A voltammetric study on drug-DNA interactions: Kinetic and thermodynamic aspects of the relations between the anticancer agent dasatinib and ds-DNA using a pencil lead graphite electrode

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.

Investigation of the ability of 3-((4-chloro-6-methyl pyrimidin-2-yl)amino) isobenzofuran-1(3H)-one to bind to double-stranded deoxyribonucleic acid

Phthalides represent a notable category of secondary metabolites that are prevalent in various plant species, certain fungi, and liverworts. The significant pharmacological properties of these compounds have led to the synthesis of a novel phthalide derivative. The current study focuses on investigating the binding interactions of a newly synthesized 3-substituted phthalide derivative, specifically 3-((4-chloro-6-methyl pyrimidine-2-yl)amino) isobenzofuran-1(3H)-one (Z11), with double-stranded deoxyribonucleic acid (dsDNA). Research in the pharmaceutical and biological fields aimed at developing more potent DNA-binding agents must take into account the mechanisms by which these newly synthesized compounds interact with DNA. This investigation seeks to explore the binding dynamics between dsDNA and our compound through a variety of analytical techniques, such as electrochemistry, UV spectroscopy, fluorescence spectroscopy, and thermal denaturation. The binding constant (Kb) of Z11 with DNA was determined using both spectroscopic and voltammetric approaches. The research revealed that Z11 employs a groove binding mechanism to associate with dsDNA. To further explore the interactions between Z11 and dsDNA, the study utilized density functional theory (DFT) calculations, molecular docking, and molecular dynamics simulations. These analyses aimed to ascertain the potential for a stable complex formation between Z11 and dsDNA. The results indicate that Z11 is situated within the minor groove of the dsDNA, demonstrating the ability to establish a stable complex. Furthermore, the findings imply that both π-alkyl interactions and hydrogen bonding play significant roles in the stabilization of this complex.

An electrochemical sensor based on carbon nanofiber and molecular imprinting strategy for dasatinib recognition

Herein, we proposed a new approach to design a MIP-based electrochemical sensor with carbon nanofiber (CNF), which could improve its conductivities as well as electrode sensitivity and successful detection of dasatinib (DAS). CNFs are capable of forming high porosity with significant interconnected porous networks. The poly(2-hydroxyethyl-methacrylate-N-methacryloyl-L-tyrosine) (PHEMA-MATyr) copolymer was synthesized in the presence of both CNF and DAS by photopolymerization. After optimization of the parameters, the modified MIP-based electrochemical sensor demonstrated the ability to determine the DAS in the linear working range of 1.0 × 10-14-1.0 × 10-13 M for the standard solution and commercial serum samples with a LOD of 1.76 × 10-15 and 2.46 × 10-15, respectively. Good linearity for DAS was observed with correlation coefficients (r) of 0.996 and 0.997 for the standard solution and commercial serum samples, respectively. The recoveries of the DAS ranged from 99.45 % to 99.53 % for the tablet dosage form and commercial serum samples, with average relative standard deviations below 1.96 % in both cases. The proposed modified sensor demonstrated significant sensitivity and selectivity for the rapid determination of DAS in commercial serum samples and tablet form.

Electroanalysis in Pharmacogenomic Studies: Mechanisms of Drug Interaction with DNA

The review discusses electrochemical methods for analysis of drug interactions with DNA. The electroanalysis method is based on the registration of interaction-induced changes in the electrochemical oxidation potential of heterocyclic nitrogenous bases in the DNA molecule and in the maximum oxidation current amplitude. The mechanisms of DNA-drug interactions can be identified based on the shift in the electrooxidation potential of heterocyclic nitrogenous bases toward more negative (cathodic) or positive (anodic) values. Drug intercalation into DNA shifts the electrochemical oxidation potential to positive values, indicating thermodynamically unfavorable process that hinders oxidation of nitrogenous bases in DNA. The potential shift toward the negative values indicates electrostatic interactions, e.g., drug binding in the DNA minor groove, since this process does not interfere with the electrochemical oxidation of bases. The concentration-dependent decrease in the intensity of electrochemical oxidation of DNA bases allows to quantify the type of interaction and calculate the binding constants.

Experimental and theoretical approaches to interactions between DNA and purine metabolism products

Deoxyribonucleic acid (DNA) is a significant target for small organic and inorganic drug molecules. Understanding the DNA interaction mechanism of these molecules is vital for new drug designs. In this work, interactions between xanthine (XT), theophylline (TP), and theobromine (TB) with calf-thymus double-strained DNA (dsDNA) were monitored via an experimental and theoretical approach. Experimentally, cyclic voltammetry (CV) and differential pulse voltammetry (DPV) techniques were used on the surface of the NiO/MWCNT/NNaM/PGE electrochemical platform in vitro. Kinetic parameters, including diffusion coefficients, surface concentrations, and standard heterogeneous rate constants, were measured in the absence and presence of DNA using scan rate studies. In the presence of DNA, kinetic parameters were observed to be reduced significantly. Thermodynamic parameters, such as DNA binding constants and standard free Gibbs energies, were calculated for each molecule using the CV and DPV techniques. Both techniques suggested a binding affinity order of XT > TB > TP. Theoretically, density functional theory was applied for geometry optimization, natural bond orbital analyses, and molecular orbital energies of XT, TP, and TB. Experimental and theoretical binding affinities confirm each other. The most energetically stable ligand-DNA complexes expressed that XT, TP, and TB interact with dsDNA via minor groove binding mode, using mostly hydrogen bonds.

The development of electrochemical DNA biosensor based on poly-l-methionine and bimetallic AuPt nanoparticles coating: Picomolar detection of Imatinib and Erlotinib

We report on the preparation of a new and simple electrochemical DNA biosensor based on DNA/AuPt/p-L-Met coating on a screen-printed carbon electrode (SPE) and its use in the determination of the cancer therapy agents, Imatinib (IMA) and Erlotinib (ERL). Poly-l-methionine (p-L-Met), gold, and platinum nanoparticles (AuPt) were successfully coated by one-step electrodeposition onto the SPE from a solution containing L-Met, HAuCl_4, and H₂PtCl₆. The immobilization of DNA was achieved by drop-casting on the surface of the modified electrode. Cyclic Voltammetry (CV), Electrochemical Impedance Spectroscopy (EIS), Field-Emission Scanning Electron Microscopy (FE-SEM), Energy-Dispersive X-ray Spectroscopy (EDX), and Atomic Force Microscopy (AFM) were used to investigate the morphology, the structure, and the electrochemical performance of the sensor. Experimental factors influencing the coating and DNA immobilization processes were optimized. The peak currents originating from guanine (G) and adenine (A) oxidation of ds-DNA were used as signals to quantify IMA and ERL in the concentration range 2.33-80 nM and 0.032-1.0 nM with the LODs of 0.18 nM and 0.009 nM, respectively. The biosensor developed was suitable for determining IMA and ERL in human serum and pharmaceutical samples.

Detection of abemaciclib, an anti-breast cancer agent, using a new electrochemical DNA biosensor

Detection of DNA molecules and possible chemotherapy-induced changes in its structure has been the goal of researchers using rapid, sensitive and inexpensive approaches. Therefore, the aim of this study was to fabricate a new electrochemical DNA biosensor using pencil graphite electrodes modified with polypyrrole/Ce doped hexagonal nickel oxide nanodisks or PP/Ce-doped H-NiO-ND composites for determination of Abemaciclib (AMC) and ds-DNA molecules. The DNA biosensor was prepared by immobilizing ds-DNA on the surface of PP/Ce-doped H-NiO-ND/PGE. Differential pulse voltammetry (DPV) was used to electrochemically detect AMC. The results elucidate the extremely high sensitivity of the ds-DNA/PP/Ce-doped H-NiO-ND/PGE biosensor to AMC, with a narrow detection limit of 2.7 nM and a lengthy linear range of 0.01–600.0 μM. The admirable performance of as-fabricated biosensor could be related to the active reaction sites and the unique electrochemical response related to the nanocomposites by enhancing ds-DNA stabilization and accelerating electron transfer on the surface of electrode.

A green and sensitive guanine-based DNA biosensor for idarubicin anticancer monitoring in biological samples: A simple and fast strategy for control of health quality in chemotherapy procedure confirmed by docking investigation

Drug efficiency can be considerably boosted while adverse effects can be reduced by precisely monitoring the concentration of anti-cancer drugs. Thus, one of the most important parameters for human health is the monitoring and detection of anticancer drugs during chemotherapy treatment. Herein, a glassy carbon electrode (GCE) was modified by Pt- and Pd-incorporated ZnO nanoparticles-decorated single-wall carbon nanotubes (Pt-Pd-ZnO/SWCNTs) nanocomposites, and ds-DNA (Calf Thymus) that was a biological recognition element, and it was aimed to be utilized as an ultrasensitive and effective electroanalytical biosensor for idarubicin (IDR) monitoring. Various physicochemical characterization techniques including transmission electron microscopy (TEM), field-emission scanning electron microscopy (FE-SEM) with energy-dispersive X-ray spectroscopy (EDS) were used to investigate the morphology and structure of the Pt-Pd-ZnO/SWCNTs nanocomposite, which was produced via straightforward chemical precipitation combined with the one-pot method. The layer-by-layer modification technique was implemented to fabricate the ds-DNA/Pt-Pd-ZnO/SWCNTs/GCE to be further utilized as a voltammetric sensor for sensitive monitoring of idarubicin in biological fluids and pharmaceutical substances. The electroanalytical method implemented to detect idarubicin was based to detect the ds-DNA's guanine base signal on the surface of the modified electrode in the absence and presence of the anticancer drug. The results explicated that the developed biosensor performed well in determining idarubicin in concentrations ranging from 1.0 nM to 65 μM, with a detection limit of 0.8 nM. The idarubicin detection ability of the modified electrode in real samples was evaluated, and the recovery data was acquired in the range of 98.0% and 104.75%. In the final step, the preferential intercalative binding mode of idarubicin drug with ds-DNA was approved by molecular docking study. This study paves the way for engineering highly sensitive DNA biosensors to be employed in the monitoring of anticancer drugs by combining the benefits of nanocomposites and valuable information of a molecular docking study.

DNA-Based Electrodes and Computational Approaches on the Intercalation Study of Antitumoral Drugs

The binding between anticancer drugs and double-stranded DNA (dsDNA) is a key issue to understand their mechanism of action, and many chemical methods have been explored on this task. Molecular docking techniques successfully predict the affinity of small molecules into the DNA binding sites. In turn, various DNA-targeted drugs are electroactive; in this regard, their electrochemical behavior may change according to the nature and strength of interaction with DNA. A carbon paste electrode (CPE) modified with calf thymus ds-DNA (CPDE) and computational methods were used to evaluate the drug–DNA intercalation of doxorubicin (DOX), daunorubicin (DAU), idarubicin (IDA), dacarbazine (DAR), mitoxantrone (MIT), and methotrexate (MTX), aiming to evaluate eventual correlations. CPE and CPDE were immersed in pH 7 0.1 mM solutions of each drug with different incubation times. As expected, the CPDE response for all DNA-targeted drugs was higher than that of CPE, evidencing the drug–DNA interaction. A peak current increase of up to 10-fold was observed; the lowest increase was seen for MTX, and the highest increase for MIT. Although this increase in the sensitivity is certainly tied to preconcentration effects of DNA, the data did not agree entirely with docking studies, evidencing the participation of other factors, such as viscosity, interfacial electrostatic interactions, and coefficient of diffusion.

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.

A New Electrochemical Platform for Dasatinib Anticancer Drug Sensing Using Fe3O4-SWCNTs/Ionic Liquid Paste Sensor

A new electrochemical platform was suggested for the sensing of the dasatinib (DA) anticancer drug based on paste electrode modification (PE) amplified with Fe₃O₄-SWCNTs nanocomposite and 1-hexyl-3-methylimidazolium tetrafluoroborate (mim-BF₄⁻). The new platform showed a linear dynamic range from 0.001–220 µM with a detection limit of 0.7 nM to determine DA at optimal condition. Electrochemical investigation showed that the redox reaction of DA is relative to changing the pH of solution. Moreover, Fe₃O₄-SWCNTs/mim-BF₄⁻/PE has improved the oxidation current of DA about 5.58 times which reduced its oxidation potential by about 120 mV at optimal condition. In the final step, Fe₃O₄-SWCNTs/mim-BF₄⁻/PE was used as an analytical platform to determine the DA in tablets and a dextrose saline spike sample, and the results showed recovery data 99.58–103.6% which confirm the powerful ability of the sensor as an analytical tool to determine the DA in real samples.