Groove Binding Mode Of Interaction Research Articles

Exploring the binding mechanism of Pomalidomide drug with CT-DNA: Insights from multi-spectroscopic, molecular docking and simulation studies

Exploration of the interaction of a thalidomide analogue immunomodulatory and anti-angiogenic drug pomalidomide (POD) with calf thymus DNA (CT-DNA) was carried out using multi-spectroscopic (UV–Vis, fluorescence, and circular dichroism), molecular docking and metadynamics simulation studies in Tris–HCl buffer (pH 7.4). The results revealed that POD binds to the nucleic acid via groove binding mode. The proposed binding mode is strongly supported by competitive dye displacement assay using ethidium bromide (EB) and rhodamine B (RB) dyes, KI quenching studies and viscosity measurements. The thermodynamic parameters such as ∆Ho (60 kJ mol−1), ∆So (297 JK−1 mol−1) and ∆Go (-22 kJ mol−1) indicated that the POD/CT-DNA interaction is spontaneous and is stabilized predominantly by hydrophobic forces. The proposed groove binding mode of interaction of POD with CT-DNA was further confirmed by a computer-aided molecular docking studies and analysis of free energy surface contour derived from the molecular simulation study.

Multi-spectroscopic, thermodynamic and molecular simulation studies on binding of pyrroloquinoline quinone with DNA: coexistence of intercalation and groove binding modes

The interaction between enzyme-like pyrroloquinoline quinone (PQQ) and calf-thymus DNA (CT-DNA) has been investigated by means of multi-spectroscopic (UV-Vis, fluorescence and circular dichroism), isothermal titration calorimetric (ITC), viscometry and molecular docking and metadynamics simulation techniques. Absorption spectral data suggested the formation of a PQQ/CT-DNA complex, which quenched the fluorescence of PQQ via the dynamic quenching process. The results of CD spectral studies coupled with viscosity measurements, competitive binding assays with Hoechst 33258 and ethidium bromide (EB), KI quenching experiments, gel electrophoresis and DNA melting studies indicated groove binding mode of interaction of PQQ with CT-DNA. ITC experiment revealed that the complex formation is a spontaneous process (ΔGo < 0) with a binding constant of 1.05 × 104 M−1. The observed ΔHo < 0 and ΔSo < 0 pointed out that the complex is stabilized by van der Waals forces along with H-bonding interactions. The outcomes of molecular docking and simulation studies confirmed the binding of PQQ with DNA. The free energy surface (FES) analysis pointed out the existence of an equilibrium between partial intercalation and groove binding modes, which is in good agreement with the competitive binding assays. Communicated by Ramaswamy H. Sarma

Synthesis and In vitro‐In silico Evaluation of Thiazolo‐triazole Hybrids as Anticancer Candidates

AbstractTo meet the growing need for stable and clinically effective chemotherapeutic agents, herein, we have synthesized a series of acyl‐functionalized thiazolo[3,2‐b]‐[1,2,4]triazole derivatives in highly efficient and regioselective manner. The structure of newly synthesized regioisomeric products was unambiguously characterized by multinuclear 2D‐NMR [(1H−13C) HMBC, (1H−13C) HMQC] spectroscopic data. To assess the anticancer and pharmacokinetic profile of the synthesized compounds, we performed in silico, and ex vivo binding studies of compounds with calf‐thymus deoxyribonucleic acid (ct‐DNA) and bovine serum albumin (BSA), respectively, and also tested their efficacy against five human cancer cell lines. viz., MCF‐7 (breast cancer), BT‐474 (breast cancer), A549 (lung cancer), MOLT4 (acute lymphoblastic leukemia), and BxPC3 (pancreatic cancer). Compounds (2‐(4‐chlorophenyl)‐6‐methylthiazolo[3,2‐b][1,2,4]triazol‐5‐yl)(4‐fluorophenyl)methanone 6 l, (4‐chlorophenyl)(2‐(4‐chlorophenyl)‐6‐methylthiazolo[3,2‐b][1,2,4]triazol‐5‐yl)methanone 6 m and (2‐(4‐chlorophenyl)‐6‐methylthiazolo[3,2‐b][1,2,4]triazol‐5‐yl)(4‐methoxyphenyl) methanone 6 q exhibited excellent anticancer potential among the screened derivatives. Furthermore, ex‐vivo mechanistic investigations showed the static mode of quenching and moderate bindings between the ligand and biomolecules; DNA (Kq=2.01‐2.24*1012 M−1 s−1) and BSA (Kq=2.25‐.2.72*1012 M−1 s−1). Moreover, fluorescence displacement assay demonstrated a groove binding mode of interaction with ct‐DNA, which was supported by UV‐Visible absorption spectrum, circular dichroism, and viscosity analysis.

Insight into the binding interactions of fluorenone-pendent Schiff base with calf thymus DNA

A novel fluorenone appended Schiff base (L) has been synthesized and utilized for studying the binding interactions with Calf Thymus DNA (ct-DNA). The mechanism of binding with ct-DNA was explored by employing various spectroscopic techniques viz. UV–Vis absorption spectroscopy, fluorescence emission spectroscopy, gel-electrophoresis, circular dichroism (CD), melting studies, viscosity arrays and molecular modeling methodology. The interpretation of UV–vis absorbance spectra pointed to binding of L within minor groove of ct-DNA with the binding constant of Kb = 0.15 × 104 M−1. Dye-displacement studies with Rhodamine-B (RhB) and Ethylene Bromide (EB) in fluorescence spectroscopy verified the groove binding mode of interaction between L and ct-DNA. Melting studies, circular dichroism, and viscosity studies further elucidated the binding modes of L with ct-DNA. Thermodynamic variable measurements taken at various temperatures such as ΔG⁰, ΔH⁰, and ΔS⁰ revealed that hydrophobic forces played a significant role in the binding process. The meticulous computational interaction demonstrated by molecular docking confirmed the minor groove binding of L with ct-DNA.

Cytotoxic activity of Ru(II)/DPEPhos/N,S-mercapto complexes (DPEPhos = bis-[(2-diphenylphosphino)phenyl]ether)

We report here on three new ruthenium(II) complexes, [Ru(DPEPhos)(mtz)(bipy)]PF6 (Ru1), [Ru(DPEPhos)(mmi)(bipy)]PF6 (Ru2) and [Ru(DPEPhos)(dmp)(bipy)]PF6 (Ru3). DPEPhos = bis-[(2-diphenylphosphino)phenyl]ether, mtz = 2-mercapto-2-thiazoline, mmi = 2-mercapto-1-methylimidazole, dmp = 4,6-diamino-2-mercaptopyrimidine and bipy = 2,2′-bipyridine. The compounds were characterized by several spectroscopic techniques, and the molecular structure of Ru1 complex was determined by single-crystal X-ray diffraction. The cytotoxicity of Ru1 – Ru3 complexes were tested against the A549 (human lung) and the MDA-MB-231 (human breast) cancer cell lines and against MRC-5 (non-tumor lung) and MCF-10A (non-tumor breast) cell lines through the MTT assay. All three complexes are cytotoxic against the cell lines studied, with IC50 values lower than those found for the cisplatin. Among them, the Ru2 complex has shown the best selectivity against MDA-MB-231 cancer cell lines, with an IC50 value 12 times lower than that on MCF-10A. The complex Ru2 was capable to induce changes in MDA-MB-231 cells morphology, with loss of cellular adhesion, inhibited colony formation and induce an accumulation of cells at the sub-G1 phase, with an increase in S-phase and decrease of cells at G2 phase. Viscosity, electrochemical and Hoechst 33258 displacement experiments for Ru1 – Ru3 complexes with calf thymus DNA (CT-DNA) showed an electrostatic and groove binding mode of interaction. Additionally, the complexes interact with the protein Human Serum Albumin (HSA) by static mechanism. The negative values for ΔH and ΔS indicate that van der Waals forces and hydrogen bonding may occurs between the complexes and HSA. Therefore, this class of complexes are promising anticancer candidates and may be selected to further detailed studies.

Elucidation of the interaction of apocarotenoids with calf thymus DNA by biophysical techniques and in vitro study in MCF-7 cells to explore their potential in cancer therapy.

DNA is one of the targets of cancer-therapeutic small molecules. Cisplatin, a DNA intercalator, is one of the first-line drugs in the cancer chemo regimen which comes with health-compromising side effects during chemotherapy. The synergistic effect of natural molecules with cisplatin can help to potentiate its anti-cancer efficacy and decrease its negative effect on health. Here, we report the interaction of cisplatin with calf thymus-DNA (ct-DNA) in combination with natural molecules like apocarotenoids which are reported for their therapeutic properties. The combinatorial effect of apocarotenoids on ct-DNA was explored through various biophysical techniques such as UV-Visible spectroscopy, circular dichroism studies, DNA melt curve analysis, viscosity measurements, and an in vitro study in MCF-7 cells by cell cycle analysis. UV-Visible spectroscopy studies suggest apocarotenoids and their combination shows a non-intercalative mode of binding. Circular dichroism analysis showed no major changes in DNA form during the interaction of DNA with apocarotenoids and their respective combinations with cisplatin, which is suggestive of the groove-binding mode of apocarotenoids. DNA melt curve analysis showed a decrease in the intensity of the fluorescence for apocarotenoids with cisplatin which indicates the possibility of DNA interaction through groove binding. Viscosity studies suggested a groove binding mode of interaction of ct-DNA with apocarotenoids and their combination as there was minimal change in the viscosity measurements. The in vitro analysis exhibits that the apocarotenoids and their combination have a considerable effect on DNA synthesis. This study provides a better perspective on the possible mode of interaction between ct-DNA and natural molecules along with cisplatin.

Imperative persistent interaction analysis of anticancer noscapine-ionic liquid with calf thymus DNA

In this study, we have shown the interaction between opium poppy alkaloid noscapine-based ionic liquid [Pip-Nos]OTf and ct-DNA using UV–visible absorption spectroscopy, fluorescence spectroscopy, CD, and computational studies. The absorption spectra showed a hypochromic shift with no shift in the absorption maxima suggesting groove or electrostatic binding. Fluorescence spectra showed an enhancement in fluorescence emission suggesting that the probable mode of binding should be groove binding. Ethidium bromide (EB) competitive and Ionic strength study showed the absence of intercalative and electrostatic modes of interaction. Further, CD analysis of ct-DNA suggested a groove binding mode of interaction of [Pip-Nos]OTf with ct-DNA. [Pip-Nos]OTf displayed a strong binding with the target ct-DNA with a molecular docking score of −41.47 kJ/mol with all 3D coordinates and full conformation. Also, molecular binding contact analyses depicted the stable binding of drug and ct-DNA with potential hydrogen bonds and hydrophobic interactions. The structural superimposition dynamics analysis showed the stable binding of [Pip-Nos]OTf with the ct-DNA model through RMSD statistics. Moreover, the ligand interaction calculations revealed the involvement of large binding energy along with a high static number of molecular forces including the hydrogen bonds and hydrophobic interactions in their complexation. These significant results report the potency of [Pip-Nos]OTf and its important futuristic role in cancer therapeutics.

Cytotoxic Ruthenium(II) Complexes Containing a Dangling Pyridine: Selectivity for Diseased Cells Mediated by pH-Dependent DNA Binding.

Ruthenium(II) complexes of the type [Ru(bpy)2(L1/L2/L3)]PF6 [where bpy = 2,2'-bipyridine, H(L1) = N-(pyrid-2-yl)salicylaldimine (1), H(L2) = N-(6-methylpyrid-2-yl)salicylaldimine (2), and H(L3) = N-(4,6-dimethylpyrid-2-yl)salicylaldimine (3)] have been isolated. The X-ray structures of 1-3 reveal distorted octahedral coordination geometry with a planar ruthenium phenolate moiety. They exhibit interpair dimeric association in their solid state such as (a) π-π-stacking interactions (1-3) and (b) C-H···π interactions (2). The 1H NMR spectral data shed light on the characteristics of metal-ligand bonding and chelate ring conformations. The complexes exhibit strong metal-to-ligand charge-transfer transitions in the visible region. The complexes also undergo two successive metal-based oxidative processes corresponding to the RuII/RuIII and RuIII/RuIV couples. Resonance Raman studies strongly suggest that the lowest unoccupied molecular orbital of 1-3 is localized at the bpy ligand. Absorption, emission, and circular dichroic spectral measurements for 1-3 with calf-thymus DNA reveal a groove binding mode of interaction. Interestingly, all of the complexes exhibit pH-dependent DNA damage, and the pH at which the damage is highest corresponds to the pH conditions of the cancer cells. The DNA damage is in the order of 3 > 2 > 1, in which a hydrolytic mechanism dominates. The protein binding properties of the complexes examined by the tryptophan quenching measurements suggest a static mechanism. The positive ΔH and ΔS values indicate that the force acting between the complexes and bovine serum albumin (BSA) is mainly a hydrophobic interaction, and thus BSA may act as a targeted drug-delivery vehicle for ruthenium(II) complexes (K ∼ 105). It is noteworthy that 3 exhibits selectivity with high cytotoxicity against breast cancer cells (EVSA-T and MCF-7), and its potency is comparable to that of cisplatin.

Synthesis of 4-((4-(4-nitrophenoxy)phenyl)diazenyl)benzene-1,3-benzoate:Experimental, DFT and, DNA binding investigation through spectral and molecular docking studies

Pharmacists and other researchers have always been fascinated by the DNA sensing evaluation. This piece of work emphasizes on the synthesis, characterization and DNA sensing of a novel azo ester (N = N, -COO) molecule. The product (1A) was synthesized employing a typical esterification reaction between previously reported resorcinol coupled azo dye and Benzoyl chloride. The structural interpretation of the synthesized ester was done by FT-IR (Fourier transform infrared), NMR (Nuclear magnetic resonance), UV/VIS (ultraviolet–visible spectroscopy), and single crystal X-ray diffraction studies. XRD analysis elucidated the Ester 1A to be in the Monoclinic system with P21/n space group. The DFT simulation experiments were also examined to investigate the structural implications of the resulting product. The higher softness (S), electrophilicity index (ω) and electronegativity (χ) values demonstrated greater polarizability and reactive nature of the compound. Further, wet and silico binding methods were employed to examine the DNA sensing ability of the synthesized molecule with SS-DNA. UV/VIS spectroscopy and hydrodynamic measurements (Viscosity) suggested Groove binding mode of interaction with a moderate value of binding constant, which was further confirmed by molecular docking techniques.

Design, synthesis, ligand’s scaffold variation and structure elucidation of Cu(II) complexes; In vitro DNA binding, morphological studies and their anticancer activity

Two new copper(II) complexes, Cu[(L)2(X)] (1) and Cu[(L)(X)2] (2) where L = 1,10-phenanthroline and X = (2-pyrimidylthio)-acetic acid (PTAA), have been synthesized and characterized utilizing physico-chemical techniques and single X-ray crystallography. Various techniques, like absorption, emission and CD spectroscopy, CV and SEM, were applied to explore drug-DNA interactions and their collaborative results revealed an electrostatic or groove binding mode of interaction of both drug candidates with ct-DNA. In addition, pBR322 cleavage activities were carried out which suggested significant oxidative cleavage with complex 1 compared to complex 2. Moreover, in vitro cytotoxic studies of complexes 1 and 2 were performed by an SRB assay against MCF-7, MDA-MB-231 and Hop-62 cancer cell lines. Both complexes showed good cytotoxic activity against all the cancer cell lines, with GI50 values < 10 μM. Interestingly, complex 1 exhibited a more efficient cytotoxic activity against MDA-MB-231 and HOP-62, even greater than that of the standard drug Adriamycin. Additionally, molecular docking studies were carried out which gave results that are in good agreement with the spectroscopic results. Furthermore, DFT calculations were performed and electrostatic maps were generated to shed light on the stability, charge density and reactivity of these complexes.

Concentration-dependent mode of binding of drug oxatomide with DNA: multi-spectroscopic, voltammetric and metadynamics simulation analysis

The interaction between antihistaminic drug oxatomide (OXT) and calf-thymus DNA (CT-DNA) has been investigated in a physiological buffer (pH 7.4) using UV–Vis, fluorescence, 1H NMR and circular dichroism spectral techniques coupled with viscosity measurements, KI quenching, voltammetry and in silico molecular modeling studies. OXT binds with CT-DNA in a concentration-dependent manner. At a lower [Drug]/[CT-DNA] molar ratio (0.6–0.1), OXT intercalates into the base pairs of CT-DNA, while at a higher [Drug]/[CT-DNA] molar ratio (13–6), the drug binds in the minor grooves of CT-DNA. The binding constants for the interaction are found to be in the order of 103–105 M−1, and the groove binding mode of interaction exhibits a slightly higher binding constant than that of intercalative mode. Thermodynamic analysis of binding constants at three different temperatures suggests that both these modes of binding are mainly driven by hydrophobic interactions (ΔH o > 0 and ΔS o > 0). Voltammetric investigations indicate that the electro-reduction of OXT is an adsorption controlled process and shifts in reduction peak potentials reiterate the concentration-dependent mode of binding of the drug with CT-DNA. The free energy landscape obtained at the all-atom level, using metadynamics simulation studies, revealed two major binding forces: partial intercalation and minor groove binding, which corroborate well with the experimental results. Communicated by Ramaswamy H. Sarma

Spectroscopic Studies on the Interaction of Naphthyridines with DNA and Fluorescent Detection of DNA in Agarose Gel.

Four new naphthyridine derivatives (R1-R4) possessing amino acid or boronic acid moieties have been synthesized and characterized using 1H and 13C NMR, FT-IR, and mass spectral techniques. The mechanism of binding of these probes with calf thymus DNA (CT-DNA) has been delineated through UV-Vis, fluorescence, and circular dichroism (CD) spectral techniques along with thermodynamic and molecular docking studies. Small hypochromicity in absorption maximum of the probes without any shift in wavelength of absorption suggests groove binding mode of interaction of these probes with CT-DNA, confirmed by CD and 1H NMR spectral data competitive binding assay with ethidium bromide (EB). CT-DNA quenches the fluorescence of these probes via a static quenching mechanism. In the case of R1 and R4, the observed ΔHo < 0 and ΔSo > 0suggest that these probes interact with CT-DNA through H-bonding and hydrophobic interactions, while in the interaction of R2 and R3, van der Walls and H-boding forces are found to be dominant (ΔHo < 0 and ΔSo < 0). Results of molecular docking investigations corroborate well with that of spectral studies, and these probes bind in the minor groove of DNA. These probes are found to be effective fluorescent staining agents for DNA in agarose gel in gel electrophoresis experiment with sensitivity comparable to that of EB, and DNA amounts as low as 37.5ng are visually detectable in the gel.

From groove binding to intercalation: unravelling the weak interactions and other factors modulating the modes of interaction between methylated phenanthroline-based drugs and duplex DNA.

Several antitumor drugs base their cytotoxicity on their capacity to intercalate between base pairs of DNA. Nevertheless, it has been established that the mechanism of intercalation of drugs in DNA starts with the prior groove binding mode of interaction of the drug with DNA. Sometimes, for some kind of flat small molecules, groove binding does not produce any cytotoxic effect and the fast transition of such flat small molecules to the cytotoxic intercalation mode is desirable. This is the case of methylated phenanthroline (phen) derivatives, where, changes in the substitution in the position and number of methyl groups determine their capability as cytotoxic compounds and, therefore, it is a way for the modulation of cytotoxic effects. In this work, we studied this modulation by means of the interaction of the [Pt(en)(phen)]2+ complex and several derivatives by methylation of phen in different number and position and the d(GTCGAC)2 DNA hexamer via groove binding using PM6-DH2 and DFT-D methods. The analysis of the geometries, electronic structure and energetics of the studied systems was compared to experimental works to gain insight into the relation structure-interaction for the studied systems with cytotoxicity. The trends are explained by means of the Non-Covalent Interaction (NCI) index, the Energy Decomposition Analysis (EDA) and solvation contributions. Our results are in agreement with the experiments, in which the methylation of position 4 of phen seems to favour the interaction via groove binding thus making the transition to the intercalation cytotoxic mode difficult. Looking at the NCI results, these interactions come not only from the CH/π and CH/n interactions of the methyl group in position 4 but also from the ethylenediamine (en) ligand, whose orientation in the Pt complex was found in such a way that it produces a high number of weak interactions with DNA, especially with the sugar and phosphate backbone.

Binding behaviour of aminoglycoside drug kanamycin with calf thymus DNA: Thermodynamic, spectroscopic and molecular modelling studies

In this work, the binding mode of antibiotic drug kanamycin with Calf thymus DNA (ctDNA) was assessed using thermodynamic, spectroscopic and molecular docking studies. Isothermal Titration Calorimetry (ITC) studies suggest that the binding is enthalpically favored with a small entropic change and a binding constant of the order of 104 mol−1 dm3, which remains almost same in the studied temperature range. Studies in the presence of osmolytes tetraethylene glycol and sucrose show no appreciable change in the binding behaviour as well as on the stability of the DNA-kanamycin complex. These finding suggests that the number of water molecule released or taken up is not significant in the binding process. Competitive fluorescence displacement assay and circular dichroism studies show that kanamycin follows groove binding mode of interaction. Molecular docking studies also supports that kanamycin prefers groove binding mode, stabilized by hydrogen bonding.

Design, synthesis, DNA binding studies and evaluation of anticancer potential of novel substituted biscarbazole derivatives against human glioma U87 MG cell line.

In this research paper, we report the design and synthesis of novel substituted biscarbazole derivatives which were characterized by 1H and 13C NMR, high resolution mass spectroscopy (HRMS). The SAR study of the compounds is reported based on different substituents and their positions in the biscarbazole scaffold. In vitro cytotoxicity of the compounds was evaluated against human glioma U87 MG cell line by MTT assay for 24h. The IC50 values of the compounds (30-35, 48-53 and 54-62) were calculated at the concentration range from 1.00µM to 500µM. The compound 34 showed the most significant in vitro cytotoxicity (IC50=3.9µM) against human glioma U87 MG cell line and was found to be better than standard drugs used for the treatment of brain tumors such as temozolomide (IC50=100µM) and carmustine (IC50=18.2µM) respectively. To determine the mode of binding of compound 34 with CT-DNA, various biophysical techniques like UV-spectrophotometer, fluorescence, circular dichroism, viscosity, topoisomerase assay and molecular docking analysis, were used. Our results demonstrated groove binding mode of interaction of the compound 34 with CT-DNA with a plausible static bio-molecular quenching rate constant (Kq) 1.7×1012 M-1s-1. The studies of biscarbazole derivatives are anticipated to develop potential novel anticancer agents against brain tumors.

Multi-spectroscopic, voltammetric and molecular docking studies on binding of anti-diabetic drug rosigiltazone with DNA.

The binding of an anti-diabetic drug rosiglitazone (RG) with calf-thymus DNA (CT-DNA) in physiological buffer (pH7.4) has been investigated using various spectral techniques such as UV-Vis, fluorescence, 1H NMR and circular dichroism (CD) coupled with viscosity measurement and molecular docking studies. The binding of RG with CT-DNA results in small hypochromism without any change in absorption maximum and fluorescence quenching with hardly any shifts in emission maximum suggesting groove binding mode of interaction. The binding constant is found to be 4.2×102 M-1 at 298K. Thermodynamic analysis reveal that the binding is spontaneous and H-bonding and van der Waals forces play predominant role in the binding of RG with CT-DNA. Competitive interaction between RG and ethidium bromide with CT-DNA, viscosity measurements, KI quenching, 1H NMR and CD studies substantiate the prosed mode of binding. Voltammetric investigations suggest that the electro-reduction of RG is an adsorption controlled process and shift of reduction peak to more negative potential, with a binding constant of 3.4×103 M-1, validates the groove binding mode of interaction between RG and CT-DNA. Molecular docking reveals that RG binds in the minor groove of DNA and the dominating interaction forces are H-bonding and hydrophobic interactions.

Synthesis, characterization, docking and electrochemical studies of nitroaromatic amides

A series of N-[4-(Nitrophenoxy)phenyl]alkanamides (N-1 to N-14) with different alky groups were synthesized following two-step procedures. The structural elucidation of the synthesized compounds was carried out by IR and NMR spectroscopic techniques along with elemental and single crystal X-ray diffraction analyses. Molecular docking study (drug-DNA binding) was carried out to check their biological potential. The docking data revealed the interaction of compounds with ds. DNA, which was further complemented by cyclic voltammetric study. The synthesized compounds showed minor groove binding mode of interaction with DNA. The increased chain length of alkyl groups did not significantly affected the compound-DNA binding.

Binding Studies of Isoxsuprine Hydrochloride to Calf Thymus DNA Using Multispectroscopic and Molecular Docking Techniques.

In the present work, the interaction of Isoxsuprine (ISX) with Calf thymus DNA (ct-DNA) under physiological conditions (Tris-HCl buffer of pH 7.4) was investigated by using electronic absorption, circular dichroism, viscosity, electrochemical studies, fluorescence techniques, salt effect studies and computational studies. Competitive fluorimetric studies with Hoechst 33258 have shown that ISX exhibit the ability to displace the DNA-bound Hoechst 33258, indicating that it binds to ct-DNA in strong competition with Hoechst 33258 for the minor groove binding. Furthermore, the resulting data showed that ISX cannot displace methylene blue or acridine orange, which are the common intercalator molecules. The viscosity of ct-DNA solution was almost unchanged on addition of ISX and circular dichroism (CD) spectra of ct-DNA showed small changes in the presence of ISX which is in agreement with groove binding mode of interaction. Thus all above studies showed that the ISX drug binds to ct-DNA in a groove binding mode.The salt-effect studies showed the non-electrostatic nature of binding of ISX to ct-DNA. Moreover, molecular docking results support the above experimental data and suggest that ISX prefers to bind on the minor groove of ct-DNA.

Synthesis and bioelectrochemical behavior of aromatic amines

Four aromatic amines 1-amino-4-phenoxybenzene (A1), 4-(4-aminophenyloxy) biphenyl (A2), 1-(4-aminophenoxy) naphthalene (A3) and 2-(4-aminophenoxy) naphthalene (A4) were synthesized and characterized by elemental, spectroscopic (FTIR, NMR), mass spectrometric and single crystal X-ray diffraction methods. The compounds crystallized in monoclinic crystal system with space group P21. Intermolecular hydrogen bonds were observed between the amine group and amine/ether acceptors of neighboring molecules. Electrochemical investigations were done using cyclic voltammetry (CV), square wave voltammetry (SWV) and differential pulse voltammetry (DPV). CV studies showed that oxidation of aromatic amines takes place at about 0.9 V (vs. Ag/AgCl) and the electron transfer (ET) process has irreversible nature. After first scan reactive intermediate were generated electrochemically and some other cathodic and anodic peaks also appeared in the succeeding scans. DPV study revealed that ET process is accompanied by one electron. DNA binding study of aromatic amines was performed by CV and UV–visible spectroscopy. These investigations revealed groove binding mode of interaction of aromatic amines with DNA.

Experimental and Computational Evidence on the Interaction of Cycloalkyl α-Aminobisphosphonates with Calf Thymus DNA

Fluorescence spectroscopy, ultraviolet-visible absorption spectroscopy, circular dichroism spectroscopy, viscometry, cyclic voltammetry, and differential pulse voltammetry were applied to investigate the competitive interaction of DNA with the three new cycloalkyl α-aminobisphosphonates (D1-D3) and spectroscopic probe, neutral red dye, and Hoechst (HO), in a Tris-hydrogen chloride buffer (pH 7.4). The spectroscopic and voltammetric studies showed that the groove binding mode of interaction is predominant in the solution containing DNA and α-aminobisphosphonates. Furthermore, the results indicated that α-aminobisphosphonate with the lengthy N alkyl chains and larger heterocyclic ring size had a stronger interaction. The principal component analysis and theoretical quantum mechanical and molecular mechanics (QM-DFT B3LYP/6-31+G* and MM-SYBYL) methods were also applied to determine the number of chemical components presented in complexation equilibrium and identify the structure complexes of DNA with the three new cycloalkyl α-aminobisphosphonates (D1-D3), respectively.