Preparation,characterizations and biological evaluations of new copper(II) complexes containing ONO pincer type ligands

A new heterocyclic Schiff bases, 6‐methyl/8methyl‐2‐oxo‐1,2‐dihydroquinoline‐3‐carboxaldehyde semicarbazones (H₂‐6MOQsc‐H) ( H ₂ L ¹ ) and (H₂‐8MOQsc‐H) ( H ₂ L ² ) and their corresponding copper(II) complexes [CuCl₂(H₂‐6MOQsc‐H)].3H₂O ( 1 ), [CuCl₂(H₂‐8MOQsc‐H)].3H₂O ( 2 ), [CuNO₃(H₂‐6MOQsc‐H)(H₂O)].NO₃ ( 3 ) and [CuNO₃(H₂‐8MOQsc‐H)(H₂O)].NO₃ ( 4 ) have been synthesized and characterized by various physicochemical techniques. The single crystal X‐ray diffraction and spectral data revealed that all of the complexes ( 1‐4 ), the ligands coordinated to the Cu(II) ion in a neutral manner via ONO donor atoms and all the complexes exhibited distorted squarepyramidal geometry. The consequence of electronegativity and ring size of nitrogen heterocyclic moiety of ONO donor type of copper(II) chelates on nucleic acid interaction and albumin binding was investigated by in vitro experiments. The interaction of compounds with calf‐thymus DNA (CT‐DNA) has been explored by absorption and emission titration, which exposed those ligands/complexes, could bind with CT‐DNA through electrostatic interaction. The results of gel electrophoresis proved the ability of complexes ( 1‐4 ) to cleave the pBR322 plasmid DNA. The interaction of serum albumin (BSA) was investigated by UV‐Vis, fluorescence, synchronous and three dimensional fluorescence spectra. In addition, radical scavenging activity, antifungal activity and cytotoxicity of the newly synthesized compounds were also evaluated. From the results of in vitro studies, it is seen that complex 3 has more potential as compared with other complexes and ligands.     

Interaction of Cationic Manganese Porphyrins with DNA. A Binding Model

The DNA cleavage properties of two cationic manganese porphyrins possessing different peripheral substituents were compared. The identical nature of the strand scission patterns of the porphyrins on a 139 base pair restriction fragment of pBR-322 DNA, along with other evidence, suggests that the porphyrin is end-on bound via the minor groove in a melted or partially melted region of DNA. This unusual binding mode underscores the potential of outisde binding cationic metalloporphyrins as probes for low melting regions of DNA     

Spectroscopic and Binding Properties of Berberine to DNA and Its Application to DNA Detection

Berberine(BER) binds to the double helical DNA with a high affinity There is only a much smaller hypochromism and no shifts in the absorption spectra when BER binds to calf thymus DNA(CT DNA) The fluorescence yields increase dramatically when BER binds to DNA, with no shifts in the emission maximum. These spectral changes are in contrast to the behavior observed with many fluorescent intercalates Groove binding rather than intercalation was suggested to be the cause of these spectral changes. Consistent with groove binding, for polyamide anion quenching studies showed that the magnitude of K_sv of the bound BER was higher than that of the free BER. The addition of salt to the solution releases the DNA-bound drug action from the groove and causes a decrease in the fluorescence yield. The results of all above studies proved the groove binding of BER to DNA. The large fluorescence enhancements observed when BER binds to DNA and the poor fluorescence yield of BER in the absence of DNA can be used for sensitive detection of DNA The linear concentration range was 0–20μg/ml The limit of detection for CT DNA was 12 ng/ml     

Influence of the size and geometry of the anion binding pocket of sugar–urea anion receptors on chiral recognition

Three new chiral urea-type anion receptors were synthesized from aromatic diamines and 1-amino-1-deoxyglucose. The anion binding properties of these receptors were studied using chiral carboxylates derived from mandelic acid and three α-amino acids. We found that the size of the anion binding pocket played an important role in chiral recognition processes. The best results were obtained for 1,8-diaminoanthracene and α-amino acid anions.     

Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package

Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations are key tools in both improving our understanding of a wide variety of biological processes and accelerating the design and optimization of therapeutics for numerous diseases. Computing power and theory have, however, long been insufficient to enable AFE calculations to be routinely applied in early stage drug discovery. One of the major difficulties in performing AFE calculations is the length of time required for calculations to converge to an ensemble average. CPU implementations of MD‐based free energy algorithms can effectively only reach tens of nanoseconds per day for systems on the order of 50,000 atoms, even running on massively parallel supercomputers. Therefore, converged free energy calculations on large numbers of potential lead compounds are often untenable, preventing researchers from gaining crucial insight into molecular recognition, potential druggability and other crucial areas of interest. Graphics Processing Units (GPUs) can help address this. We present here a seamless GPU implementation, within the PMEMD module of the AMBER molecular dynamics package, of thermodynamic integration (TI) capable of reaching speeds of >140 ns/day for a 44,907‐atom system, with accuracy equivalent to the existing CPU implementation in AMBER. The implementation described here is currently part of the AMBER 18 beta code and will be an integral part of the upcoming version 18 release of AMBER. © 2018 Wiley Periodicals, Inc.     

Multispectroscopic DNA interaction and Docking studies

Two new water soluble oxovanadium(IV) complexes with formulae Na[VO(his)(met)SO₄] (1) and Na[VO(gly)(met)SO₄] (2), (gly=glycine his=histidine, and met=metformin) were synthesized and characterized by LCMS, UV‐Visible absorption, infrared spectra, magnetic moment, elemental analysis, thermal analysis and electronic spectral studies. The metal center was found in an octahedral geometry. DNA binding interaction of these complexes with CT DNA has been explored by UV‐Visible absorption, fluorescence, viscosity measurements and cleavage studies. Finally the binding of the complexes with CT‐DNA could be surface binding, mainly in the groove binding. The complexes were docked in to B‐DNA sequence, 5’(D*AP*CP*CP*GP*AP*CP*GP*TP*CP*GP*GP*T)‐3’ retrieved from protein data bank (PDB ID: 423D), using Discovery Studio 2.1 software.     

Sequential-dissociation kinetics of non-covalent complexes of DNA with multiple proteins in separation-based approach: General theory and its application

Binding of multiple proteins to DNA is crucial in many regulatory cellular processes. The kinetics of assembly and disassembly of DNA–multiple protein complexes is very difficult to study in detail due to the lack of suitable experimental approaches. A separation-based approach has been recently proposed to resolve disassembly kinetics of such complexes. While conceptually simple, the separation-based approach generates experimental data with very complex patterns. The analysis of these patterns is a challenging problem on its own. Here we report on a mathematical approach that can extract a solution for the experimental data obtained in separation-based analysis of sequential dissociation of a DNA complex with multiple proteins. This case describes the dissociation of proteins one-by-one from the complex. Generally speaking, a mathematical solution of such problems requires calculations of multiple integrals. Our approach reduces this procedure to taking double integrals and constructing their superposition. We tested this approach with the experimental data obtained for three-step sequential dissociation of complexes of DNA with two protein copies.     

Synergic approach to XAFS analysis for the identification of most probable binding motifs for mononuclear zinc sites in metalloproteins

In the present work a data analysis approach, based on XAFS data, is proposed for the identification of most probable binding motifs of unknown mononuclear zinc sites in metalloproteins. This approach combines multiple‐scattering EXAFS analysis performed within the rigid‐body refinement scheme, non‐muffin‐tin ab initio XANES simulations, average structural information on amino acids and metal binding clusters provided by the Protein Data Bank, and Debye–Waller factor calculations based on density functional theory. The efficiency of the method is tested by using three reference zinc proteins for which the local structure around the metal is already known from protein crystallography. To show the applicability of the present analysis to structures not deposited in the Protein Data Bank, the XAFS spectra of six mononuclear zinc binding sites present in diverse membrane proteins, for which we have previously proposed the coordinating amino acids by applying a similar approach, is also reported. By comparing the Zn K‐edge XAFS features exhibited by these proteins with those pertaining to the reference structures, key spectral characteristics, related to specific binding motifs, are observed. These case studies exemplify the combined data analysis proposed and further support its validity.     

Novel materials for bioanalytical and biomedical applications: Environmental response and binding/release capabilities of amphiphilic hydrogels with shape‐persistent dendritic junctions

The binding and release capabilities of a hydrogel series, constructed of hydrophilic poly(ethylene glycol) segments and hydrophobic dendritic junctions [poly (benzyl ether)s], are evaluated in aqueous media. The environmental response of the amphiphilic networks is also tested in water at three pH values: 1.5, 7.0, and 10.1. The highest swelling ratio is observed under acidic conditions and varies between 3.7 and 6.5, depending on the crosslinking density and dendrimer generation. Gel specimens with embedded indicators react within 3–6 s with a clear color switch to the change in the pH of the surrounding medium. The experiments with model anionic and cationic indicators and stains show that the hydrogels have basic interiors. The gel binding capabilities depend on the water solubility of the substrate and on the size of the incorporated dendritic fragments. Model release studies have been performed at 37 °C and pHs 1.5, 7.0, and 10.1. The observed phenomena are explained by the transformations in the structure and charge that both the networks and the model compounds undergo with the changes in the pH of the aqueous medium. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 4017–4029, 2005