Spectrophotometric study on binding of 2-thioxanthone acetic acid with ct-DNA

Electrochemical and computational studies on the interaction between calf-thymus DNA and skin whitening agent arbutin

The interaction between double-stranded calf thymus DNA (ctDNA) and the skin whitening agent arbutin (AR) examined by applying electrochemical and computational methods for the first time in literature. A single-use pencil graphite electrode via cyclic (CV) and differential pulse voltammetry (DPV) techniques were applied to determine the kinetic and thermodynamic parameters in the absence and presence of ctDNA. To examine the interaction process, oxidation peak currents and potentials of AR were observed prior to the addition of various ctDNA concentrations. The binding constants (KAR-DNA) and Gibbs free energy (ΔG°) values for the AR-DNA complex were determined as 1.82 × 104L/mol and -24.30 kJ/mol at 298 K, respectively. Temperature evaluation of the interaction was examined using thermodynamic parameters (ΔH°: -30.30 kJ/mol and ΔS°: -0.00197 kJ/mol) applying the Van't Hoff equation. The local interaction sites in the molecule structure were determined by applying Fukui functions and second-order perturbation theory in view of potential hydrogen binding centers. The optimized structure of AR was applied with a DNA structure revealing the binding position for AR-DNA complex. Experimental and computational examinations suggested that AR-DNA binds to ctDNA through a minor groove mode via conventional hydrogen bonds, hydrophobic interactions and van der Waals forces.

Functionalization of Fe3O4/rGO magnetic nanoparticles with resveratrol and in vitro DNA interaction

Based on the previous research, we found that the magnetic nanocomposite Fe₃O₄/rGO (reduced graphene oxide) has a good drug loading effect. Therefore, in this paper, we studied the positive role of Fe₃O₄/rGO as a drug carrier in the interaction between resveratrol (RES) and calf-thymus DNA (ct-DNA). The fluorescence experiment is used to evaluate by the Stern-Volmer equation, the quenching constant of RES - ct-DNA system with and without Fe₃O₄/rGO decreases with the increasing temperature. It was found the quenching mode of RES - ct-DNA and Fe₃O₄/rGO - RES - ct-DNA systems were all static quenching, but the binding constant of RES -ct-DNA increased from 4.14 ± 0.21 × 10⁴ L mol^-1 to 10.12 ± 0.02 × 10⁴ L mol^-1. It was found that Fe₃O₄/rGO formed a ternary complex with RES and ct-DNA by ultraviolet spectrum (UV-vis), resonance light scattering experiments (RLS) and scanning electron microscope (SEM). Meanwhile, Fourier transform infrared (FT-IR) and circular dichroism (CD) experiments show that Fe₃O₄/rGO and Fe₃O₄/rGO loaded with RES have effect on the secondary structure of ct-DNA and change the conformation of ct-DNA. On the cellular level, the comet assay shows that Fe₃O₄/rGO and Fe₃O₄/rGO - RES could not cause DNA strand break to the mouse hepatocytes after 24 co-incubation. These results confirm that Fe₃O₄/rGO nanocomposites have good application potential, which can be used as a good drug carrier in a wide range of therapeutic methods.

Acridine Based N-Acylhydrazone Derivatives as Potential Anticancer Agents: Synthesis, Characterization and ctDNA/HSA Spectroscopic Binding Properties

A series of novel acridine N-acylhydrazone derivatives have been synthesized as potential topoisomerase I/II inhibitors, and their binding (calf thymus DNA—ctDNA and human serum albumin—HSA) and biological activities as potential anticancer agents on proliferation of A549 and CCD-18Co have been evaluated. The acridine-DNA complex 3b (-F) displayed the highest Kb value (Kb = 3.18 × 103 M−1). The HSA-derivatives interactions were studied by fluorescence quenching spectra. This method was used for the calculation of characteristic binding parameters. In the presence of warfarin, the binding constant values were found to decrease (KSV = 2.26 M−1, Kb = 2.54 M−1), suggesting that derivative 3a could bind to HSA at Sudlow site I. The effect of tested derivatives on metabolic activity of A549 cells evaluated by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide or MTT assay decreased as follows 3b(-F) > 3a(-H) > 3c(-Cl) > 3d(-Br). The derivatives 3c and 3d in vitro act as potential dual inhibitors of hTopo I and II with a partial effect on the metabolic activity of cancer cells A594. The acridine-benzohydrazides 3a and 3c reduced the clonogenic ability of A549 cells by 72% or 74%, respectively. The general results of the study suggest that the novel compounds show potential for future development as anticancer agents.

Revealing the binding properties between resorcinol and DNA

Resorcinol (1,3-dihydroxybenzene) is a common coupling agent in permanent hair dyes, and has arrested people's attention for its potential hazard to human health. However, the action mechanism of resorcinol and human DNA has not been elucidated. In this research, the binding properties between resorcinol and calf thymus DNA (ct-DNA) were studied for the first time through various spectral and molecular docking techniques. Spectral studies showed that the initial fluorescence quenching of resorcinol against DNA was a static one. The result of ΔH < 0 and ΔS > 0 was produced from thermodynamic experimental data, therefore it could be concluded that electrostatic force was the major driving force, while binding constant K_b was 1.56 × 10⁴  M^-1 at 298 K. The electrostatic binding network between resorcinol and ct-DNA was established explicitly through competitive substitution analysis and other spectral approaches. The results of FT-IR absorption spectra indicated that resorcinol had bound to the DNA phosphate skeleton. Molecular docking clearly revealed that binding occurred between hydroxyl groups of resorcinol and phosphorus oxygen bonds (P-O) of the DNA skeleton. These findings may deepen our understanding of the action mechanism between resorcinol and ct-DNA and provide some useful data on the effect of resorcinol on human diseases.

What Can Electrochemical Methods Offer in Determining DNA-Drug Interactions?

The interactions of compounds with DNA have been studied since the recognition of the role of nucleic acid in organisms. The design of molecules which specifically interact with DNA sequences allows for the control of the gene expression. Determining the type and strength of such interaction is an indispensable element of pharmaceutical studies. Cognition of the therapeutic action mechanisms is particularly important for designing new drugs. Owing to their sensitivity, simplicity, and low costs, electrochemical methods are increasingly used for this type of research. Compared to other techniques, they require a small number of samples and are characterized by a high reliability. These methods can provide information about the type of interaction and the binding strength, as well as the damage caused by biologically active molecules targeting the cellular DNA. This review paper summarizes the various electrochemical approaches used for the study of the interactions between pharmaceuticals and DNA. The main focus is on the papers from the last decade, with particular attention on the voltammetric techniques. The most preferred experimental approaches, the electrode materials and the new methods of modification are presented. The data on the detection ranges, the binding modes and the binding constant values of pharmaceuticals are summarized. Both the importance of the presented research and the importance of future prospects are discussed.

Tetracyclic Thioxanthene Derivatives: Studies on Fluorescence and Antitumor Activity

Thioxanthones are bioisosteres of the naturally occurring xanthones. They have been described for multiple activities, including antitumor. As such, the synthesis of a library of thioxanthones was pursued, but unexpectedly, four tetracyclic thioxanthenes with a quinazoline–chromene scaffold were obtained. These compounds were studied for their human tumor cell growth inhibition activity, in the cell lines A375-C5, MCF-7 and NCI-H460. Photophysical studies were also performed. Two of the compounds displayed GI₅₀ values below 10 µM for the three tested cell lines, and structure–activity relationship studies were established. Three compounds presented similar wavelengths of absorption and emission, characteristic of dyes with a push-pull character. The structures of two compounds were elucidated by X-ray crystallography. Two tetracyclic thioxanthenes emerged as hit compounds. One of the two compounds accumulated intracellularly as a bright fluorescent dye in the green channel, as analyzed by both fluorescence microscopy and flow cytometry, making it a promising theranostic cancer drug candidate.

Natural DNA Intercalators as Promising Therapeutics for Cancer and Infectious Diseases

Cancer and infectious diseases are one of the greatest challenges of modern medicine. An unhealthy lifestyle, the improper use of drugs, or their abuse are conducive to the increase of morbidity and mortality caused by these diseases. The imperfections of drugs currently used in therapy for these diseases and the increasing problem of drug resistance have forced a search for new substances with therapeutic potential. Throughout history, plants, animals, fungi and microorganisms have been rich sources of biologically active compounds. Even today, despite the development of chemistry and the introduction of many synthetic chemotherapeutics, a substantial part of the new compounds being tested for treatment are still of natural origin. Natural compounds exhibit a great diversity of chemical structures, and thus possess diverse mechanisms of action and molecular targets. Nucleic acids seem to be a good molecular target for substances with anticancer potential in particular, but they may also be a target for antimicrobial compounds. There are many types of interactions of small-molecule ligands with DNA. This publication focuses on the intercalation process. Intercalators are compounds that usually have planar aromatic moieties and can insert themselves between adjacent base pairs in the DNA helix. These types of interactions change the structure of DNA, leading to various types of disorders in the functioning of cells and the cell cycle. This article presents the most promising intercalators of natural origin, which have aroused interest in recent years due to their therapeutic potential.

Structural investigation, DNA interactions and in vitro anticancer studies of transition metal complexes of 3-(2-(2, 4-dihydroxy benzylidene) hydrazinyl) quinoxalin-2(1H) -one

The Schiff base ligand, 3-(2-(2, 4-dihydroxybenzylidene) hydrazinyl) quinoxalin-2(1H)-one (RHQO) has been synthesized and characterized by spectral and single crystal X-ray analysis. The Mn(II), Ni(II) and Cu(II) complexes of RHQO have been synthesized and characterized by FT-IR, UV-VIS, mass, EPR spectra, CHN, thermo gravimetric analysis, magnetic susceptibility and conductivity measurements. The morphology of the ligand and complexes is studied by Scanning Electron Microscopy. The metal complexes formed were found to be polymeric in nature. The abilities of the ligand and its metal complexes to interact and bind with calf thymus DNA (CT-DNA) has been studied by electronic absorption spectroscopy and their quantitative binding strength was evaluated in terms of their intrinsic binding constant (K_b). The cleavage interaction of the ligand and its metal complexes with super coiled pBR 322 DNA has been investigated by agarose gel electrophoresis. Cytotoxicity of the Cu(II) and Ni(II) complexes was evaluated using various cancer cell lines, Human cervical cancer cell line (Hela), B16 melanoma F10(B16-F10), Human ovarian cancer cell (SKOV3) and Breast cancer cell line (MCF7) by MTT assay. The results indicated that the ligand and its metal complexes bind with CT-DNA by groove binding mode and cleaved the supercoiled pBR 322 DNA in to nicked form. The Ni(II) and Cu(II) complexes exhibited anticancer activity without affecting the normal CHO-K1 cell lines. Communicated by Vsevolod Makeev.

The interaction of light-activatable 2-thioxanthone thioacetic acid with ct-DNA and its cytotoxic activity: Novel theranostic agent

In this study, a thioxanthone derivative, 2-Thioxanthone Thioacetic Acid (TXSCH₂COOH) was used to analyze the type of binding to calf thymus DNA in a physiological buffer (Tris-HCl buffer solution, pH:7.0). Several spectroscopic techniques were employed including UV-Vis absorption and fluorescence emission spectroscopy and viscosity measurements were also used to clarify the binding mode of TXSCH₂COOH to ct-DNA. The intrinsic binding constant Kb of TXSCH₂COOH-ct-DNA was found as 2.5 × 10³ M^-1 from the absorption studies. Increasing of fluorescence emission intensity was found approximately 74.4% by adding ct-DNA to the TXSCH₂COOH solution. Fluorescence microscopy was employed to display imaging of the TXSCH₂COOH-ct-DNA solution. Increasing of the iodide quenching effect was observed when TXSCH₂COOH was added to the double stranded DNA and the calculated quenching constants of TXSCH₂COOH and TXSCH₂COOH-ct-DNA were found to be 1.89 × 10³ M^-1 and 1.19 × 10⁴ M^-1, respectively. Additionally, the iodide quenching experiment was conducted with single stranded DNA which led to a high Ksv value. All the experimental results including the viscosity values of ct-DNA with TXSCH₂COOH demonstrated that the binding of TXSCH₂COOH to ct-DNA was most likely groove binding. Furthermore, TXSCH₂COOH was found to be an A-T rich minor groove binder. This was confirmed by the displacement assays with Hoechst 33258 compared to Ethidium Bromide. The in vitro cytotoxic activity measurements were performed by MTT assay on HT29 cell line for 72 h. TXSCH₂COOH exhibited notable cytotoxic activities compared to the standard chemotherapy drugs, fluorouracil (5-FU), cisplatin in tumorigenic HT29 cell line. The 50% growth-inhibitory concentration (IC₅₀) for TXSCH₂COOH was 19,8 μg/mL while 5-FU and cisplatin were 28.9 μg/mL, 20 μg/mL, respectively. The increase in cytotoxic effect when TXSCH₂COOH is activated by light indicates the potential of being theranostic cancer drug candidate.

Study on the interactions between B-norcholesteryl benzimidazole compounds with ct-DNA

The study of molecule-DNA interaction is very important for designing an improved therapeutic agent. In previous studies, we synthesized some B-norcholesteryl benzimidazole compounds, and the tests on cancer cells showed that these compounds had good in vitro anti-cancer activities. In order to further investigate mechanism of their actions, three different B-norcholesteryl benzimidazole compounds were selected and interaction of these compounds with the calf thymus DNA (ct-DNA) was monitored by using various methods including UV-Vis and fluorescence spectroscopic techniques, viscosity measurement, and circular dichroism (CD). The results proved a hypochromic effect accompanied with a slight red-shift due to the interaction of the molecules with ct-DNA. According to the UV-Vis and fluorescence spectra, the mentioned compounds were bound to DNA, preferentially through partial intercalation into the DNA helix. Moreover, the ethidium bromide (EB) and Hoechst 33258 competitive binding experiments were also used to confirm the interaction mode of the compounds with ct-DNA. In the Hoechst 33258 displacement experiment, no significant change in the fluorescence intensity was observed. Additional assays such as iodide quenching, viscosity, and CD spectroscopy further confirmed that intercalation should be the major binding mode of the selected compounds with DNA. The cytotoxicity of these three compounds was also evaluated by MTT method, and the results confirmed that binding ability of these compounds to DNA was consistent with their cytotoxicity behavior. The experimental results indicated a higher binding affinity for compound 3 compared to the other compounds. This research provided a better understanding on the molecular mechanism of the interaction between B-norcholesteryl benzimidazole compounds and tumor cells, and offered a beneficial perspective to the designation of novel B-norsteroidal anticancer compounds.

Assessment on the binding characteristics of dasatinib, a tyrosine kinase inhibitor to calf thymus DNA: insights from multi-spectroscopic methodologies and molecular docking as well as DFT calculation

The binding characteristics of calf thymus DNA (ct-DNA) with dasatinib (DSTN), a tyrosine kinase inhibitor was assessed through multi-spectroscopic methodologies and viscosity measurement combined with molecular docking as well as DFT calculation to understand the binding mechanism, affinity of DSTN onto ct-DNA, effect of DSTN on ct-DNA conformation, and among others. The results confirmed DSTN bound onto ct-DNA, leading to forming the DSTN-ct-DNA complex with the binding constant of 4.82 × 10³ M^-1 at 310 K. DSTN preferentially inserted to the minor groove of ct-DNA with rich A-T region, that was the binding mode of DSTN onto ct-DNA was groove binding. The enthalpic change (ΔH⁰) and entropic change (ΔS⁰) during the binding process of DSTN with ct-DNA were 128.9 kJ mol^-1 and 489.2 J mol^-1 K^-1, respectively, confirming clearly that the association of DSTN with ct-DNA was an endothermic process and the dominative driven-force was hydrophobic interaction. Meanwhile, the results also indicated that there was a certain extent of electrostatic force and hydrogen bonding, but they maybe play an auxiliary role. The CD measurement results confirmed the alteration in the helical configuration of ct-DNA but almost no change in the base stacking after binding DSTN. The results revealed that there was the obvious change in the conformation, the dipole moment, and the atomic charge distribution of DSTN in the B-DNA complexes, compared with free DSTN, to satisfy the conformational adaptation. From the obtained fronitier molecular orbitals of DSTN, it can be inferred that the nature of DSTN alters with the change of the environment around DSTN. Communicated by Ramaswamy H. Sarma.

Determination of the DNA binding properties of a novel PARP inhibitor MK-4827 with calf-thymus DNA by molecular simulations and detailed spectroscopic investigations

The binding interaction of niraparib (MK-4827), a poly(ADP-ribose) polymerase inhibitor, with calf thymus deoxyribonucleic acid (ctDNA) has been explored by various theoretical and experimental techniques.

Drug Effect of Thulium(III)-Arsenazo III Complex on Herring Sperm DNA

To assess the potential cytostatic properties of the thulium(III)-arsenazo III complex as a probe of rare earth complex antitumor drugs, the interaction information of the thulium(III)-arsenazo III complex with DNA was obtained by using spectroscopy, viscosity measurements, and voltammetric methods. The thermodynamic functions demonstrated that the binding constants of the thulium(III)-arsenazo III complex with DNA were Kθ298.15K = 4.84 × 106 L·mol−1 and Kθ308.15K = 4.48 × 106 L·mol−1, and the binding process was enthalpy driven. The increase in relative viscosity of DNA with the addition of the thulium(III)-arsenazo III complex and the results from Scatchard and voltammetric methods showed that the interaction mode between the thulium(III)-arsenazo III complex and DNA was groove binding along with weak intercalative binding.