead-compound for structural modification by adding different substituted thiosemicarbazide moieties. Eight new (Z)-2-(acridin-9-ylmethylene)-N-phenylhydrazinecarbothioamide derivatives (3a-h) were synthesized, their antiproliferative activities were evaluated, and DNA binding properties were performed with calf thymus DNA (ctDNA) by electronic absorption and fluorescence spectroscopies. Both hyperchromic and hypochromic effects, as well as red or blue shifts were demonstrated by addition of ctDNA to the derivatives. The calculated binding constants ranged from 1.74 × 10(4) to 1.0 × 10(6) M(-1) and quenching constants from -0.2 × 10(4) to 2.18 × 10(4) M(-1) indicating high affinity to ctDNA base pairs. The most efficient compound in binding to ctDNA in vitro was (Z)-2-(acridin-9-ylmethylene)-N- (4-chlorophenyl) hydrazinecarbothioamide (3f), while the most active compound in antiproliferative assay was (Z)-2-(acridin-9-ylmethylene)-N-phenylhydrazinecarbothioamide (3a). There was no correlation between DNA-binding and in vitro antiproliferative activity, but the results suggest that DNA binding can be involved in the biological activity mechanism. This study may guide the choice of the size and shape of the intercalating part of the ligand and the strategic selection of substituents that increase DNA-binding or antiproliferative properties.

Targeting DNA with small molecules: a comparative study of a library of azonia aromatic chromophores

The fluorescence, DNA binding and DNA sequence selectivity properties of a library of azonia aromatic cations have been studied.

Efficient inhibition of human AP endonuclease 1 (APE1) via substrate masking by abasic site-binding macrocyclic ligands

Bis-naphthalene macrocycles bind to abasic sites in DNA, leading to efficient inhibition of their cleavage by human AP endonuclease 1 (APE1).

Improved DNA equilibrium binding affinity determinations of platinum(ii) complexes using synchrotron radiation circular dichroism

The DNA binding affinity of a range of Pt(ii) complexes was reinvestigated using SRCD and a new method was implemented for determining the binding constant, saving time and minimising data collection.