Pharmaceuticals and related drugs

Pharmacogenomic study using bio- and nanobioelectrochemistry: Drug-DNA interaction

Small molecules that bind genomic DNA have proven that they can be effective anticancer, antibiotic and antiviral therapeutic agents that affect the well-being of millions of people worldwide. Drug-DNA interaction affects DNA replication and division; causes strand breaks, and mutations. Therefore, the investigation of drug-DNA interaction is needed to understand the mechanism of drug action as well as in designing DNA-targeted drugs. On the other hand, the interaction between DNA and drugs can cause chemical and conformational modifications and, thus, variation of the electrochemical properties of nucleobases. For this purpose, electrochemical methods/biosensors can be used toward detection of drug-DNA interactions. The present paper reviews the drug-DNA interactions, their types and applications of electrochemical techniques used to study interactions between DNA and drugs or small ligand molecules that are potentially of pharmaceutical interest. The results are used to determine drug binding sites and sequence preference, as well as conformational changes due to drug-DNA interactions. Also, the intention of this review is to give an overview of the present state of the drug-DNA interaction cognition. The applications of electrochemical techniques for investigation of drug-DNA interaction were reviewed and we have discussed the type of qualitative or quantitative information that can be obtained from the use of each technique.

Determination of the cationic amphiphilic drug-DNA binding mode and DNA-assisted fluorescence resonance energy transfer amplification

Understanding the mechanism of drug-DNA binding is crucial for predicting the potential genotoxicity of drugs. Agarose gel electrophoresis, absorption, steady state fluorescence, and circular dichroism have been used in exploring the interaction of cationic amphiphilic drugs (CADs) such as amitriptyline hydrochloride (AMT), imipramine hydrochloride (IMP), and promethazine hydrochloride (PMT) with calf thymus or pUC19 DNA. Agarose gel electrophoresis assay, along with absorption and steady state fluorescence studies, reveal interaction between the CADs and DNA. A comparative study of the drugs with respect to the effect of urea, iodide induced quenching, and ethidium bromide (EB) exclusion assay reflects binding of CADs to the DNA primarily in an intercalative fashion. Circular dichroism data also support the intercalative mode of binding. Besides quenching, there is fluorescence exchange energy transfer (FRET) in between CADs and EB using DNA as a template.

DNA binding properties and biological evaluation of dihydropyrimidinones derivatives as potential antitumor agents

The binding properties of two medicinally important dihydropyrimidinones derivatives 5-(Ethoxycarbonyl)-6-methyl-4-phenyl-3,4-dihydropyrimidin-2(1H)-one (EMPD) and 5-(Ethoxycarbonyl)-6-methyl-4-(4-chlorophenyl)-3,4-dihydropyrimidin-2(1H)-one (EMCD) with calf-thymus DNA (ctDNA) were investigated by spectroscopy, viscosity, isothermal titration calorimetry (ITC) and molecular modeling techniques. Simultaneously, their biological activities were evaluated with MTT assay method. The binding constants determined with spectroscopic titration and ITC were found to be in the same order of 10(4)M(-1). According to the results of viscosity studies, fluorescence competitive binding experiment and ITC investigations, intercalative binding was evaluated as the dominant binding modes between the two compounds and ctDNA. Furthermore, the results of molecular modeling corroborated those obtained from spectroscopic, viscosimetric and ITC investigations. Evaluation of the antitumor activities of the two derivatives against different tumor cell lines proved that they exhibited significant tumor cell inhibition rate, accordingly blocking DNA transcription and replication. The present results favor the development of potential drugs related with dihydropyrimidinones derivatives in the treatment of some diseases.

DNA interaction studies of an antiviral drug, ribavirin, using different instrumental methods

Interaction of ribavirin with CT-DNA was investigated by emission, absorption, circular dichroism, and viscosity studies to determine the binding mode and binding constant of this drug with DNA. The calculated binding constant, K(b), obtained from UV-vis absorption studies was 4.6 × 10(3) M(-1). In fluorimetric studies, the enthalpy (ΔH<0) and entropy (ΔS>0) of the reaction between ribavirin and CT-DNA showed a hydrophobic interaction. In addition, in the circular dichroism spectrum, the drug induces a B → A structural transition of CT-DNA. These results demonstrate that ribavirin interacts with CT-DNA via the groove binding mode. It was observed that the drug has ability to cleave supercoiled plasmid DNA.

Inhibition of transcription factor assembly and structural stability on mitoxantrone binding with DNA

MTX (mitoxantrone) is perhaps the most promising drug used in the treatment of various malignancies. Comprehensive literature on the therapeutics has indicated it to be the least toxic in its class, although its mechanism of action is still not well defined. In the present study, we have evaluated the associated binding interactions of MTX with naked DNA. The mechanism of MTX binding with DNA was elucidated by steady-state fluorescence and a static-type quenching mechanism is suggested for this interaction. Thermodynamic parameters from van 't Hoff plots showed that the interaction of these drugs with DNA is an entropically driven phenomenon. The binding mode was expounded by attenuance measurements and competitive binding of a known intercalator. Sequence specificity of these drug–DNA complexes was analysed by FTIR (Fourier-transform infrared) spectroscopy and molecular modelling studies. CD spectroscopy and the plasmid nicking assay showed that the binding of this drug with DNA results in structural and conformational perturbations. EMSA (electrophoretic mobility-shift assay) results showed that these drug–DNA complexes prevent the binding of octamer TF (transcription factor) to DNA. In summary, the study implicates MTX-induced conformational instability and transcription inhibition on DNA binding.

Electroanalytical and spectroscopic procedures for examination of interactions between double stranded DNA and intercalating drugs

A method is presented for the electroanalytical characterization of interactions of dsDNA with a drug, under conditions that both agents are dissolved in the phosphate buffer solution and both are electroactive. Normal pulse, square wave, differential pulse, and cyclic voltammetries were employed in the measurements of the drug and dsDNA oxidation signals at carbon electrodes. UV-Vis spectroscopy was used as a non-electrochemical method to support the electroanalytical data. An anticancer drug, C-1311 (5-diethylaminoethyl-amino-8-hydroxyimidazoacridinone), has been selected for the examination. Normal pulse voltammetry was particularly useful in showing that under the conditions employed neither dsDNA nor the drug were adsorbed at the electrode surface. Necessary conditions for the appearance of the well-defined dsDNA voltammetric signal (guanine peak) are: rigorous chemical and biological purity in the cell and appropriate purity of DNA. An analysis of the obtained results confirmed that there were two modes of interaction between C-1311 and dsDNA: by intercalation and electrostatically. In the presence of excess NaCl the electrostatic interactions deteriorate. The binding constants (K (1) and K (2), respectively) and the number (n) of nucleic base pairs (bp) and the number (m) of phosphate groups (pg) interacting with one molecule of drug have been determined. For strong interactions (intercalation) the values of the binding constant, K (1), and the binding-site size, n, equal 3.7 x 10(4) M(-1) and 2.1, respectively. For the weak electrostatic interactions the K (2) and m parameters equal 0.28 x 10(4) M(-1) and 4.7. The intercalation process is rather slow and its rate (the conditions of pseudo-first-order reaction) was estimated to equal 7 x 10(-4) s(-1). The possibility of independent determination of both interacting agents was very useful in the study.

Interaction of anticancer drug mitoxantrone with DNA analyzed by electrochemical and spectroscopic methods

Cyclic voltammetry coupled with different spectroscopic (UV/Vis, fluorescence and Raman) techniques were used to study the interaction of mitoxantrone (MTX), an antitumor drug, with calf thymus DNA in acetate buffer solutions (pH 4.5). The interaction of MTX with DNA could result a considerable decrease in the MTX peak currents and a hypochromic and bathochromic shift in the maximum adsorption bands of MTX as well as the emission quenching in the MTX fluorescence spectra. The variations in the electrochemical and spectral characteristics of MTX indicated MTX bind to DNA by an intercalative mode. This conclusion was reinforced by Raman data. The merely particular vibrations were affected in Raman, suggesting that only a portion of the chromophore of MTX was involved in the intercalation into DNA duplex. These studies are valuable for a better understanding the detailed mode of MTX-DNA interaction, which should be important in deeper insight into the therapeutic efficacy of MTX and design of new DNA targeted drug.

Interaction of echinomycin with guanine: electrochemistry and spectroscopy studies

The interaction of antitumor antibiotic, echinomycin (Echi) with guanine (Gua) was thoroughly investigated by adsorptive transfer stripping cyclic voltammetry, ultraviolet and visible adsorption spectra (UV/Vis) and Fourier-transform infrared spectroscopy (FTIR). Electrochemistry provided a simple tool for verifying the occurrence of interaction between Echi and Gua. Echi could be accumulated from the solution and give well-defined electrochemical signals in 0.1 M phosphate buffer solution (pH 7.0) only when Gua was present on the surface of the electrochemically pretreated glass carbon electrode (GCE), suggesting a strong binding of Echi to Gua. All the acquired spectral data showed that a new adduct between Echi and Gua was formed, and two pairs of adjacent intermolecular hydrogen bonds between the Ala backbone atoms in Echi and Gua (Ala-NH to Gua-N3 and Gua-NH2 to Ala-CO) played a dominating role in the interaction. Electrochemistry coupled with spectroscopy techniques could provide a relatively easy way to obtain useful insights into the molecular mechanism of drug-DNA interactions, which should be important in the development of new anticancer drugs with specific base recognition.

Rapid pharmacokinetic screening for the selection of new drug discovery candidates using a generic isocratic liquid chromatography--atmospheric pressure ionization tandem mass spectrometry method

A generic isocratic HPLC-APCI-MS-MS method has been developed for the determination of plasma concentrations of bioactive compounds for the selection of potential new drug discovery candidates. A 4.6 x 50 mm cyano phase column eluted with an acetonitrile/water mobile phase containing 20 mM ammonium acetate and 0.4% TFA produces retention times of 1 min or less for a wide range of compounds. This is a great advantage in new drug discovery where many compounds are analyzed once and eliminated. No time is consumed developing chromatographic conditions for each new compound. The mass spectrometer can be optimized and the samples can be processed and analyzed, all in the same day. Multiple assays can be run consecutively without changing the column or mobile phase between assays.

Determination of nonsteroidal anti-inflammatory drugs in biological fluids by automatic on-line integration of solid-phase extraction and capillary electrophoresis

A new, automatic method for the clean-up, preconcentration, separation, and quantitation of nonsteroidal anti-inflammatory drugs (NSAIDs) in biological samples (human urine and serum) using solid-phase extraction coupled on-line to capillary electrophoresis is proposed. Automatic pretreatment is carried out by using a continuous flow system operating simultaneously with the capillary electrophoresis equipment, to which it is linked via a laboratory-made mechanical arm. This integrated system is controlled by an electronic interface governed via a program developed in GWBasic. Capillary electrophoresis is conducted by using a separation buffer consisting of 20 mM NaHPO4, 20 mM beta-cyclodextrin and 50 mM SDS at pH 9.0, an applied potential of 20 kV and a temperature of 20 degrees C. The analysis time is 10 min and the detection limits were between 0.88 and 1.71 microg mL(-1). Automatic clean-up and preconcentration is accomplished by using a C-18 minicolumn and 75% methanol as eluent. The limit of detection of NSAIDs can be up to 400-fold improved when using sample clean-up. The extraction efficiency for these compounds is between 71.1 and 109.7 microg mL(-1) (RSD 2.0-7.7%) for urine samples and from 77.2 to 107.1 microg mL(-1) (RSD 3.5-7.1%) for serum samples.

Determination of C-21 ketosteroids in serum using trifluoromethanesulfonic acid catalyzed precolumn dansylation and 1,1'-oxalyldiimidazole postcolumn peroxyoxalate chemiluminescence detection

A new procedure for the quantitation of C-21 ketosteroids using trifluoromethanesulfonic acid-catalyzed precolumn dansylation and coupled column liquid chromatographic separation, followed by postcolumn 1,1'-oxalyldiimidazole peroxyoxalate chemiluminescence detection is presented. In the simultaneous optimization of chromatographic resolution and chemiluminescence intensity, a coupled column chromatographic system and a stopped-flow system were used. An eluent containing 20 mM phosphate buffer at pH 6.7 accomplished an efficient separation of 3 alpha-hydroxy-5 beta-pregnan-20-one from a mixture containing 10 C-21 ketosteroids. Phosphate buffer also proved to be the most advantageous, among the six buffers tested, for sensitive detection. Experimental design and multivariate data analysis were used to characterize and optimize the postcolumn reaction chemistry in the chromatographic system. A valid full factorial design with excellent predictability showed that the flow rates for both 1,1'-oxalyldiimidazole and hydrogen peroxide were the factors most strongly affecting the sensitivity of the system. The theoretical plate numbers were above 11,000 for all 10 dansylated ketosteroids. The 3 sigma detection limit estimated from 3 alpha-hydroxy-5 beta-pregnan-20-one calibration curve data was 1.6 pmol (n = 4, 125 microL injected) and spiked serum containing 0-74 pmol of this compound showed overall recoveries of 73 +/- 9% (n = 12). Quantitation of 3 alpha-hydroxy-5 beta-pregnan-20-one was finally carried out on 45 serum samples and the results compared to those from a radioimmunoassay (RIA) method. The data acquired with the procedure described in this work compare well with the results from RIA, which confirms the reliability of the new analytical procedure.