Effect of spermine conjugation on the interaction of acridine with alternating purine-pyrimidine oligodeoxyribonucleotides studied by CD, fluorescence and absorption spectroscopies

Synthesis and Photophysics of Water-Soluble Psoralens with Red-Shifted Absorption

8-Methoxypsoralen (8-MOP) serves as a PUVA (psoralen + UV-A) agent in the treatment of certain skin diseases. Derivatives of 8-MOP with cationic aromatic substituents at the five positions were synthesized and characterized by steady-state, femtosecond and nanosecond spectroscopy as well as cyclic voltammetry. The aromatic substituents' positive charge increases the water solubility and the affinity toward intercalation into DNA. The aromatic substituents were supposed to lower the psoralen S₁ energy and thereby suppress a photo-induced electron transfer (PET) with guanine-bearing DNA. Such a suppression of this PET is expected to increase the propensity of psoralens to photo-addition to DNA. For derivatives bearing methylpyridinium residues, femtosecond spectroscopy revealed an intramolecular PET occurring on the picosecond time scale. This PET precludes the population of the triplet state. As triplet states are the precursor state for the photo-addition to DNA, their intermolecular PET renders these derivatives ineffective in terms of PUVA. For two derivatives bearing trimethylphenylammonium moieties, such an intramolecular PET does not occur and the triplet state is populated. Surprisingly, these compounds also exhibit no PUVA activity. Based on these findings, implications for further optimization of PUVA agents are discussed.

Bacterial rRNA A-site recognition by DAPI: Signatures of intercalative binding

The bacterial A-site RNA is one of the key targets towards the development of new antibacterials including new treatment options for tuberculosis. Using DAPI as a prototype, we have explored the potential of bisamidines as a potential chemical motif for bacterial A-site recognition. We have demonstrated that the binding of DAPI shows a concentration-dependent thermal stabilization of the bacterial A-site RNA (ΔT_m = 9.9 °C). The binding, however, does not show pH-dependent changes upon lowering of pH. Both UV-vis and CD experiments show that the DAPI binding involves base stacking with the RNA bases in a manner that is analogous to intercalation. Scatchard analysis of the UV-vis titration data revealed a micromolar affinity of the DAPI to the bacterial rRNA A-Site (K_a = 1.14 × 10⁶ M^-1) which was corroborated by the FID-based relative binding affinity comparison with aminoglycosides. The molecular docking studies showed binding poses consistent with polar and stacking interactions with the RNA. These studies highlight the role of amidines in bacterial A-site recognition and the need for the development of their structural analogs towards the making of aminoglycoside mimics.

Binding interaction of N-acetylated acridine conjugate with ct-DNA and β-cyclodextrin: Synthesis and photophysical studies

In the present work we are reporting the synthesis and binding interaction of a saturated fatty acid containing 9-aminoacridine derivative (AC-PA) with ct-DNA and β-cyclodextrin (β-CD). From Steady-state fluorescence experiments this newly synthesized 9-aminoacridine derivative, AC-PA, shows more efficient binding interaction with ct-DNA as compared to the 9-aminoacridine (AC). The extent of interaction of AC-PA and AC with ct-DNA was found out by calculating the fluorescence quenching by using Stern-Volmer quenching equation. The calculated quenching constants of AC-PA and AC are (4.5 ± 0.5) × 10³M^-1 (3.7 ± 0.5) × 10³M^-1 respectively. The mechanism of fluorescence quenching of AC-PA and AC, were understand by using Stern-Volmer plots as well as time-resolved fluorescence experiments. The fluorescence quenching of AC-PA and AC by ct-DNA are static in nature and take place by formation of ground state complexes. The binding mode between AC-PA and AC were understood by DNA melting analysis experiment. The DNA melting analysis experiments were reveals that the binding interactions between fluorophores (AC-PA and AC) with ct-DNA are intercalative in nature. The melting temperature and mode of binding intercalative mode of binding between AC-PA and AC were further confirmed by DSC and CD experiments. The steady-state and time-resolved fluorescence parameters of AC-PA are quite sensitive towards the formation of inclusion complexes between AC-PA and β-CD. Long hydrophobic tail containing acridine conjugate (AC-PA) shows more efficient binding interactions with the β-CD and the calculated binding constants value of AC-PA is 0.51 × 10²M^-1. Whereas, the parent molecule, AC not showing any binding interactions with β-CD.

Synthesis and characterisation of arsenic nanoparticles and its interaction with DNA and cytotoxic potential on breast cancer cells

Therapeutic applications of arsenic trioxide (ATO) are limited due to their severe adverse effects. However, nanoparticles of ATO might possess inimitable biologic effects based on their structure and size which differ from their parent molecules. Based on this conception, AsNPs were synthesized from ATO and comparatively analysed for their interaction mechanism with DNA using spectroscopic & electrochemical techniques. Finally, anti-proliferative activity was assessed against different breast cancer cells (MDA-MB-231 & MCF-7) and normal non-cancerous cells (HEK-293). The DNA interaction study revealed that AsNPs and ATO exhibit binding constant values in the order of 10⁶ which indicates strong binding interaction. Binding of AsNPs did not disturb the structural integrity of DNA, on the other hand an opposing effect was observed with ATO through biophysical techniques. Further, in vitro study, confirms cytotoxicity of ATO and AsNPs against different cells, however at particular concentration ATO exhibits more cytotoxicity than that of AsNPs. Furthermore, cytotoxicity was confirmed through acridine orange and comet assay. In conclusion, AsNPs are safer than ATO with comparable efficacy and might be a suitable candidate for the development of novel therapeutic agent against breast cancer and other solid tumours.

Interaction studies between biosynthesized silver nanoparticle with calf thymus DNA and cytotoxicity of silver nanoparticles

The interaction of calf thymus DNA (CTDNA) with silver nanoparticles (SNP) has been investigated following spectroscopic studies, analysis of melting temperature (Tm) curves and hydrodynamic measurement. In spectrophotometric titration and thermal denaturation studies of CTDNA it was found that SNP can form a complex with double-helical DNA and the increasing value of Tm also supported the same. The association constant of SNP with DNA from UV-Vis study was found to be 4.1×10(3) L/mol. The fluorescence emission spectra of intercalated ethidium bromide (EB) with increasing concentration of SNP represented a significant reduction of EB intensity and quenching of EB fluorescence. The results of circular dichroism (CD) suggested that SNP can change the conformation of DNA. From spectroscopic, hydrodynamic, and DNA melting studies, SNP has been found to be a DNA groove binder possessing partial intercalating property. Cell cytotoxicity of SNP was compared with that of normal silver salt solution on HeLa cells. Our results show that SNP has less cytotoxicity compared to its normal salt solution and good cell staining property.

Synthesis, characterization, and cytotoxicity studies of a novel palladium(II) complex and evaluation of DNA-binding aspects

A new water-soluble palladium(II) complex, [Pd(bpy)(pyr-Ac]NO₃ in which bpy = 2,2'-bipyridine and pyr-Ac is 1-pyrrolacetato, has been synthesized and characterized by spectroscopic methods (¹H NMR, FT-IR, and UV-Vis), molar conductivity measurements, and elemental analysis. The results obtained from elemental analysis and conductivity measurements confirmed the stoichiometry of ligand and its complex while the characteristic peaks in UV-Vis and FT-IR and resonance peaks in (¹H NMR spectra confirmed the formation of ligand frameworks around the palladium ion. The 50% cytotoxic concentration (Ic₅₀) of new synthesized Pd(II) complex was determined by using MTT assay against human breast cancer cell line, T47D. The interaction between the Pd(II) complex with calf thymus DNA was studied at different temperatures by using absorption spectroscopy, fluorescence titration spectra, ethidium bromide displacement, and gel chromatography studies. The results obtained by absorption spectroscopy revealed that the Pd(II) complex can bind to DNA cooperatively at low concentrations. Several binding parameters in the above interaction were calculated by the fluorescence quenching method. The quenching mechanism was suggested to be the static quenching. The thermodynamic parameters: enthalpy change (ΔH °), entropy change (ΔS °), and Gibbs free energy (ΔG °), showed that van der Waals and hydrogen binding are predominant intermolecular forces between Pd(II) complex and DNA. These results were also consistent with the results obtained from Scatchard's plots.

A novel CUG(exp)·MBNL1 inhibitor with therapeutic potential for myotonic dystrophy type 1

Myotonic dystrophy type 1 (DM1) is caused by an expanded CUG repeat (CUG(exp)) that sequesters muscleblind-like 1 protein (MBNL1), a protein that regulates alternative splicing. CUG(exp) RNA is a validated drug target for this currently untreatable disease. Herein, we develop a bioactive small molecule (1) that targets CUG(exp) RNA and is able to inhibit the CUG(exp)·MBNL1 interaction in cells that model DM1. The core of this small molecule is based on ligand 2, which was previously reported to be active in an in vitro assay. A polyamine-derivative side chain was conjugated to this core to make it aqueous-soluble and cell-penetrable. In a DM1 cell model this conjugate was found to disperse CUG(exp) ribonuclear foci, release MBNL1, and partially reverse the mis-splicing of the insulin receptor pre-mRNA. Direct evidence for ribonuclear foci dispersion by this ligand was obtained in a live DM1 cell model using time-lapse confocal microscopy.

DNA binding acridine-thiazolidinone agents affecting intracellular glutathione

Three new acridine-thiazolidinone derivatives (2a-2c) have been synthesized and their interactions with calf thymus DNA and a number of cell lines (leukemic cells HL-60 and L1210 and human epithelial ovarian cancer cell lines A2780) were studied. The compounds 2a-2c possessed high affinity to calf thymus DNA and their binding constants determined by spectrofluorimetry were in the range of 1.37 × 10(6)-5.89 × 10(6) M(-1). All of the tested derivatives displayed strong cytotoxic activity in vitro, the highest activity in cytotoxic tests was found for 2c with IC(50) = 1.3 ± 0.2 μM (HL-60), 3.1 ± 0.4 μM (L1210), and 7.7 ± 0.5 μM (A2780) after 72 h incubation. The cancer cells accumulated acridine derivatives very fast and the changes of the glutathione level were confirmed. The compounds inhibited proliferation of the cells and induced an arrest of the cell cycle and cell death. Their influence upon cells was associated with their reactivity towards thiols and DNA binding activity.

Interaction studies between a 1,10-phenanthroline adduct of palladium(II) dithiocarbamate anti-tumor complex and calf thymus DNA. A synthesis spectral and in-vitro study

The interaction of calf thymus DNA (CT-DNA) with a novel synthesized and characterized Palladium (II) complex with the formula of [Pd (Et-dtc) (phen)] NO(3) (where phen is 1,10-phenanthroline and Et-dtc is ethyldithiocarbamate) was extensively studied by various spectroscopic techniques. UV-vis studies imply that there is a set of 6 binding sites for the complex on DNA with positive cooperativity in the binding process. This complex unexpectedly denatures the DNA at very low concentration (approximately 9.8 microM). Gel filtration studies indicate that the binding of metal complex with DNA is strong enough not to readily break. Fluorescence studies show that the palladium complex intercalates in DNA through the planar 1,10-phenanthroline ligand presented in its structure. Several binding and thermodynamic parameters are also described. Furthermore, anti-tumor studies of this water soluble complex against human cell tumor lines (K562) have been done. It shows 50% cytotoxic concentration (Ic(50)) value much lower than that of cisplatin.

Diimine platinum(II) and palladium(II) complexes of dithiocarbamate derivative as potential antitumor agents: synthesis, characterization, cytotoxicity, and detail dna-binding studies

The synthesis and chemical characterization of two structurally related platinum(II) and palladium(II) complexes, [M(2,2'-bipyridine)(morpholinedithiocarbamate)]NO(3) or [M(bpy)(mor-dtc)]NO(3), where M = Pt(II) or Pd(II), are described. Studies of anti-tumor activities of these complexes against human cell tumor lines (K(562)) have been carried out. They show 50% cytotoxic concentration (Cc(50)) values much lower than that of cisplatin. Both of these water soluble complexes have been shown to interact with calf thymus DNA (ct-DNA) using difference absorption-, fluorescence-, and circular dichroism-titration techniques. These studies showed that both complexes exhibit cooperative binding and presumably intercalate in DNA. These complexes unexpectedly denature DNA at very low concentrations (50-100 microM). Several binding and thermodynamic parameters are also described.

2,2'-Bipyridinebutyldithiocarbamatoplatinum(II) and palladium(II) complexes: synthesis, characterization, cytotoxicity, and rich DNA-binding studies

Butyldithiocarbamate sodium salt (Bu-dtcNa) and its two complexes, [M(bpy)(Bu-dtc)]NO3 (M=Pt(II) or Pd(II) and bpy=2,2'-bipyridine), have been synthesized and characterized on the basis of elemental analysis, molar conductivities, IR, 1H NMR, and UV-vis spectra. In these complexes, the dithiocarbamato ligand coordinates to Pt(II) or Pd(II) center as bidentate with two sulfur atoms. These complexes show 50% cytotoxic concentration (Cc(50)) values against chronic myelogenous leukemia cell line, K562, much lower than that of cisplatin. The interaction of these complexes with calf thymus DNA was extensively investigated by a variety of spectroscopic techniques. These studies showed that both complexes presumably intercalate in DNA. UV-vis studies imply that they cooperatively bind with DNA and unexpectedly denature the DNA at very low concentrations (approximately 100 microL). Palladium complex breaks the DNA into two unequal fragments and binds stronger to the lighter fragment than to the heavier one. In the interaction studies between the Pt(II) and Pd(II) complexes with DNA, several binding and thermodynamic parameters have been determined, which may provide deeper insights into the mechanism of action of these types of complexes with nucleic acids.