Study on the Interaction of an Anthracycline Disaccharide with DNA by Spectroscopic Techniques and Molecular Modeling

Study the interaction between juglone and calf thymus DNA by spectroscopic and molecular docking techniques

Juglone (Jug) is one of the main active substances of Cortex Juglandis Mandshuricae in a folk anti-cancer prescription. Previously, there were few studies on its interaction with DNA and mechanism of action. The present paper studied, the mechanism of action between Jug and calf thymus DNA (ctDNA) by fluorescence spectroscopy, together with ethidium bromide (EB) fluorescence probe, UV-vis absorption spectroscopy, salt effect and ctDNA melting point (T_m) experiment, resonance scattering spectroscopy and molecular docking under the simulated human physiological conditions. The experimental findings indicated that Jug quiescently quenched the fluorescence of EB-ctDNA system, characteristic absorption peak intensity of ctDNA presented a decolorization effect after the interaction of ctDNA and Jug, the interaction with ctDNA enhanced of Jug resonance scattering peak and generated new resonance scattering peak, the salt exerted less effect on the interaction between Jug and ctDNA molecules, and the interaction with Jug increased the T_m value of ctDNA by 5.0 °C The binding constant (K_A) between Jug and ctDNA was 2.12 × 10⁵ L/mol (310 K) and the number of binding sites (n) was about 1. The interaction between Jug and ctDNA was an entropically driven spontaneous and endothermic process. The results of molecular docking further showed that the naphthoquinone plane was embedded in the region between the two TA bases in the ctDNA groove, and the 5'-hydroxyl and 4-naphthoquinone groups extended to the outside of the ctDNA double helix.

Temozolomide-Doxorubicin Conjugate as a Double Intercalating Agent and Delivery by Apoferritin for Glioblastoma Chemotherapy

We designed a conjugated compound by coupling temozolomide (TMZ) with doxorubicin (DOX) via an acylhydrazone linkage as a potential prodrug used for glioblastoma multiforme (GBM) treatment. Viscosity and spectroscopic studies revealed that the drug conjugate could act as a nonclassical double intercalating agent. Although free TMZ is an inefficient DNA binder in comparison to DOX, the TMZ moiety interacted with DNA as an induced intercalator, arising from the synergistic effect of DOX moiety that mediated conformational changes of the DNA helix. Two binding modes were proposed to interpret the double intercalating effect of the drug conjugate on intra- and inter-DNA interactions that could cause DNA cross-linking and fibril aggregates. We also developed a delivery nanoplatform with a loading efficiency of 83% using copper-bound apoferritin as a nanocarrier. In sharp contrast to the short half-life of free TMZ, the nanocomposite was stable under physiological conditions without detectable drug decomposition after a 2 week storage, and drug release was activatable in the presence of glutathione at millimolar levels. The antitumor effect of the drug conjugate and nanocomposite against GBM cells was reported to demonstrate the potential therapeutic applications of double intercalating materials.

Monitoring ZEO apoptotic potential in 2D and 3D cell cultures and associated spectroscopic evidence on mode of interaction with DNA

Recognizing new anticancer compounds to improve Breast cancer treatment seems crucial. Essential oil of Zataria Multiflora (ZEO) is a secondary metabolite with some biological properties, yet underlying cellular and molecular anticancer properties of ZEO is unclear. GC/MS analysis revealed that carvacrol is the major ingredient of the essential oil. ZEO increasingly suppressed viability in MDA-MB-231, MCF-7 and T47D Breast cancer cells while nontoxic to L929 normal cells in monolayer cell cultures (2D), whereas MDA-MB-231 multicellular spheroids (3D) were more resistant to inhibition. ZEO significantly induced cell apoptosis confirmed by fluorescent staining, flow cytometry analysis and DNA fragmentation in MDA-MB-231 2D and 3D cell cultures. ZEO increased ROS generation and subsequent loss of ΔΨm, caspase 3 activation and DNA damage which consequently caused G1 and G2/M cell cycle arrest in a dose- and time-dependent manner in 2D. S phase arrest occurred in cell spheroids therefore ZEO possible DNA interaction with gDNA was investigated and revealed ZEO binds DNA via intercalation. Altogether, these data corroborate anticancer properties of ZEO and suggest that cell culture format (2D monolayer vs. 3D spheroid) plays a critical role in drug response and provides new insights into the mechanisms underlying ZEO cytotoxicity effect on Breast cancer cells.

Mass spectrometric approaches for the identification of anthracycline analogs produced by actinobacteria

Anthracyclines are a well-known chemical class produced by actinobacteria used effectively in cancer treatment; however, these compounds are usually produced in few amounts because of being toxic against their producers. In this work, we successfully explored the mass spectrometry versatility to detect 18 anthracyclines in microbial crude extract. From collision-induced dissociation and nuclear magnetic resonance spectra, we proposed structures for five new and identified three more anthracyclines already described in the literature, nocardicyclins A and B and nothramicin. One new compound 8 (4-[4-(dimethylamino)-5-hydroxy-4,6-dimethyloxan-2-yl]oxy-2,5,7,12-tetrahydroxy-3,10-dimethoxy-2-methyl-3,4-dihydrotetracene-1,6,11-trione) was isolated and had its structure confirmed by (1) H nuclear magnetic resonance. The anthracyclines identified in this work show an interesting aminoglycoside, poorly found in natural products, 3-methyl-rhodosamine and derivatives. This fact encouraged to develop a focused method to identify compounds with aminoglycosides (rhodosamine, m/z 158; 3-methyl-rhodosamine, m/z 172; 4'-O-acethyl-3-C-methyl-rhodosamine, m/z 214). This method allowed the detection of four more anthracyclines. This focused method can also be applied in the search of these aminoglycosides in other microbial crude extracts. Additionally, it was observed that nocardicyclin A, nothramicin and compound 8 were able to interact to DNA through a DNA-binding study by mass spectrometry, showing its potential as anticancer drugs. Copyright © 2016 John Wiley & Sons, Ltd.

Picking Out Logic Operations in a Naphthalene β-Diketone Derivative by Using Molecular Encapsulation, Controlled Protonation, and DNA Binding

On–off switching and molecular logic in fluorescent molecules are associated with what chemical inputs can do to the structure and dynamics of these molecules. Herein, we report the structure of a naphthalene derivative, the fashion of its binding to β-cyclodextrin and DNA, and the operation of logic possible using protons, cyclodextrin, and DNA as chemical inputs. The compound crystallizes out in a keto-amine form, with intramolecular N−H⋅⋅⋅O bonding. It shows stepwise formation of 1:1 and 1:2 inclusion complexes with β-cyclodextrin. The aminopentenone substituents are encapsulated by β-cyclodextrin, leaving out the naphthalene rings free. The binding constant of the β-cyclodextrin complex is 512 m⁻¹. The pK_a value of the guest molecule is not greatly affected by the complexation. Dual input logic operations, based on various chemical inputs, lead to the possibility of several molecular logic gates, namely NOR, XOR, NAND, and Buffer. Such chemical inputs on the naphthalene derivative are examples of how variable signal outputs based on binding can be derived, which, in turn, are dependent on the size and shape of the molecule.

The role of encapsulation by β-cyclodextrin in the interaction of raloxifene with macromolecular targets: a study by spectroscopy and molecular modeling

We report the binding of the drug raloxifene with Calf thymus DNA (ctDNA) and bovine serum albumin (BSA) in the presence and absence of β-cyclodextrin (β-CD) and explain the influence of β-cyclodextrin on the binding of the drug to macromolecules. UV-Vis absorption, fluorescence, proton nuclear magnetic resonance and two-dimensional rotating-frame nuclear overhauser effect spectroscopic techniques are used to study the stoichiometry and the binding strength of the complexes. Molecular modeling is used in combination with other techniques to propose the structure of the inclusion complex and the interaction with ctDNA. The Stern-Volmer quenching constants of the interaction of raloxifene with ctDNA in aqueous and in β-CD solution are compared. The competition for binding of ctDNA with raloxifene and Methylene Blue is studied. The apparent binding constant and the number of binding sites for the binding of raloxifene with BSA in aqueous solution are significantly different from those in the presence of β-CD. The influence of β-CD on the binding of the small molecules with biological macromolecules is discussed. We infer that the binding strengths between raloxifene and macromolecules, viz., ctDNA and BSA are influenced by the β-CD encapsulation. These results may suggest new ways to tune the drug binding to biomacromolecules by encapsulating specific moieties of drugs.

In vitro DNA binding studies of anticancer drug idarubicin using spectroscopic techniques

The interaction between idarubicin and double stranded deoxyribonucleic acid (ds-DNA) was investigated by UV-VIS spectrophotometry, fluorescence and Raman spectroscopy techniques. The absorption spectra of idarubicin with ds-DNA showed a slight red shift and hypochromic effect. In the fluorescence experiments, emission peaks were decreased by adding ds-DNA. Using ethidium bromide (ETB) as a fluorescence probe, fluorescence quenching of the emission peak was observed in the ETB-DNA system when idarubicin was added. Moreover, similar results were obtained in Raman spectroscopy. Binding constants of idarubicin with ds-DNA were determined as 5.14×10(5) M(-1) and 5.8×10(5) M(-1) for UV-VIS spectrophotometry and fluorescence spectroscopy, respectively. The large binding constant indicated that idarubicin has a high affinity with ds-DNA. All the evidences indicated that the binding mode of idarubicin with DNA was an intercalative binding. Furthermore, quantitative determination of idarubicin in pharmaceutical formulation was done.

The Unusual Fluorescence Quenching of Coumarin 314 by β-Cyclodextrin and the Effect of β-Cyclodextrin on its Binding with Calf Thymus DNA

This paper discusses the binding of a laser dye, Coumarin 314 with β-cyclodextrin, studied mainly by UV-visible spectroscopy, 2D rotating-frame nuclear Overhauser effect spectroscopy (ROESY), steady-state spectroscopy and time-resolved fluorescence spectroscopy. The role of β-cyclodextrin on the binding of Coumarin 314 with calf thymus DNA was investigated. Coumarin 314 shows a hyperchromic shift of absorption and a quenching of fluorescence due to binding with β-cyclodextrin. The fluorescence quenching is non-linear and the reason for the non-linearity is discussed. The unusual fluorescence quenching on Coumarin 314–β-cyclodextrin binding is rationalised from the effect of acidity on absorption, fluorescence, and molecular modelling studies. Additional proof for the mode of binding is given by 2D ROESY. The capped and exposed portions of the Coumarin 314 molecule in the Coumarin 314–β-cyclodextrin complex when binding with calf thymus DNA were visualised based on spectral and molecular modelling studies.

Binding characteristics of salbutamol with DNA by spectral methods

Salbutamol interacting with deoxyribonucleic acid (DNA) was examined by fluorescence, UV absorption, viscosity measurements, and DNA melting techniques. The binding constants and binding sites were obtained at different temperatures by fluorescence quenching. The Stern-Volmer plots showed that the quenching of fluorescence of salbutamol by DNA was a static quenching. To probe the binding mode, various analytical methods were performed and the results were as follows: hyperchromic effect was shown in the absorption spectra of salbutamol upon addition of DNA; there was no appreciable increase in melting temperature of DNA when salbutamol was presented in DNA solution; the fluorescence intensity of salbutamol-DNA decrease with the increasing ionic strength; the relative viscosity of DNA did not change in the presence of salbutamol; the binding constant of salbutamol with double strand DNA (dsDNA) was much higher than that of it with single strand DNA (ssDNA). All these results indicated that the binding mode of salbutamol to DNA should be groove binding. The thermodynamic parameters suggested that hydrogen bond or van der Waals force might play an important role in salbutamol binding to DNA. According to the Förster energy transference theory, the binding distance between the acceptor and donor was 3.70 nm.

Binding interactions of naringenin and naringin with calf thymus DNA and the role of β-cyclodextrin in the binding

The interaction of naringenin (Nar) and its neohesperidoside, naringin (Narn), with calf thymus deoxyribonucleic acid (ctDNA) in the absence and the presence of β-cyclodextrin (β-CD) was investigated. The interaction of Nar and Narn with β-CD/ctDNA was analyzed by using absorption, fluorescence, and molecular modeling techniques. Docking studies showed the existence of hydrogen bonding, electrostatic and phobic interaction of Nar and Narn with β-CD/DNA. 1:2 stoichiometric inclusion complexes were observed for Nar and Narn with β-CD. With the addition of ctDNA, Nar and Narn resulted into the fluorescence quenching phenomenon in the aqueous solution and β-CD solution. The binding constant K(b) and the number of binding sites were found to be different for Nar and Narn bindings with DNA in aqueous and β-CD solution. The difference is attributed to the structural difference between Nar and Narn with neohesperidoside moiety present in Narn.

Surface plasmon resonance detection of silver ions and cysteine using DNA intercalator-based amplification

We report the development of a surface plasmon resonance sensor based on the silver ion (Ag(+))-induced conformational change of a cytosine-rich, single-stranded DNA for the detection of Ag(+) and cysteine (Cys) in aqueous solutions. In the free state, single-stranded oligonucleotides fold into double-helical structures through the addition of Ag(+) to cytosine–cytosine (C–C) mismatches. However, in the presence of Cys, which competitively binds to Ag(+), the formation of the C–Ag(+)–C assembly is inhibited, resulting in free-state, single-stranded oligonucleotides. To enhance sensitivity, the DNA intercalator, daunorubicin, was employed to achieve signal enhancement. The detection limit for Ag(+) was 10 nM with a measurement range of 50–2,000 nM, and the detection limit for Cys was 50 nM with a measurement range of 50–2,000 nM. This simple assay was also used to individually determine the spiked Ag(+) concentration in water samples and Cys concentrations in biological fluid samples.

Intercalation and induction of strand breaks by adriamycin and daunomycin: a study with human genomic DNA

The anticancer drugs Adriamycin (ADR) and Daunomycin (DNM) of the anthracycline family are effective in treating a variety of cancers. Although their interactions with other cellular targets may play a role in the selective cytotoxicity of these drugs, it is generally believed that intercalation with DNA is essential for their activity. However, a relationship has not yet been established between intercalation and cellular processes leading to cytotoxicity. The present study was designed to investigate the relationship, if any, between intercalation and DNA strand breaks. ADR and DNM were observed to be strong intercalators of human genomic DNA by absorption and fluorimetric methods that were further substantiated by rise in thermal melting temperature. DNM is the better intercalator of the two, which is also evident from circular dichroic spectral changes. DNA strand breaks, considered to be an index of genotoxicity, was assayed by single cell gel electrophoresis (SCGE; comet assay). ADR and DNM induced equivalent genotoxicity in normal human lymphocytes at a clinically used dose, which was observed to be independent of intercalation efficiency though positively correlated to yield of reactive oxygen species.

New synthesis of 6[3-(1-adamantyl)-4-methoxyphenyl]-2-naphthoic acid and evaluation of the influence of adamantyl group on the DNA binding of a naphthoic retinoid

6[3-(1-Adamantyl)-4-methoxyphenyl]-2-naphthoic acid (Adapalene®), a synthetic aromatic retinoid specific for RARβ and RARγ receptors, has been prepared utilizing a Pd/C-mediated Suzuki coupling between 6-bromo-2-naphthoic acid and 4-methoxyphenyl boronic acid, followed by introduction of an adamantyl group in the position 3 of the formed 6-(4-methoxyphenyl)-2-naphthoic acid. The interaction of 6-(4-methoxyphenyl)-2-naphthoic acid/ethyl ester and the 3-adamantyl analogs with DNA was studied in aqueous solution at physiological conditions by UV-vis spectroscopy. The calculated binding constants K(ligand-DNA) ranged between 1.1×10(4) M(-1) and 1.1×10(5) M(-1), the higher values corresponding to those of the adamantylated compounds. Molecular modeling studies have emphasized that the intercalative binding of adapalene and its derivatives to DNA is mainly stabilized by hydrophobic interactions related to the presence of the adamantyl group.