Determination of the drug–DNA binding modes using fluorescence-based assays

Insight into the intercalation of N-substituted acridine-9-amines into DNA based on spectroscopic and calorimetric analysis

The study delves into the binding properties of acridine-9-amine and its selected, mainly N-substituted derivatives (A9As), with calf thymus deoxyribonucleic acid (CT-DNA). This investigation, conducted using UV-Vis spectrophotometry, steady-state fluorescence spectroscopy and isothermal titration calorimetry, provides insights into the relationship between their structure and activity. The absorption spectra of the A9As exhibited a slight red shift and significant hypochromic effects, while the fluorescence emission intensities decreased in the presence of CT-DNA. These results suggest that all fluorescent substrates intercalate into the double helix of native DNA to varying degrees. The binding constants for the A9As/CT-DNA complexes (log(KA) were determined using various techniques in the range from 2.59 to 5.50). The thermodynamic parameters of A9As binding to DNA were obtained from ITC measurements (ΔG from - 7.51 to - 6.75 kcal·mol-1, ΔH from - 11.58 to - 3.83 kcal·mol-1, and TΔS from - 4.83 to 3.68 kcal·mol-1) and indicated that the formation of all the investigated A9As-DNA complexes is an enthalpy-driven process. The study also discusses the influence of the emitters' structure and electronic properties of substituents on intercalation efficiency. This knowledge serves as a guide for further research and offers directions for functionalising new acridines as potential reagents. It also provides the latest information on the ability of intercalation to DNA, which can be instrumental in studies on the mechanism of binding small aromatic molecules to DNA and can potentially contribute to new anticancer drug designs.

Deciphering the Effect of a Cu(II)-hydrazone Complex on Intracellular Cell Signalling Pathways in a Human Osteosarcoma 2D and 3D Models

New therapeutic strategies for osteosarcoma (OS) have demonstrated the potential efficacy of copper compounds as anticancer drugs and as a substitute for the often used platinum compounds. OS is a type of bone cancer, primarily affecting young adults and children.The main objective of this work is to discover the molecular targets and cellular pathways related to the antitumor properties of a Cu(II)-hydrazone toward human OS 2D and 3D systems. Cell viability study using MG-63 cells was evaluated in OS monolayer and spheroids. CuHL significantly reduced cell viability in OS models (IC50 2D: 2.6±0.3 μM; IC50 3D: 9.9±1.4 μM) (p<0.001). Also, CuHL inhibits cell proliferation and it induces cells to apoptosis. The main mechanism of action found for CuHL are the interaction with DNA, genotoxicity, the ROS generation and the proteasome activity inhibition. Besides, 67 differentially expressed proteins were found using proteomic approaches. Of those 67 proteins, 40 were found overexpressed and 27 underexpressed. The response to stress and to unfolded protein, as well as ATP synthesis were the most affected biological process among upregulated proteins, whilst proteins related to DNA replication and redox homeostasis were downregulated.

Promising Dual Anticancer and Antimetastatic Action by a Cu(II) Complex Derived from Acylhydrazone on Human Osteosarcoma Models

Osteosarcoma cancers are becoming more common in children and young adults, and existing treatments have low efficacy and a very high mortality rate, making it pressing to search for new chemotherapies with high efficacy and high selectivity index. Copper complexes have shown promise in the treatment of osteosarcoma. Here, we report the synthesis, characterization, and anticancer activity of [Cu(N-N-Fur)(NO3)(H2O)] complex where N-N-Fur is (E)-N'-(2-hydroxy-3-methoxybenzylidene)furan-2-carbohydrazide. The [Cu(N-N-Fur)(NO3)(H2O)] complex was characterized via X-ray diffraction and electron spin resonance (ESR), displaying a copper center in a nearly squared pyramid environment with the nitrate ligand acting as a fifth ligand in the coordination sphere. We observed that [Cu(N-N-Fur)(NO3)(H2O)] binds to DNA in an intercalative manner. Anticancer activity on the MG-63 cell line was evaluated in osteosarcoma monolayer (IC50 2D: 1.1 ± 0.1 μM) and spheroids (IC50 3D: 16.3 ± 3.1 μM). Selectivity assays using nontumoral fibroblast (L929 cell line) showed that [Cu(N-N-Fur)(NO3)(H2O)] has selectivity index value of 2.3 compared to cis-diamminedichloroplatinum(II) (CDDP) (SI = 0.3). Additionally, flow cytometry studies demonstrated that [Cu(N-N-Fur)(NO3)(H2O)] inhibits cell proliferation and conveys cells to apoptosis. Cell viability studies of MG-63 spheroids (IC50 = 16.3 ± 3.1 μM) showed that its IC50 value is 4 times lower than for CDDP (IC50 = 65 ± 6 μM). Besides, we found that cell death events mainly occurred in the center region of the spheroids, indicating efficient transport to the microtumor. Lastly, the complex showed dose-dependent reductions in spheroid cell migration from 7.5 to 20 μM, indicating both anticancer and antimetastatic effects.

Finding New Molecular Targets of Two Copper(II)-Hydrazone Complexes on Triple-Negative Breast Cancer Cells Using Mass-Spectrometry-Based Quantitative Proteomics

Breast cancer is the most common cancer in women, with a high incidence estimated to reach 2.3 million by 2030. Triple-Negative Breast Cancer (TNBC) is the greatest invasive class of breast cancer with a poor prognosis, due to the side-effects exerted by the chemotherapy used and the low effectivity of novel treatments. In this sense, copper compounds have shown to be potentially effective as antitumor agents, attracting increasing interest as alternatives to the usually employed platinum-derived drugs. Therefore, the aim of this work is to identify differentially expressed proteins in MDA-MB-231 cells exposed to two copper(II)-hydrazone complexes using label-free quantitative proteomics and functional bioinformatics strategies to identify the molecular mechanisms through which these copper complexes exert their antitumoral effect in TNBC cells. Both copper complexes increased proteins involved in endoplasmic reticulum stress and unfolded protein response, as well as the downregulation of proteins related to DNA replication and repair. One of the most relevant anticancer mechanisms of action found for CuHL1 and CuHL2 was the down-regulation of gain-of-function-mutant p53. Moreover, we found a novel and interesting effect for a copper metallodrug, which was the down-regulation of proteins related to lipid synthesis and metabolism that could lead to a beneficial decrease in lipid levels.

Effect of ancillary ligand on DNA and protein interaction of the two Zn (II) and Co (III) complexes: experimental and theoretical study

In the present work we have developed one mononuclear Zn(II) complex [Zn(L)(H2O)] (Complex 1) by utilizing a tetracoordinated ligand H₂L, formed by simple condensation of 2, 2 dimethyl 1,3 diamino propane and 3- ethoxy salicylaldehyde and one newly designed mononuclear Co (III) complex [Co(L)(L1)] (complex 2) by utilizing (H₂L) and 3- ethoxy salicylaldehyde(HL1) as an ancillary ligand. The newly developed complex 2 have been spectroscopically characterized. An interesting phenomenon has been noticed that in presence of ancillary ligand, the solubility in buffer solution and the thermal stability of complex 2 comparatively increases than 1. To check the effect of ancillary ligand, present in complex 2 towards the DNA and HSA binding efficacy, both the complexes have been taken into consideration to inspect their binding potentiality with the macromolecules. The 'on', 'off' fluorescence changes in presence of DNA and HSA, the binding constant values, obtained from electronic spectral titration, iodide induced quenching, competitive binding assay, circular dichroism (CD) spectral titration, time resolved fluorescence experiment unambiguously assure the better binding efficacy of complex 2 with the signal of minor groove binding mode with DNA along with no significant conformational changes of the macromolecules. The strong and spontaneous binding of complex 2 with CT-DNA is further supported by the Isothermal Titration Calorimetry (ITC) study. Furthermore TDDFT calculation of DNA with and without complex 2 significantly authorize the formation of complex 2-DNA adduct during the association. Finally Molecular Docking study properly verifies the experimental findings and provides justified explanation behinds experimental findings.

The Study of Interaction Activity of Nickel (ll) Phthalocyanine Complex Bearing Tetra Substituted Phenoxy-3-Methoxybenzoic Acid Groups with DNA

Nickel phthalocyanine complex containing 4-(3,4-dicyanophenoxy)-3-methoxybenzoic acid group was synthesized and specified by way of FT-IR, NMR, UV/Vis procedures. The binding of PcNi complex to CT-DNA was examined via electronic absorption titration, emission titration, melting temperature, viscosity measurement, and agarose gel electrophoresis technics, respectively. The DNA interaction activity of PcNi against CT-DNA was studied by way of UV/Vi titrations, fluorescence spectra, farther by conducting melting point, viscosity procedures in the buffer of a pH 7.02. The obtained outcomes from these methods demonstrated that PcNi indicated substantial binding affinity to the DNA via intercalating by the binding constant of 1.31 x 106 m-1. Further, the interaction activity of the complex on CT-DNA was investigated by which the electrophoresis technique and this procedure indicated that PcNi complex exhibits strong binding affinity on the DNA.

Synthesis, Characterization, Biological Evaluation and DNA Interaction Studies of 4-Aminophenol Derivatives: Theoretical and Experimental Approach

In the present study, five 4-aminophenol derivatives (4-chloro-2-(((4-hydroxyphenyl)imino)methyl)phenol(S-1), 4-((4-(dimethylamino)benzylidene)amino)phenol(S-2), 4-((3-nitrobenzylidene)amino)phenol(S-3), 4-((thiophen-2-ylmethylene)amino)phenol(S-4) and 4-(((E)-3-phenylallylidene)amino)phenol(S-5)) were synthesized and characterized by FT-IR, ¹H-NMR, ¹³C-NMR and elemental analyses. The synthesized compounds were tested for their antimicrobial (Gram-positive and Gram-negative bacteria and Saccharomyces cervesea fungus) and antidiabetic (α-amylase and α-glucosidase inhibitory) activities. All the compounds showed broad-spectrum activities against the Staphylococcus aureus (ATCC 6538), Micrococcus luteus (ATCC 4698), Staphylococcus epidermidis (ATCC 12228), Bacillus subtilis sub. sp spizizenii (ATCC 6633), Bordetella bronchiseptica (ATCC 4617) and Saccharomyces cerevisiae (ATCC 9763) strains. The newly synthesized compounds showed a significant inhibition of amylase (93.2%) and glucosidase (73.7%) in a concentration-dependent manner. Interaction studies of Human DNA with the synthesized Schiff bases were also performed. The spectral bands of S-1, S-2, S-3 and S-5 all showed hyperchromism, whereas the spectral band of S-4 showed a hypochromic effect. Moreover, the spectral bands of the S-2, S-3 and S-4 compounds were also found to exhibit a bathochromic shift (red shift). The present studies delineate broad-spectrum antimicrobial and antidiabetic activities of the synthesized compounds. Additionally, DNA interaction studies highlight the potential of synthetic compounds as anticancer agents. The DNA interaction studies, as well as the antidiabetic activities articulated by the molecular docking methods, showed the promising aspects of synthetic compounds.

Anticancer and Biological Properties of New Axially Disubstituted Silicon Phthalocyanines

This study reports the synthesis of three novel axially disubstituted silicon phthalocyanines (1-3-Si) and their quaternized phthalocyanines (1-3-QSi). The resulting compounds were characterized by applying spectroscopic techniques including 1H NMR,...

Anticancer Activity and Mechanism of Action Evaluation of an Acylhydrazone Cu(II) Complex toward Breast Cancer Cells, Spheroids, and Mammospheres

The purpose of this work was to screen the anticancer activity and mechanisms of action of Cu(II)-acylhydrazone complex [Cu(HL)(H₂ O)](NO₃ )⋅H₂ O, (CuHL), to find a potential novel agent for breast chemotherapies. Cytotoxicity studies on MCF7 cells demonstrated that CuHL has stronger anticancer properties than cisplatin over breast cancer cell models. Computational simulations showed that CuHL could interact in the minor groove of the DNA dodecamer, inducing a significant genotoxic effect on both cancer cells from 0.5 to 1 μM. In this sense, molecular docking and molecular dynamics simulations showed that the compound could interact with 20S proteasome subunits. Also, cell proteasome experiments using breast cancer cells revealed that the complex can inhibit proteasomal activity. Moreover, CuHL induced apoptosis in breast cancer cells at very low micromolar concentrations (0.5-2.5 μM) and displayed relevant anticancer activity over spheroids derived from MCF7 cells. Ultimately, CuHL diminished the number of mammospheres formed, disturbing their morphology and size.

Förster Resonance Energy Transfer from Carbon Nanoparticles to a DNA-Bound Compound: A Method to Detect the Nature of Binding

A drug molecule can bind in various orientations to a DNA strand. Nature of the binding decides the functionality and efficacy of the drug. To innovate a new method to detect the nature of binding of a drug to DNA strands, herein we have used the dipole-dipole interaction driven Förster resonance energy transfer (FRET) between carbon nanoparticles (CNPs) and a DNA-bound small molecule, (E)-3-ethyl-2-(4-(pyrrolidin-1-yl)styryl)benzo[d]thiazol-3-ium (EPSBT), which belongs to the hemicyanine family and binds typically to the minor groove of a DNA duplex. EPSBT was designed to obtain appreciable fluorescence quantum yield, which constructed an efficient FRET pair with the synthesized CNPs. The tested compound prefers the thymine nucleobase to bind to the DNA strand. Orientation of its dipole on attachment to the DNA strand and the donor-acceptor distance dictate the FRET efficiency with the CNPs. The results provided a precise estimation of the nature of binding of EPSBT to the DNA backbone and, hence, supposedly will help in deciding the functional efficacy.

Copper(II) N,N,O-Chelating Complexes as Potential Anticancer Agents

Three novel dinuclear Cu(II) complexes based on a N,N,O-chelating salphen-like ligand scaffold and bearing varying aromatic substituents (−H, −Cl, and −Br) have been synthesized and characterized. The experimental and computational data obtained suggest that all three complexes exist in the dimeric form in the solid state and adopt the same conformation. The mass spectrometry and electron paramagnetic resonance results indicate that the dimeric structure coexists with the monomeric form in solution upon solvent (dimethyl sulfoxide and water) coordination. The three synthesized Cu(II) complexes exhibit high potentiality as ROS generators, with the Cu(II)/Cu(I) redox potential inside the biological redox window, and thus being able to biologically undergo Cu(II)/Cu(I) redox cycling. The formation of ROS is one of the most promising reported cell death mechanisms for metal complexes to offer an inherent selectivity to cancer cells. In vitro cytotoxic studies in two different cancer cell lines (HeLa and MCF7) and in a normal fibroblast cell line show promising selective cytotoxicity for cancer cells (IC₅₀ about 25 μM in HeLa cells, which is in the range of cisplatin and improved with respect to carboplatin), hence placing this N,N,O-chelating salphen-like metallic core as a promising scaffold to be explored in the design of future tailor-made Cu(II) cytotoxic compounds.

Three novel dinuclear Cu(II) complexes based on a N,N,O-chelating salphen-like ligand scaffold and bearing varying aromatic substituents (−H, −Cl, and −Br) have been synthesized and characterized. They three exhibit high potentiality as reactive oxygen species (ROS) generators, with the Cu(II)/Cu(I) redox potential inside the biological redox window. In vitro studies in two different cancer cell lines (HeLa and MCF7) and in a normal fibroblast cell line show promising selective cytotoxicity for cancer cells.

Multispectroscopic and molecular docking studies on DNA binding of guaifenesin drug

The interaction mechanism of guaifenesin drug; (RS)-3-(2-methoxyphenoxy)propane-1,2-diol; and calf thymus DNA was characterized by multiple spectroscopic and molecular docking approaches. The changes in drug electronic absorption with increasing DNA concentration and also the observed significant quenching of guaifenesin emission in the presence of DNA proved the complex formation between guaifenesin and DNA during the interactions. Both the binding constant and thermodynamic parameters for the interaction have been calculated in 283, 298, and 310 K at pH 7.4. The results Δ H 0  = 17.87 kJ/mol and Δ S 0  = 143.31 J/mol.K confirmed the role of hydrophobic force in the guaifenesin-DNA interaction. Circular dichroism study showed that guaifenesin causes decrease in the negative band of CT-DNA and at the same time the positive band increases which indicated the transition of DNA conformation from B to A. KI quenching experiment specifies that guaifenesin binds to DNA via nonintercalative mode. The competitive studies based on known Hoechst 33258 and methylene blue probes proved the groove binding mode in guaifenesin-DNA adduct. Further, full agreement of molecular docking simulation with the experimental results of binding constant and interaction mode, support high accuracy of the results.

Neto JDB, de Abreu FC, Figueiredo IM, Carinhanha C. Santos J, Pessoa CDÓ, da Silva-Júnior EF, de Araújo-Júnior JX, M. de Aquino T. Synthesis of hybrids thiazole–quinoline, thiazole–indole and their analogs: in vitro anti-proliferative effects on cancer cell lines, DNA binding properties and molecular modeling

A quinoline–thiazole hybrid was synthesized, which showed cytotoxicity against the HL-60 cell line. Electrochemical and spectroscopic experiments suggested DNA as the biological target.

Spectroscopic and viscometric determination of DNA-binding modes of some bioactive dibenzodioxins and phenazines

Push-pull dibenzodioxins and phenazines having ‘anthracene-like’ planar structures and good charge transfer character had been previously synthesised in our laboratory. The dibenzodioxins had earlier proven their anti-proliferative nature against HeLa tumor cell lines. Since phenazines are structural analogues of the former, these molecules were evaluated in course of the current study for their cytotoxic action against HeLa cell lines and they exhibited strong anti-tumor activity. This behavior could be related to their good DNA binding property. The DNA binding modes of molecules 1–4 (Fig. 1) were evaluated using various experimental techniques and they interacted with DNA in a non-covalently by both intercalative as well as groove binding mechanisms. Molecule 1 follows predominantly intercalative binding mode whereas molecules 2 and 3 have nearly equal and opposite preferences for both groove binding and intercalative modes. For molecule 4, groove binding is preferred mode of binding to DNA. A rationale for such differential binding behaviour is provided based on the subtle structural differences in our synthesised dibenzodioxins and phenazines. Elucidation of the mode of a molecule-DNA-binding event is relevant for understanding the mechanism of action of these molecules and will help promote further research into designing better DNA targeting small molecules.

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DNA binding modes of push-pull planar dibenzodioxins and phenazines were elucidated.

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DNA binding mechanistic details were obtained by spectroscopic and viscometric techniques.

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The molecular shape and geometry has a bearing on its choice of binding mode.

Synthesis of a 3,4-Disubstituted 1,8-Naphthalimide-Based DNA Intercalator for Direct Imaging of Legionella pneumophila

The development of organic molecules to target nucleic acid is an active area of research at the interface of chemistry and biochemistry, which involves DNA binding, nuclear imaging, and antitumor studies. These molecules bind with DNA through covalent interactions, electrostatic interactions, or intercalation. However, they are less permeable to membrane, and they have a significant cytotoxicity, which limits their application under in vivo conditions. In the present work, various mono- and disubstituted 1,8-naphthalimides-based derivatives (S-12, S-13, S-15, and S-21) have been synthesized and characterized through various spectroscopic techniques. Among these, 3-amino-4-bromo-1,8-naphthalimide (S-15) was found to have an attractive water solubility and act as a nuclear imaging agent. The spectroscopic absorption and emission data showed that S-15 has a strong affinity for salmon sperm DNA with a binding constant of 6.61 × 10⁴ M^-1, and the ratiometric fluorescence intensity (I ₄₈₉/I ₅₅₂) of S-15 has a linear relationship in the 0-50 μM range of DNA concentrations. It intercalates with DNA through the hydrophobic planar naphthalimide core as confirmed through cyclic voltammetry, circular dichroism, ¹H NMR titration, and thermal denaturation studies. Positively charged amine groups also participate in H-bonding with the bases and backbone of DNA. The S-15 intercalator showed a large Stokes shift and photostability, which made it attractive for direct imaging of Legionella pneumophila, without the need for a prior membrane permeabilization.

4-Acetamidophenol Binding Mechanism with DNA by UV-Vis and FTIR Techniques Based on Binding Energy, LUMO and HOMO Orbitals and Geometry of Molecule

Present study was conducted to appraise the interaction mechanism of 4-acetamidophenol (4-AP) with DNA based on UV-Vis and FTIR techniques based on binding energy, isolated atomic energy, LUMO and HOMO orbitals gap and geometry of molecule. Analysis revealed the groove binding and intercalation mode of interaction between 4-AP and DNA since hyperchromic and bathochromic shifts were observed in response of interaction of DNA. The planar part of interacting molecule intercalated with DNA and non-planar part of 4-acetamidophenol bounded with DNA (groove binding). The constants for binding between 4-AP and DNA were calculated and 20.12 × 103 mol−1 dm3 binding constant was recorded at pH 4.7, whereas this value was 5.32 × 103 mol−1 dm3 for the pH 7.4. The binding constant value for interaction of 4-AP with DNA revealed the possibility of oral administration of 4-AP. The 4-AP binding with DNA is spontaneous process, which was confirmed from negative value of free energy at room temperature. FTIR study revealed that C–H and C=C (aromatic) functional groups were involved in binding at pH 4.7 and C=O (amide) was involved in groove binding, whereas C–H (aromatic) was responsible for intercalation at pH 7.4 and C–H (alkaline) and C=O (amide) were responsible for groove binding at pH 4.7.

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

Thioxanthone and its derivatives are the most remarkable molecules due to their vast variety of application such as radiation curing that is, until using them as a therapeutic drug. Therefore, in this study it was intended to use 2-Thioxanthone acetic acid with and without NaCl in Tris HCl buffer solution (pH:7.0) to represent the interaction with ct-DNA. The UV-vis absorption spectra of TXCH₂COOH in the presence of ct-DNA showed hypochromism and the intrinstic binding constant (K_b) was determined as 6 × 10³ L mol^-1. The fluoresence intensity of TXCH₂COOH with ct-DNA clearly increased up to 101% which indicated that the fluorescence intensity was very sensitive to ct-DNA concentration. The binding constant (K) and the values of number of binding sites (n) and were calculated as 1.8 × 10³ L mol^-1 and 0.69, respectively. When the quenching constants (K_sv) of free TXCH₂COOH and TXCH₂COOH, which were bonded with ct-DNA were compared, slightly changed values of Ksv were seen. Moreover, displacement assay with Hoechst 33,258 and viscosity measurements in the presence and absence of NaCl salt also confirmed the binding mode which noted the electrostatic interaction following groove binding between TXCH₂COOH and ct-DNA. Last but not least, the salt effect was examined on ct-DNA binding with TXCH₂COOH. The results of the experiments indicated that the groove binding was strengthened by NaCl whereas in the high NaCl concentration, the binding ability of TXCH₂COOH to ct-DNA was inversely affected.

The efficacy assessments of alkylating drugs induced by nano-Fe3O4/CA for curing breast and hepatic cancer

A new method to evaluate the anticancer activity at the molecular level has been developed. In our assay, the interaction between alkylating anticancer drugs-Fe₃O₄/CA with DNA has been investigated for the Resonance Light Scattering (RLS) signal enhancement. Water-based nano-Fe₃O₄, as a probe, has the ability of good solubility, biodegradability and low bulk resistivity etc. The experimental results show that, the activity order of three kinds of drugs is Nimustine (ACNU)>Semustine (Me-CCNU)>Chlormethine (HN2), which is satisfied with the results of the cell apoptosis experiment and the IC₅₀ by MTT method. This assay is simple, sensitive and high efficient. And the theoretical basics for the development of new anticancer drugs as well as the assessments of their efficacy to cure breast and hepatic cancer have been provided.

Analytical approaches for clarification of DNA-double decker phthalocyanine binding mechanism: As an alternative anticancer chemotherapeutic

In the present study a novel water soluble double-decker phthalocyanine was synthesized and calf thymus DNA interaction of the synthesized double-decker phthalocyanine was investigated. 5-(3-pyridyl)-1,3,4-oxadiazole substituted phthalonitrile 1 was prepared by a nucleophilic displacement reaction of 4-nitrophthalonitrile with 5-(3-pyridyl)-1,3,4-oxadiazole-2-thiol. Lutetium(III) double-decker phthalocyanine 2 was prepared by cyclotetramerization of compound 1. Water soluble lutetium(III) double-decker phthalocyanine 3 was prepared with quaternarization of compound 2. The synthesized double-decker phthalocyanine and calf thymus DNA interaction was investigated with UV-vis titrimetric methods, gel electrophoresis, and viscosity measurements. The fluorometric ethidium bromide replacement assay was conducted to clarify the binding mode of water soluble double-decker phthalocyanine. The thermodynamic parameters for interaction, K, ΔG⁰, ΔH⁰ and ΔS⁰ were calculated between the temperature ranges of 25°C-75°C. To the best of our knowledge, this is the first study about a double-decker phthalocyanine and DNA interaction.

Fluorescent probes based on side-chain chlorinated benzo[a]phenoxazinium chlorides: Studies of interaction with DNA

The interaction of DNA with six water soluble benzo[a]phenoxazinium chlorides mono- or di-substituted with 3-chloropropyl groups at the O and N of 2- and 9-positions, along with methyl, hydroxyl and amine terminal groups at 5-positions, was investigated by photophysical techniques. The results indicated that almost all compounds intercalated in DNA base pairs at phosphate to dye ratio higher than 5. At lower values of this ratio, electrostatic binding mode with DNA was observed. Groove binding was detected mainly for the benzo[a]phenoxazinium dye with NH₂·HBr terminal. The set of six benzo[a]phenoxazinium chlorides proved successful to label the migrating DNA in agarose gel electrophoresis assays. These finding proves the ability of these benzo[a]phenoxazinium dyes to strongly interact with DNA.

Studies of the binding mode of TXNHCH2COOH with calf thymus DNA by spectroscopic methods

In this study, a thioxanthone derivative named 2-(9-oxo-9H-thioxanthen-2ylamino) acetic acid (TX-NHCH2COOH) was used to investigate small molecule and DNA binding interactions. Absorption and fluorescence emission spectroscopy were used and melting studies were used to explain the binding mode of TXNHCH2COOH-DNA. Intrinsic binding constant Kb TXNHCH2COOH was found 6×10(5)M(-1)from UV-Vis absorption spectroscopy. Fluorescence emmision intensity increased by adding ct-DNA to the TXNHCH2COOH and KI quenching experiments resulted with low Ksv value. Additionally, 3.7°C increase for Tm was observed. The observed quenching of EB and ct-DNA complex and increase viscosity values of ct-DNA by addition of TXNHCH2COOH was determined. All those results indicate that TXNHCH2COOH can intercalate into DNA base pairs. Fluorescence microscopy helped to display imaging of the TXNHCH2COOH-DNA solution.

A Quinacrine Analogue Selective Against Gastric Cancer Cells: Insight from Biochemical and Biophysical Studies

One of the earliest synthetic antimalarial drugs, quinacrine, was recently reported as interesting for the treatment of acute myeloid leukemia. Inspired by this and similar findings, we evaluated a set of quinacrine analogues against gastric (MKN-28), colon (Caco-2), and breast (MFC-7) cancer cell lines and one normal human fibroblast cell line (HFF-1). All the compounds, previously developed by us as dual-stage antimalarial leads, displayed antiproliferative activity, and one of the set stood out as selective toward the gastric cancer cell line, MKN-28. Interestingly, this compound was transported across an in vitro MKN-28 model cell line in low amounts, and approximately 80 % was trapped inside those cells. Nuclear targeting of the same compound and its interactions with calf thymus DNA were assessed through combined fluorescence microscopy, spectroscopy, and calorimetry studies, which provided evidence for the compound's ability to reach the nucleus and to interact with DNA.

Electrochemical monitoring of the interaction between Temozolamide and nucleic acids by using disposable pencil graphite electrodes

Temozolomide (TMZ) is an anticancer drug used for the treatment of adult brain tumour and skin cancer. The biomolecular interaction between TMZ and DNA was investigated for the first time in this study using disposable pencil graphite electrodes (PGEs) in combination with electrochemical techniques. The surface confined interactions between TMZ and different type of nucleic acids were performed. Before/after surface confined interaction process, the oxidation signals of TMZ, guanine and adenine were measured using differential pulse voltammetry (DPV) and PGE and accordingly, the changes at the oxidation signals were evaluated. The detection limit (DL) was also estimated based on the oxidation signal of TMZ. The interaction of TMZ with single stranded poly [A], poly [G], or double stranded poly [A]-poly[T] and poly [G]-poly[C] was also explored. Moreover, cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) techniques were utilized for detection the interaction between TMZ and DNA. The features of this single-use electrochemical sensor was discussed in comparison to other reports that were developed for TMZ detection.

Binding studies of terbutaline sulfate to calf thymus DNA using multispectroscopic and molecular docking techniques

The interaction of terbutaline sulfate (TS) with calf thymus DNA (ctDNA) were investigated by fluorescence quenching, UV-vis absorption, viscosity measurements, ionic strength effect, DNA melting experiments and molecular docking. The binding constants (Ka) of TS to ctDNA were determined as 4.92×10(4), 1.26×10(4) and 1.16×10(4) L mol(-1) at 17, 27 and 37 °C, respectively. Stern-Volmer plots suggested that the quenching of fluorescence of TS by ctDNA was a static quenching. The absorption spectra of TS with ctDNA revealed a slight blue shift and hyperchromic effect. The relative viscosity ctDNA was hardly changed by TS, and melting temperature varied slightly. For the system of TS-ctDNA, the intensity of fluorescence decreased with the increase of ionic strength. Also, the Ka for TS-double stranded DNA (dsDNA) was clearly weaker than that for TS-single stranded DNA (ssDNA). All these results revealed that the binding mode of TS with ctDNA should be groove binding. The enthalpy change and entropy change suggested that van der Waals force or hydrogen bonds was a main binding force between TS and ctDNA. Furthermore, the quantum yield of TS was measured by comparing with the standard solution. Based on the Förster energy transference theory (FRET), the binding distance between the acceptor and donor was calculated. Molecular docking showed that TS was a minor groove binder of ctDNA and preferentially bound to A-T rich regions.

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.

Electrochemical sensors based on multi-walled nanotubes for investigating the damage and action of 6-mercaptopurine on double-stranded DNA

Clear damage to dsDNA caused by 6-MP was observed. The damage to adenine was more severe than to guanine.

A monofunctional platinum(II)-based anticancer agent from a salicylanilide derivative: Synthesis, antiproliferative activity, and transcription inhibition

Cationic monofunctional platinum(II)-based anticancer agents with a general formula of cis-[Pt(NH3)2(N-donor)Cl](+) have recently drawn significant attention due to their unique mode of action, distinctive anticancer spectrum, and promising antitumor activity both in vitro and in vivo. Understanding the mechanism of action of novel monofunctional platinum compounds through rational drug design will aid in the further development of active agents. In this study, we synthesized and evaluated a monofunctional platinum-based anticancer agent SA-Pt containing a bulky salicylanilide moiety. The antiproliferative activity of SA-Pt was close to that of cisplatin. Mechanism studies revealed that SA-Pt entered HeLa cells more efficiently than cisplatin, blocked the cell cycle at the S-phase, and induced apoptosis. The compound bound to DNA as effectively as cisplatin, but did not block RNA polymerase II-mediated transcription as strongly as cisplatin, indicating that once the compound formed Pt-DNA lesions, the salicylanilide group was more easily recognized and removed. This study not only enriches the family of monofunctional platinum-based anticancer agents but also guides the design of more potent monofunctional platinum complexes.

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.

Strong inhibition of thioredoxin reductase by highly cytotoxic gold(I) complexes. DNA binding studies

Biological properties of a series of aminophosphine-thiolate gold(I) complexes [Au(SR)(PPh2NHpy)] [Ph2PNHpy=2-(diphenylphosphinoamino)pyridine; HSR=2-mercaptopyridine (2-HSpy) (3), 2-mercaptonicotinic acid (2-H2-mna) (4), 2-thiouracil (2-HTU) (5) or 2-thiocytosine (2-HTC) (6)] and [Au(SR){PPh2NH(Htrz)}] [Ph2PNH(Htrz)=3-(diphenylphosphinoamino)-1,2,4-triazole]; HSR=2-mercaptopyridine (2-HSpy) (7), 2-thiocytosine (2-HTC) (8) or 6-thioguanine (6-HTG) (9) have been studied. Their antitumor properties have been tested in vitro against two tumor human cell lines, HeLa (derived from cervical cancer) and MCF-7 (derived from breast cancer), using a metabolic activity test (3-(4,5-dimethyl-thiazol-2-yl)-2,5-diphenyl tetrazolium bromide, MTT). Some of them showed excellent cytotoxic activity. With the aim to obtain more information about the mechanisms of action of these derivatives, the interactions of complexes 3, 5, 7 and 9 with thioredoxin reductase in HeLa cells were studied. They showed a potent inhibition of thioredoxin reductase activity. In order to complete this study, interactions of the complexes with calf thymus (CT-) DNA and with different bacterial DNAs, namely the plasmid pEMBL9 and the promoter region of the furA (ferric uptake regulator A) gene from Anabaena sp. PCC 7120 were investigated. Although interactions of complexes with CT-DNA have been verified, none of them cause significant changes in its structure.

Study on the interaction between quinine sulfate and DNA by multiple spectral methods and their analytical applications

The interaction of quinine sulfate (QS) and DNA has been investigated by spectra methods including fluorescence spectroscopy and resonance light scattering (RLS) technique in aqueous solutions. The QS showed an obvious decrease of fluorescence intensity upon the addition of trace amounts of DNA, and the quenching mechanism was suggested to be static quenching according to the Stern-Volmer equation. Under the acidic condition of pH 2.5, the quenched fluorescence intensity of the QS-DNA system was linearly dependent on the concentration of ctDNA ranging from 0.02 to 2.5 mg/L. The interaction between QS and DNA as well as the detection of DNA was further confirmed by RLS technique, and the results showed that enhanced RLS intensity was linearly related to the concentration of ctDNA from 0.01 to 3.5 mg/L. Therefore, two spectral methods for the detection of ctDNA have been established with the use of a QS small molecular probe.