The disaccharide anthracycline MEN 10755 binds human serum albumin to a non-classical drug binding site

The interaction of the novel disaccharide anthracycline MEN 10755 with human serum albumin (HSA) was investigated by visible absorption and fluorescence spectroscopies and by ultrafiltration. Notably, MEN 10755 binds serum albumin far stronger than doxorubicin. Albumin binding results into a drastic quenching of the intrinsic fluorescence of MEN 10755; a binding constant of 1.1 x 10(5) was determined from fluorescence data. To localize the HSA binding site of MEN 10755 competition experiments were carried out with ligands that are selective for the different drug binding sites of the protein. No relevant competition effects were seen in the case of warfarin, diazepam and hemin, known ligands of sites I, II and III, respectively. Modest effects were observed following addition of palmitic acid that targets the several fatty acid binding sites of the protein. In contrast, extensive displacement of the bound anthracycline was achieved upon addition of ethacrinic acid. On the basis of these results, it is proposed that MEN 10755 binds serum albumin tightly to a non-canonical surface binding site for which it competes specifically with ethacrinic acid.     

DNA binding studies of PdCl<Subscript>2</Subscript>(LL)(LL = chelating diamine ligand: N,N-dimethyltrimethylenediamine) complex

The interaction of native calf thymus DNA with the Pd(II) complex, PdCl2(LL) (LL = chelating diamine ligand: N,N-dimethyltrimethylenediamine), in 10 mM Hepes aqueous solutions at neutral pH has been monitored as a function of metal complex/DNA molar ratio by UV absorption spectrophotometry, circular dichroism (CD), viscosimetry, and fluorescence spectroscopy. The results support two modes of interaction. In particular, this complex showed absorption hypochromism and then hyperchromism, increase in melting temperature, and some structural changes in specific viscosity when bound to calf thymus DNA. The binding constant determined using absorption measurement is 2.69.10(3) M(-1). As evidenced by the increasing fluorescence of methylene blue-DNA solutions in the presence of increasing amounts of metal complex, PdCl(2)(LL) is able to displace the methylene blue intercalated into DNA, but not so completely, as indicated by partial intercalation. CD spectral changes in two steps and viscosity decrease confirm our conclusions.     

Synthesis, characterization, antioxidative and antitumor activities of solid quercetin rare earth(III) complexes

Eight rare earth metal(II) complexes with quercetin ML3 x 6H2O [L=quercetin (3-OH group deprotonated); M = La, Nd, Eu, Gd, Tb, Dy, Tm and Y] have been synthesized and characterized by elemental analysis, complexometric titration, thermal analysis, conductivity, IR, UV, 1HNMR and fluorescence spectra techniques as well as cyclic voltammetry. The quercetin:metal stoichiometry and the equilibrium stability constant for metal binding to quercetin have been determined. The antioxidative and antitumor activities of quercetin x 2H2O and the complexes were tested by both the MTT and SRB methods. The results show that the suppression ratio of the complexes against the tested tumour cells are superior to quercetin x 2H2O. The property of LaL3 x 6H2O reacting with calf thymus DNA was studied by fluorescence methods. The La-complex binding to DNA has been determined by fluorescence titration in 0.05 M Tris-HCl, 0.5 M NaCl buffer (pH 7.0). The results indicate that the interaction of the complex with DNA is very evident.     

Interaction of diazinon with DNA and the protective role of selenium in DNA damage

The interaction of native calf thymus DNA with Diazinon, an organophophorus insecticide, in HEPES buffer at neutral pH, was monitored by UV absorption spectrophotometry, circular dichroism (CD), electrochemical technique, and fluorescence spectroscopy. UV spectra showed hyperchromicity and blue shift with the increase of Diazinon concentration. Fluorescence spectroscopy results indicated that the probable quenching mechanism of DNA-ethidium bromide (EB) fluorescence by Diazinon is a dynamic quenching procedure, because the Stern-Volmer quenching constant (K(SV)) increased with the temperature rising. Unchanging of the CD signal around 280 nm with increasing ratio of Diazinon to DNA is an important evidence for non-intercalative-binding mode of Diazinon with DNA. Stoichiometry measurement of the DNA-nDiazinon indicated that a stable 1:2 complex of DNA-Diazinon was formed under the selected conditions. The electrochemical study of the Diazinon-DNA interaction was carried out by incubation of DNA with Diazinon in the presence of varying amounts of selenium (Se). This technique revealed that Se is able to diminish the DNA damage effect of Diazinon.     

Characteristics of the binding of the anticancer agents mitoxantrone and ametantrone and related structures to deoxyribonucleic acids

The binding constants for interaction of the anticancer agents mitoxantrone and ametantrone and several congeners with calf thymus DNA and the effects of ionic strength changes have been determined spectrophotometrically. The agents show a preference for certain sequences, particularly those with GC base pairs, and the magnitude of the specificity depends on the specific substituents on the anthraquinone ring system. The binding constant for mitoxantrone with calf thymus DNA in 0.1 M Na+, pH 7, is approximately 6 X 10(6) M-1, and the rate constant for the sodium dodecyl sulfate driven dissociation of mitoxantrone from its calf thymus DNA complex under the same solution conditions and 20 degrees C was determined to be 1.3 s-1. The unwinding angle of mitoxantrone determined independently by viscosity measurements and by a novel assay employing calf thymus topoisomerase shows excellent agreement for a value of 17.5 degrees. The viscosity increase of sonicated calf thymus DNA varies considerably with the substituent on the anthraquinone ring system. Binding studies employing T4 and phi w-14 DNAs in which the major groove is occluded and the reverse experiment with anthramycin-treated calf thymus DNA indicate at least part of the mitoxantrone molecule may lie in the minor groove.     

Steady-state fluorescence and molecular-modeling studies of tomaymycin-DNA adducts

The interaction of tomaymycin and 8-O-methyltomaymycin with calf thymus DNA was studied by steady-state fluorescence techniques. The 8-phenolic proton of tomaymycin has a pK = 8.0, and the phenolate anion is essentially nonfluorescent. However, the fluorescence of the DNA adduct does not decrease until pH greater than 10.5, when the DNA double helix denatures. Acrylamide quenches the fluorescence of the free antibiotic with a quenching rate constant kq = 7 x 10(9) M-1 s-1. In DNA adducts, the quenching rate constant is reduced about 50-fold, indicating that the aromatic ring of the drug is shielded from the solvent. The four possible binding modes of the antibiotics were modeled on a 6-mer duplex by molecular mechanics calculations in the absence and presence of water and counterions. The modeling studies show that the antibiotic is buried in the minor groove in all binding modes, with the 8-substituent pointing away from the DNA core. Three or five waters are displaced from the minor groove, depending on the orientation of the drug on the DNA.     

The Interaction Mode of Groove Binding Between Quercetin and Calf Thymus DNA Based on Spectrometry and Simulation

Quercetin, a ubiquitous flavanoid, has numerous pharmacological effects, such as antioxidant and antitumor. Previous studies showed nucleic acids were the potential biological targets for antitumor medicine. For exploring the mechanism of DNA‐target medicine, the interaction between quercetin and calf thymus DNA was studied based on the method of spectrometry and simulation in our study. Firstly, the interaction between quercetin and calf thymus DNA was confirmed by fluorescence spectrometry. Furthermore, circular dichroism, fluorescence polarization, competitive displacement assay, and salt concentration dependence assay were applied to search the interaction mode of quercetin‐calf thymus DNA, which proved the existence of groove binding and electrostatic interaction. Meanwhile, quenching constant K_sv, binding constant K_a and the number of binding sites n was calculated, inferring that the fluorescence quenching occurred by static quenching process, and the main acting force was hydrogen bond. Finally, molecular docking was used to simulate and analyze the interaction between quercetin and calf thymus DNA.     

The crystal structure of the complex between a disaccharide anthracycline and the DNA hexamer d(CGATCG) reveals two different binding sites involving two DNA duplexes

The crystal structure of the complex formed between the anthracycline antibiotic 3'-deamino-3'- hydroxy-4'-(O-L-daunosaminyl)-4-demethoxydoxo rubicin (MEN 10755), an active disaccharide analogue of doxorubicin, and the DNA hexamer d(CGATCG) has been solved to a resolution of 2.1 A. MEN 10755 exhibits a broad spectrum of antitumor activities, comparable with that of the parent compound, but there are differences in the mechanism of action as it is active in doxorubicin-resistant tumors and is more effective in stimulating topoisomerase DNA cleavage. The structure is similar to previously crystallised anthracycline- DNA complexes. However, two different binding sites arise from drug intercalation so that the two halves of the self-complementary duplex are no longer equivalent. In one site both sugar rings lie in the minor groove. In the other site the second sugar protrudes out from the DNA helix and is linked, through hydrogen bonds, to guanine of a symmetry-related DNA molecule. This is the first structure of an anthracycline-DNA complex where an interaction of the drug with a second DNA helix is observed. We discuss the present findings with respect to the relevance of the amino group for DNA binding and to the potential role played by the second sugar in the interactions with topoisomerases or other cellular targets.     

A multi-spectroscopic and molecular docking approach to investigate the interaction of antiviral drug oseltamivir with ct-DNA

The possible interaction between the antiviral drug oseltamivir and calf thymus DNA at physiological pH was studied by spectrophotometry, competitive spectrofluorimetry, differential pulse voltammogram (DPV), circular dichroism spectroscopy (CD), viscosity measurements, salt effect, and computational studies. Intercalation of oseltamivir between the base pairs of DNA was shown by a sharp increase in specific viscosity of DNA and a decrease of the peak current and a positive shift in differential pulse voltammogram. Competitive fluorescence experiments were performed using neutral red (NR) as a probe for the intercalation binding mode. The studies showed that oseltamivir is able to release the NR.     

Role of the amino sugar in the DNA binding of disaccharide anthracyclines: crystal structure of the complex MAR70/d(CGATCG)

Disaccharide anthracyclines analogues have been shown to exhibit different antitumour activity as compared with parents compounds doxorubicin and daunomycin. Here we report the crystal structure of the disaccharide analog MAR70 complexed with the DNA hexamer d(CGATCG). The structure has been solved at 1.54A resolution and is similar to previous crystallized anthracycline-DNA complexes with both sugar rings of the disaccharide chain lying in the DNA minor groove. Comparison with the structure of MEN10755 another disaccharide anthracycline co-crystallized with the same DNA hexamer suggests a correlation between the position of the amino sugar on the disaccharide chain and the conformation of this moiety when binding to DNA. This is discussed with respect to the influence on drug activity and on the possible interaction with other cellular targets.     

Molecular docking and spectroscopic studies on the interaction of new fifth-generation antibacterial drug ceftobiprole with calf thymus DNA

Abstract

The interaction of the cefobiprole drug with calf thymus DNA (ct-DNA) at physiological pH was investigated by UV-visible spectrophotometry, fluorescence measurement, dynamic viscosity measurements, circular dichroism spectroscopy and molecular modeling. The binding constant obtained of UV–visible was 4?×?10⁴ L mol^?1. Moreover, the results of circular dichroism (CD) and viscosity measurements displayed that the binding of the cefobiprole to ct-DNA can change the conformation of ct-DNA. Furthermore, thermodynamic parameters indicated that hydrogen bond and van der waals play main roles in the binding of cefobiprole to ct-DNA. Optimal results of docking, it can be concluded that ceftobiprole-DNA docked model is in approximate correlation with our experimental results.     

Spectroscopic and molecular docking investigation of polynucleotides and DNA binding affinity to Nile blue dye

We used UV-vis absorption spectroscopy, fluorescence spectrophotometry and molecular docking calculations to investigate intermolecular interaction between the cationic dye, Nile blue (NB), and synthetic polynucleotides, poly(A-T), poly(G-C) and calf thymus DNA (Ct-DNA) at physiological pH. Strong hypsochromic absorbance and fluorescence quenching were observed that showed strong binding of NB to these polynucleotides and DNA. The binding affinity values derived from maximum absorption of the spectra of NB bound to various polynucleotides and Ct-DNA concentrations suggests that NB exhibits greater binding affinity to poly(G-C) than to poly(A-T). The thermodynamic parameters suggested that hydrogen bonds and van der Waals forces might play a major role in the binding of NB to DNA. The molecular docking results suggested that NB was an intercalator of the stacked base pairs of Ct-DNA.     

Thermodynamic investigation of M-DNA: a novel metal ion-DNA complex

The thermodynamics of formation of a novel divalent metal ion-DNA complex known as M-DNA have been investigated using an ethidium bromide (EB) fluorescence assay, and with isothermal titration calorimetry. The process of M-DNA formation was observed from the EB assay to be strongly temperature-dependent. The binding of Zn(2+) to calf thymus (42% GC content) and Escherichia coli (50% GC content) DNA at pH 8.5 exhibited an endothermic cooperative binding process at Zn(2+) concentrations of approximately 0.1 mM, indicating an entropy driven process. This binding process is consistent with a site-specific binding interaction, similar in nature to Z-DNA formation; however, the interaction occurs at much lower metal ion concentrations. The enthalpy of M-DNA formation for calf thymus DNA was determined to be 10.5+/-0.7 and 9+/-2 kJ/mbp at DNA concentrations of 100 and 50 microg ml(-1), respectively. An enthalpy of 13+/-3 kJ/mbp was obtained for M-DNA formation for 50 microg ml(-1) E. coli DNA. No evidence of M-DNA formation was observed in either DNA at pH 7.5 with Zn(2+) or at either pH 7.5 or 8.5 with Mg(2+).     

Spectroscopic studies on the interaction of quercetin-terbium(III) complex with calf thymus DNA

The interaction of native calf thymus DNA (CT-DNA) with quercetin-terbium(III) [Q-Tb(III)] complex at physiological pH was monitored by UV absorption spectrophotometry, circular dichroism, fluorescence spectroscopy, and viscosimetric techniques. The complex displays binding properties to the CT-DNA and was found to interact with CT-DNA through outside binding, demonstrated by a hypochromic effect of Q-Tb(III) on the UV spectra of CT-DNA and the calculated association constants (K). Also, decrease in the specific viscosity of CT-DNA, decrease in the fluorescence intensity of Q-Tb(III) solutions in the presence of increasing amounts of CT-DNA, and detectable changes in the circular dichroism spectrum of CT-DNA are other evidences to indicate that Q-Tb(III) complex interact with CT-DNA through outside binding.     

The interaction of native DNA with Zn(II) and Cu(II) complexes of 5-triethyl ammonium methyl salicylidene orto-phenylendiimine

The interaction of native calf thymus DNA with the Zn(II) and Cu(II) complexes of 5-triethyl ammonium methyl salicylidene orto-phenylendiimine (ZnL(2+) and CuL(2+)), in 1 mM Tris-HCl aqueous solutions at neutral pH, has been monitored as a function of the metal complex-DNA molar ratio by UV absorption spectrophotometry, circular dichroism (CD) and fluorescence spectroscopy. The results support for an intercalative interaction of both ZnL(2+) and CuL(2+) with DNA, showing CuL(2+) an affinity of approximately 10 times higher than ZnL(2+). In particular, the values of the binding constant, determined by UV spectrophotometric titration, equal to 7.3x10(4) and 1.3x10(6)M(-1), for ZnL(2+) and CuL(2+), respectively, indicate the occurrence of a marked interaction with a binding size of about 0.7 in base pairs. The temperature dependence of the absorbance at 258 nm suggests that both complexes strongly increase the DNA melting temperature (Tm) already at metal complex-DNA molar ratios equal to 0.1. As evidenced by the quenching of the fluorescence of ethidium bromide-DNA solutions in the presence of increasing amounts of metal complex, ZnL(2+) and CuL(2+) are able to displace the ethidium cation intercalated into DNA. A tight ZnL(2+)-DNA and CuL(2+)-DNA binding has been also proven by the appearance, in both metal complex-DNA solutions, of a broad induced CD band in the range 350-450 nm. In the case of the CuL(2+)-DNA system, the shape of the CD spectrum, at high CuL(2+) content, is similar to that observed for psi-DNA solutions. Such result allowed us to hypothesize that CuL(2+) induces the formation of supramolecular aggregates of DNA in aqueous solutions.     

Preparation, characterization, and DNA binding studies of water-soluble quercetin--molybdenum(VI) complex

DNA binding studies of flavonoids are needed to understand the reaction mechanism and improve drugs that target DNA. Quercetin (Q) is one of the most common flavonoids that can chelate metal ions and interact with double-stranded DNA. In the present work, UV absorption spectrophotometry, viscosimetry, circular dichroism, and fluorescence spectroscopic techniques were employed to study the interaction of water-soluble quercetin--molybdenum(VI) complex [Q-Mo(VI)] with calf thymus DNA. The binding constants (K(b)) for the complex with DNA were estimated to be 2.9?×?10(3) through spectroscopic titrations. Upon addition of the complex, significant decreases were observed in the viscosity of calf thymus DNA. Circular dichroic spectra indicated that there are certain detectable conformational changes in the DNA double helix when complex was added. Further, competitive methylene blue binding studies with fluorescence spectroscopy have shown that the complex can bind to DNA through nonintercalative mode. The experimental results suggest that Q-Mo(VI) binds to DNA via an outside binding mode.     

One-pot solvent free synthesis and DNA binding studies of thieno[2,3-b]-1,8-naphthyridines

With the aim of evaluating interaction between double-stranded calf thymus (ds)DNA and sulphur containing fused planar rings, the derivatives of 1,8-naphthyridine containing thiono groups were synthesized by the condensation of 2-mercapto-3-formyl[1,8]naphthyridines using 1-chloroacetone, 2-chloroacetamide, chloroaceticacid, and 2-chloro-1-phenylethanone in the presence of anhydrous potassium carbonate as s catalyst under solvent free microwave irradiation. The structures of the compounds were elucidated on the basis of elemental analysis, IR, (1)H NMR, and mass spectra. The interaction of thieno[2,3-b]-1,8-naphthyridine-2-carboxylic acid (TNC) (3a) with ct-DNA was studied by UV-Vis spectrophotometry, viscosity, thermal denaturation, as well as cyclic voltammetry experiments. On binding to DNA, the absorption spectrum underwent bathochromic and hypochromic shifts. Binding parameters, determined from spectrophotometric measurements indicated a binding constant of Kb=2.1 x 10(6) M(-1). The thieno[2,3-b]-1,8-naphthyridine-2-carboxylic acid (3a) increases the viscosity of sonicated rod-like DNA fragments. The binding of TNC to DNA increased the melting temperature by about 4 degrees C. The decrease in peak current heights and shifts of peak potential values are observed by the addition of calf thymus DNA in cyclic voltammetry studies.     

DNA binding studies of tartrazine food additive

The interaction of native calf thymus DNA with tartrazine in 10?mM Tris-HCl aqueous solution at neutral pH 7.4 was investigated. Tartrazine is a nitrous derivative and may cause allergic reactions, with a potential of toxicological risk. Also, tartrazine induces oxidative stress and DNA damage. Its DNA binding properties were studied by UV-vis and circular dichroism spectra, competitive binding with Hoechst 33258, and viscosity measurements. Tartrazine molecules bind to DNA via groove mode as illustrated by hyperchromism in the UV absorption band of tartrazine, decrease in Hoechst-DNA solution fluorescence, unchanged viscosity of DNA, and conformational changes such as conversion from B-like to C-like in the circular dichroism spectra of DNA. The binding constants (K(b)) of DNA with tartrazine were calculated at different temperatures. Enthalpy and entropy changes were calculated to be +37 and +213 kJ mol(-1), respectively, according to the Van't Hoff equation, which indicated that the reaction is predominantly entropically driven. Also, tartrazine does not cleave plasmid DNA. Tartrazine interacts with calf thymus DNA via a groove interaction mode with an intrinsic binding constant of 3.75?×?10(4) M(-1).     

Studies of the interaction of the fluorophores harmine and harmaline with calf thymus DNA.

The binding to calf thymus DNA of the hallucinogen harmine and one of its analogues harmaline was studied by absorption spectrophotometry and fluorescence quenching analysis. Viscosity measurements were also carried out. For both molecules, quenched and unquenched sites on DNA are present. For each type of binding site, the value of the product of the number of sites times the association constant was determined. Harmine is more strongly bound than harmaline. Viscosity measurements indicate intercalation in the case of harmine only.     

DNA interaction studies of sesamol (3,4-methylenedioxyphenol) food additive

The interaction of native calf thymus DNA (CT-DNA) with sesamol (3,4-methylenedioxyphenol) in Tris–HCl buffer at neutral pH 7.4 was monitored by absorption spectrophotometry, viscometry and spectrofluorometry. It is found that sesamol molecules could interact with DNA outside and/or groove binding modes, as are evidenced by: hyperchromism in UV absorption band, very slow decrease in specific viscosity of DNA, and small increase in the fluorescence of methylene blue (MB)-DNA solutions in the presence of increasing amounts of sesamol, which indicates that it is able to partially release the bound MB. Furthermore, the enthalpy and entropy of the reaction between sesamol and CT-DNA showed that the reaction is enthalpy-favored and entropy-disfavored (ΔH = ?174.08 kJ mol^?1; ΔS = ?532.92 J mol^?1 K^?1). The binding constant was determined using absorption measurement and found to be 2.7 × 10⁴ M^?1; its magnitude suggests that sesamol interacts to DNA with a high affinity.