Synthesis of organic–inorganic sorbent containing phenylboronic acid as glucose-binding ligand

A copolymer with N-allylaminophenylboronic acid has been synthesized from a water-soluble N-vinylpyrrolidone–acrolein diethyl acetal copolymer. Immobilization of the obtained copolymer on silica gel afforded an organic–inorganic sorbent capable of sorbing glucose from model solutions.     

Anion binding by pyrrole–pyridine-based macrocyclic polyamides

The synthesis, characterisation and anion-binding properties of new pyrrole–pyridine-based macrocyclic polyamides 7a and 7b are presented. Chloride anion templation in the macrocyclisation reaction has been shown to control [1 + 1] acylation. The anion-binding properties of the receptors have been determined by UV–vis titrations in a DMSO solution and compared with systems with a similar design. The new receptors have been found to display a 10-fold selectivity for hydrogensulphate, dihydrogenphosphate and acetate anions over other anions studied.     

Synthesis of cyclodextrin–pyrrole conjugates possessing tuneable carbon linkers

Cyclodextrins are naturally occurring cyclic oligosaccharides consisting of glucose units. The main feature of cyclodextrins is the ability to accommodate various lipophilic compounds in their interior, which determines them to be popular helpers to the mankind. However, there is still a demand for new derivatives for advanced applications. Herein, we report the synthesis of β-cyclodextrin–pyrrole conjugates. Their preparation is based on an amide bond formation or copper(I)-catalysed azide-alkyne cycloaddition between β-cyclodextrin and pyrrole derivatives. The main advantage of the synthetic approach lies in the possibility to attach the substituent in β-position, because polypyrroles possessing a substituent in this position are generally more conductive than the N-substituted ones. Moreover, the presented synthetic route is general and allows tuning the properties (various types of connections and lengths) of a linker. The presented cyclodextrin–pyrrole derivatives thus open the door for new applications in the field of sensors or tissue engineering.     

The intricacies of the stacking interaction in a pyrrole–pyrrole system

Extensive calculations of potential energy surfaces for parallel-displaced configurations of pyrrole–pyrrole systems have been carried out by the use of a dispersion-corrected density functional. System geometries associated with the energy minima have been found. The minimum interaction energy has been calculated as ?5.38 kcal/mol. However, bonding boundaries appeared to be relatively broad, and stacking interactions can be binding even for ring centroid distances larger than 6 Å. Though the contribution of the correlation energy to intermolecular interaction in pyrrole dimers appeared to be relatively small (around 1.6 smaller than it is in a benzene–benzene system), this system’s minimum interaction energy is lower than those calculated for benzene–benzene, benzene–pyridine and even pyridine–pyridine configurations. The calculation of the charges and energy decomposition analysis revealed that the specific charge distribution in a pyrrole molecule and its relatively high polarization are the significant source of the intermolecular interaction in pyrrole dimer systems.     

Importance of inter-residue interactions in ligand—receptor binding

In the present study, the role of inter-residue interactions in ligand binding and the ligand—receptor interactions were examined. Computational chemistry methods of ligand docking and molecular dynamics simulations were used to study the binding of β-funaltrexamine (β-FNA) and N-methyl-β-funaltrexamine (N-methyl-β-FNA) to μ- and κ-opioid receptors and to the μ-receptor with Lys303^6.58Glu mutation. It was found that inter-residue interactions Lys233^5.39—Glu303^6.58 in the mutant receptor and Lys227^5.39—Asp223^5.35 in the κ-receptor are more likely to prevent covalent bond formation between β-FNA and the receptor than the ligand-receptor interactions. This emphasizes the importance of inter-residue interactions in ligand binding as well as the effects of point-mutations.     

Analysis of mismatched DNA by mismatch binding ligand (MBL)–Sepharose affinity chromatography

Mismatch binding molecules (MBLs), strongly and selectively bound to the mismatched base pair in duplex DNA, were immobilized on Sepharose. Three MBL–Sepharose columns were prepared with three MBLs, naphthyridine dimer (ND), naphthyridine–azaquinolone (NA), and aminonaphthyridine dimer (amND), which exhibited different binding profiles to the mismatched base pairs. These three MBL–Sepharose columns showed characteristic elution profiles for DNA duplexes containing mismatched base pairs. The ND–Sepharose column separated the G–G and G–A mismatched DNA from fully matched duplexes. The NA–Sepharose column separated the A–A and G–A mismatched DNA from other DNA duplexes. The amND–Sepharose column separated the C–C mismatched DNA. These chromatographic profiles were very consistent with the binding preference of each MBL. By changing the elution conditions from sodium hydroxide to sodium chloride, MBL–Sepharose columns were also able to separate the mismatched DNA that weakly bound to the MBL from fully matched DNA duplex. Figure MBL-Sepharose affinity chromatography successfully separates the mismatched duplex DNA from fully matched duplex.     

Synthesis of a mixed carboxylate–phosphinate AAZTA-like ligand and relaxometric characterization of its Gd complex

The synthesis of the new polydentate ligand AAZ2A2P^Et derived from the heptadentate polyaminocarboxylic ligand AAZTA (6-amino-6-methylperhydro-1,4-diazepine-N,N′,N″,N″-tetraacetic acid) in which two acetate groups were replaced by methyleneethylphosphinic pendant arms is reported. The relaxometric behavior of the corresponding mono-aquo Gd^III complex was also investigated.     

Synthesis,characterization, and DNA damaging of bivalent metal complexes incorporating tetradentate dinitrogen–dioxygen ligand as potential biocidal agents

A new symmetrical tetradentate Schiff base was prepared by the condensation of 5-nitro-o-vanillin and diaminoethane. Its complexes were synthesized and characterized by elemental analysis, magnetic moment, molar conductance, UV-Vis, IR, ¹H NMR, ESI-mass, and EPR spectra. The DNA-binding behavior of these complexes was investigated by absorption spectra, cyclic voltammetry, and viscosity measurements. The DNA-binding constants for Co(II), Ni(II), Cu(II), and Zn(II) complexes were 1.58?×?10⁴, 1.65?×?10⁴, 2.71?×?10⁴, and 1.83?×?10⁴ (mol?L^?1)^?1, respectively. The results suggest that the complexes intercalate between DNA base pairs. Further, all these complexes exhibit moderate to high ability to cleave pUC19 DNA. The ligand and its complexes have been screened for antimicrobial activities using the disc diffusion method against selected bacteria and fungi. Antibacterial activity was greater against Gram-positive than Gram-negative bacteria for Cu(II) complex and antifungal activity was greater against Aspergillus niger and Candida albicans for the Cu(II) complex.     

Synthesis of rhodium–carbonyl complexes bearing a novel P,N-chelating ligand of Schiff-base type

Schiff-base type N,P-chelating ligands, phosphorus analogues of imino–anilido ligands, were designed and synthesized as a new type of ligands toward transition metals, and the rhodium–carbonyl complexes bearing the novel imino–phosphido and phosphaalkenyl-anilido ligands were synthesized as stable crystalline compounds. Their structures were definitively revealed by X-ray crystallographic analysis, showing the unique electronic features of the ligands. In addition, the effective trans-influence of the phosphorus atom was suggested on the basis of the structural parameters and spectroscopic features of the isolated complexes.     

Analysis of Fas–ligand interactions using a molecular model of the receptor–ligand interface

A molecular model of the complex between Fas and its ligand was generated to better understand the location and putative effects of site-specific mutations, analyze interactions at the Fas–FasL interface, and identify contact residues. The modeling study was conservative in the sense that regions in Fas and its ligand which could not be predicted with confidence were omitted from the model to ensure accuracy of the analysis. Using the model, it was possible to map four of five N-linked glycosylation sites in Fas and FasL and to study 10 of 11 residues previously identified by mutagenesis as important for binding. Interactions involving six of these residues could be analyzed in detail and their importance for binding was rationalized based on the model. The predicted structure of the Fas–FasL interface was consistent with the experimentally established importance of these residues for binding. In addition, five previously not targeted residues were identified and predicted to contribute to binding via electrostatic interactions. Despite its limitations, the study provided a much improved basis to understand the role of Fas and FasL residues for binding compared to previous residue mapping studies using only a molecular model of Fas.     

Assessing protein–ligand binding modes with computational tools: the case of PDE4B

In a first step in the discovery of novel potent inhibitor structures for the PDE4B family with limited side effects, we present a protocol to rank newly designed molecules through the estimation of their IC\(_{50}\) values. Our protocol is based on reproducing the linear relationship between the logarithm of experimental IC\(_{50}\) values [\(\log\)(IC\(_{50}\))] and their calculated binding free energies (\(\Delta G_\mathrm{binding}\)). From 13 known PDE4B inhibitors, we show here that (1) binding free energies obtained after a docking process by AutoDock are not accurate enough to reproduce this linear relationship; (2) MM-GB/SA post-processing of molecular dynamics (MD) trajectories of the top ranked AutoDock pose improves the linear relationship; (3) by taking into account all representative structures obtained by AutoDock and by averaging MM-GB/SA computations on a series of 40 independent MD trajectories, a linear relationship between \(\log\)(IC\(_{50}\)) and the lowest \(\Delta G_\mathrm{binding}\) is achieved with \(R^2=0.944\).     

Recent progress in the design of G-quadruplex–based electrochemical aptasensors

Aptamer-based electrochemical sensors are now developed for the detection of a wide variety of analytes including ions, low-molecular-weight molecules, proteins, and living cells. An aptamer-based sensor is an analytical device whose bio-sensing element (i.e. the aptamer) is immobilized on a transducer surface. Aptasensors have attracted great attention because of their high selectivity, sensitivity, and stability; they could be miniaturized and are of low production cost and offer extraordinary flexibility in the design of their assemblies. This review will emphasize recent developments of aptasensors using aptamers that are able to adopt the particular G-quadruplex (G4) conformations, which are secondary DNA structures formed from guanine-rich sequences. Indeed, G4 exhibits notable recognition properties inherent to their particular structuration.     

NMR-based analysis of protein–ligand interactions

Physiological processes are mainly controlled by intermolecular recognition mechanisms involving protein–protein and protein–ligand (low molecular weight molecules) interactions. One of the most important tools for probing these interactions is high-field solution nuclear magnetic resonance (NMR) through protein-observed and ligand-observed experiments, where the protein receptor or the organic compounds are selectively detected. NMR binding experiments rely on comparison of NMR parameters of the free and bound states of the molecules. Ligand-observed methods are not limited by the protein molecular size and therefore have great applicability for analysing protein–ligand interactions. The use of these NMR techniques has considerably expanded in recent years, both in chemical biology and in drug discovery. We review here three major ligand-observed NMR methods that depend on the nuclear Overhauser effect—transferred nuclear Overhauser effect spectroscopy, saturation transfer difference spectroscopy and water–ligand interactions observed via gradient spectroscopy experiments—with the aim of reporting recent developments and applications for the characterization of protein–ligand complexes, including affinity measurements and structural determination.     

Synthesis of Spiro[pyrrole–pyrrolizidines] by 1,3-Dipolar Cycloaddition of Azomethine Ylides to 3-Ylidenepyrrol-2-ones

Russian Journal of Organic Chemistry - The Knoevenagel condensation of 1H-pyrrole-2,3-diones with malononitrile gave 3-(dicyanomethylidene)-2,3-dihydro-1H-pyrrole-2-ones which were brought into...     

Prediction of protein–ligand binding affinity by free energy simulations: assumptions,pitfalls and expectations

Many limitations of current computer-aided drug design arise from the difficulty of reliably predicting the binding affinity of a small molecule to a biological target. There is thus a strong interest in novel computational methodologies that claim predictions of greater accuracy than current scoring functions, and at a throughput compatible with the rapid pace of drug discovery in the pharmaceutical industry. Notably, computational methodologies firmly rooted in statistical thermodynamics have received particular attention in recent years. Yet free energy calculations can be daunting to learn for a novice user because of numerous technical issues and various approaches advocated by experts in the field. The purpose of this article is to provide an overview of the current capabilities of free energy calculations and to discuss the applicability of this technology to drug discovery.     

Synthesis and Evaluation of Coumarin–Resveratrol Hybrids as 15-Lipoxygenaze Inhibitors

A series of coumarin–resveratrol hybrids, 3-arylcoumarin derivatives 3a–u, were synthesized through the intermolecular condensation reaction of various salicylaldehydes and phenylacetic acids in the presence of 1,4-diazabicyclo[2.2.2]octane under solvent-free conditions. All the synthesized compounds were screened for their inhibitory potency against soybean 15-lipoxygenase. Among them, three compounds (3c, 3j, and 3q) showed good enzyme-inhibitory activities.     

Baeyer–Villiger rearrangement of a substituted pyrrole by Oxone

Pyrroloxyls have been reported to exhibit very narrow EPR spectral lines, essential for in vivo imaging. En route to pyrroloxyls, we observed an unexpected Baeyer–Villiger rearrangement, leading to loss of aromaticity and formation of a 4,5-dihydro-1H-ketopyrrole.     

Polyaphrons as Templates for the Sol–Gel Synthesis of Macroporous Silica

Macroporous silica was synthesized using polyaphrons as shape-directing templates in a sol–gel hydrolysis scheme using tetraethyl orthosilicate (TEOS). Polyaphrons are a special class of high internal phase ratio emulsions (HIPRE) that can potentially be used in the continuous processing of long range ordered macroporous solids. The structures so formed were examined using a scanning electron microscope after thermal curing to 400C. The majority of the pores in the silica structures were in the range between 0.1 and 10 m. Key parameters affecting the polyaphrons template characteristics were varied and their effects on the final silica structure were studied.     

Selenium Dioxide–Mediated Synthesis of Fused 1,2,4-Triazoles as Cytotoxic Agents

A series of fused 1,2,4-triazoles has been prepared by oxidative intramolecular cyclization of heterocyclic hydrazones with selenium dioxide. General applicability of this practical protocol was confirmed by the synthesis of moderate to good yields of 1,2,4-triazolo[4,3-a]pyridines, 1,2,4-triazolo[4,3-a]pyrimidines, 1,2,4-triazolo[4,3-a]pyramidines, and 1,2,4-triazolo-[4,3-a]quinoxa lines. All compounds were tested in vitro for their cytotoxic activity against HCT-116, A549, and Colo-205 cell lines. Two compounds, 3-(4-methoxyphenyl)-7-methyl-[1,2,4]triazolo[4,3-a]pyridine and 1-(4-methoxyphenyl)-[1,2,4]triazolo[4,3-a]quinoxaline, showed potent antiproliferative activity against the three cell lines.