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Despite the rise of sophisticated new targeting strategies in cancer chemotherapy, many classic DNA‐binding drugs remain on the front line of the therapy against cancer. Based on examples primarily from the author's laboratory, this article reviews the capabilities of several DNA‐binding drugs to alter gene expression. Research is ongoing about the molecular bases of the inhibition of gene expression and how alteration of the cellular transcriptome can commit cancer cells to die. The development of a variety of omic techniques allows us to gain insights into the effect of antitumor drugs. Genome‐wide approaches provide unbiased genomic data that can facilitate a deeper understanding of the cellular response to DNA‐binding drugs. Moreover, the results of large‐scale genomic studies are gathered in publicly available databases that can be used in developing precision medicine in cancer treatment. [ABSTRACT FROM AUTHOR]

[Display omitted] • Understanding of the binding mode of an important drug, Imiquimod (IMQ), with Calf Thymus Deoxyribonucleic Acid (ct-DNA). • Fluorescence quenching, time-resolved emission, steady state anisotropy technique, ethidium bromide displacement assay and circular dichroism studies provided evidences for intercalation mechanisms. • The DNA sequence dependent binding interactions are visualized with the help of molecular docking studies followed by molecular dynamics simulation. Herein the manuscript, we report the interaction of an important drug, Imiquimod (IMQ), with Calf Thymus Deoxyribonucleic Acid (ct-DNA). Despite of being used IMQ in multiple medicinal applications such as immune response modifier, antitumor and antiviral drug its interaction with DNA is not studied yet. To understand their interaction and characterize the binding mechanism between groove and intercalation modes, we used various spectroscopic tools. Fluorescence quenching, time-resolved emission, steady state anisotropy technique, ethidium bromide (EtBr), and 4′,6-diamidino-2-phenylindole (DAPI) displacement assays provided us biophysical aspects of IMQ-DNA interactions. All the above studies revealed the binding mode as intercalation mechanism. Circular Dichroism (CD) also well corroborated the intercalation of IMQ into DNA. Thermodynamic parameters of these binding interactions were interpreted with the help of temperature dependent spectroscopic studies characterizing the interaction as enthalpy driven. Further, the binding interactions is explored with the help of molecular docking studies. Based on experimental and computational studies it was concluded that the drug binds to DNA via intercalation mode in AT-rich DNA sequences. These biophysical investigations not only improve our comprehension of IMQ's therapeutic effectiveness but also clarifies the sequence dependent binding processes underlying comparable drug-DNA interactions. [ABSTRACT FROM AUTHOR]

Mitoxantrone (1,4-dihydroxy-5,8-bis[2-(2-hydroxyethylamino)ethylamino]-anthracene-9,10-dione) is a clinically-relevant synthetic anthracenedione that functions as a topoisomerase II poison by trapping DNA double-strand break intermediates. Mitoxantrone binds to DNA via both stacking interactions with DNA bases and hydrogen bonding with the sugar-phosphate backbone. It has been shown that mitoxantrone inhibits apurinic/apyrimidinic (AP) endonuclease 1 (APE1)-catalyzed incision of DNA containing a tetrahydrofuran (THF) moiety and more recently, that mitoxantrone forms Schiff base conjugates at AP sites in DNA. In this study, mitoxantrone-mediated inhibition of APE1 at THF sites was shown to be consistent with preferential binding to, and thermal stabilization of DNA containing a THF site as compared to non-damaged DNA. Investigations into the properties of mitoxantrone at AP and 3′ α,β-unsaturated aldehyde sites demonstrated that in addition to being a potent inhibitor of APE1 at these biologically-relevant substrates (∼ 0.5 μM IC 50 on AP site-containing DNA), mitoxantrone also incised AP site-containing DNA by catalyzing β- and β/δ-elimination reactions. The efficiency of these reactions to generate the 3′ α,β-unsaturated aldehyde and 3′ phosphate products was modulated by DNA structure. Although these cell-free reactions revealed that mitoxantrone can generate 3′ phosphates, cells lacking polynucleotide kinase phosphatase did not show increased sensitivity to mitoxantrone treatment. Consistent with its ability to inhibit APE1 activity on DNAs containing either an AP site or a 3′ α,β-unsaturated aldehyde, combined exposures to clinically-relevant concentrations of mitoxantrone and a small molecule APE1 inhibitor revealed additive cytotoxicity. These data suggest that in a cellular context, mitoxantrone may interfere with APE1 DNA repair functions. • Mitoxantrone has the capacity to interfere with the processing of AP sites. • Mitoxantrone stabilizes AP site-containing DNA against thermal denaturation. • Mitoxantrone catalyzes β- and δ-elimination reactions on AP site-containing DNA. • The efficiency of mitoxantrone-catalyzed nicking is modulated by DNA structure. • Mitoxantrone inhibits APE1 DNA repair activities. [ABSTRACT FROM AUTHOR]

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.

Ftorafur is an antimetabolite antitumour drug successfully used for treatment of various tumours. It is generally accepted that ftorafur is converted to 5-fluoruracil. However, some data indicate direct interactions of the compound with DNA. To test this hypothesis we have performed spectrophotometric study of DNA interactions of ftorafur and some of its elementoorganic derivatives with DNA. UV-VIS spectra of the tested compounds were recorded in absence and presence of increasing amounts of DNA. DNA caused a hypochromic effect in spectra of ftorafur, similar, but weaker effect was observed in 5-fluoruracil spectra. Trimethylgermyl derivative of ftorafur manifested a higher DNA-binding capacity compared to ftorafur. To reveal possible mechanism of interaction between the tested nucleosides and DNA ethidium bromide extrusion experiments were performed. It was shown that the compounds did not compete with EBr for intercalation. Fourier transformation infrared spectroscopy analyses revealed decrease in intensity of several bands in spectra of ftorafur, its trimethylgermyl derivative and fluorouracil in presence of DNA indicating again interactions between the compounds and DNA. Docking experiments reveal interactions of the tested nucleosides with the DNA minor groove. Thus ftorafur is capable to interact directly with DNA; further modifications of the molecule enhance this capacity. [ABSTRACT FROM AUTHOR]

Abstract: The interaction of cis-diamminedichloroplatinum(II) (cis-DDP) and the potential novel chemotherapeutic agent, cis-bis(3-aminoflavone)dichloroplatinum(II) (cis-BAFDP) was studied electrochemically with calf thymus double-stranded DNA (dsDNA) by using differential pulse voltammetry (DPV) with disposable pencil graphite electrode (PGE) at the surface. These studies were prompted by beneficial biological properties of cis-BAFDP in comparison with cis-DDP, which were proven in vitro both in human normal and cancer cells and in vivo. The changes in the experimental parameters such as the concentration of cis-DDP and cis-BAFDP were studied by using DPV; in addition, the reproducibility of this genosensor and the detection limit for each compound were determined. After the interaction of cis-DDP with dsDNA, the DPV signal of guanine and adenine was found to be decreasing. In comparison with cis-DDP, a dramatic decrease at adenine signal was also obtained after the interaction of cis-BAFDP and dsDNA. Similar results were also found in solution phase after the latter compound interacts with poly[A]. The features of the proposed electrochemical method for the detection of cis-BAFDP with DNA in comparison with cis-DDP are discussed and compared with those methods previously reported for the other type of DNA-targeted agents in the literature. [Copyright &y& Elsevier]

Developing a molecular view of the thermodynamics of DNA recognition is essential to the design of ligands for regulating gene expression. In a first comprehensive attempt at sketching an atlas of DNA–drug energetics, we present here a detailed thermodynamic view of minor-groove recognition by small molecules via a computational study on 25 DNA–drug complexes. The studies are configured in the MMGBSA (Molecular Mechanics-Generalized Born-Solvent Accessibility) framework at the current state of the art and facilitate a structure–energy component correlation. Analyses were conducted on both energy minimized structures of DNA–drug complexes and molecular dynamics trajectories developed for the purpose of this study. While highlighting the favorable role of packing, shape complementarity, and van der Waals and hydrophobic interactions of the drugs in the minor groove in conformity with experiment, the studies reveal an interesting annihilation of favorable electrostatics by desolvation. Structural modifications attempted on the ligands point to the requisite physico-chemical factors for obtaining improved binding energies. Hydrogen bonds predicted to be important for specificity based on structural considerations do not always turn out to be significant to binding in post facto analyses of molecular dynamics trajectories, which treat thermal averaging, solvent, and counterion effects rigorously. The strength of the hydrogen bonds retained between the DNA and drug during the molecular dynamics simulations is ∼1 kcal/mol. Overall, the study reveals the compensatory nature of the diverse binding free energy components, possible threshold limits for some of these properties, and the availability of a computationally viable free energy methodology which could be of value in drug-design endeavors. [Copyright &y& Elsevier]

The binding of Hoechst 33258 and DAPI to five different (A/T)4 sequences in a stable DNA hairpin was studied exploiting the substantial increase in dye fluorescence upon binding. The two dyes have comparable affinities for the AATT site (e.g. association constant Ka=5.5×108 M−1 for DAPI), and their affinities decrease in the series AATT≫ TAAT≈ATAT>TATA≈TTAA. The extreme values of Ka differ by a factor of 200 for Hoechst 33258 but only 30 for DAPI. The binding kinetics of Hoechst 33258 were measured by stopped-flow under pseudo-first order conditions with an (A/T)4 site in excess. The lower-resolution experiments can be well represented by single exponential processes, corresponding to a single-step binding mechanism. The calculated association-rate parameters for the five (A/T)4 sites are similar (2.46×108 M−1 s−1 to 0.86×108 M−1 s−1) and nearly diffusion-controlled, while the dissociation-rate parameters vary from 0.42 s−1 to 96 s−1. Thus the association constants are kinetically controlled and are close to their equilibrium-determined values. However, when obtained with increased signal-to-noise ratio, the kinetic traces for Hoechst 33258 binding at the AATT site reveal two components. The concentration dependencies of the two time constants and amplitudes are consistent with two different kinetically equivalent two-step models. In the first model, fast bimolecular binding is followed by an isomerization of the initial complex. In the second model, two single-step associations form two complexes that mutually exclude each other. For both models the four reaction-rate parameters are calculated. Finally, specific dissociation kinetics, using poly[d(A-5BrU)], show that the kinetics are even more complex than either two-step model. We correlate our results with the different binding orientations and locations of Hoechst 33258 in the DNA minor groove found in several structural studies in the literature. [Copyright &y& Elsevier]

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. [ABSTRACT FROM AUTHOR]