Identification of ligands that target the HCV-E2 binding site on CD81

Hepatitis C is a global health problem. While many drug companies have active R&D efforts to develop new drugs for treating Hepatitis C virus (HCV), most target the viral enzymes. The HCV glycoprotein E2 has been shown to play an essential role in hepatocyte invasion by binding to CD81 and other cell surface receptors. This paper describes the use of AutoDock to identify ligand binding sites on the large extracellular loop of the open conformation of CD81 and to perform virtual screening runs to identify sets of small molecule ligands predicted to bind to two of these sites. The best sites selected by AutoLigand were located in regions identified by mutational studies to be the site of E2 binding. Thirty-six ligands predicted by AutoDock to bind to these sites were subsequently tested experimentally to determine if they bound to CD81-LEL. Binding assays conducted using surface Plasmon resonance revealed that 26 out of 36 (72 %) of the ligands bound in vitro to the recombinant CD81-LEL protein. Competition experiments performed using dual polarization interferometry showed that one of the ligands predicted to bind to the large cleft between the C and D helices was also effective in blocking E2 binding to CD81-LEL.     

How mobile NMR can help with the conservation of paintings

The conservation of paintings is fundamental to ensure that future generations will have access to the ideas of the grand masters who created these art pieces. Many factors, such as humidity, temperature, light, and pollutants, pose a risk to the conservation of paintings. To help with painting conservation, it is essential to be able to noninvasively study how these factors affect paintings and to develop methods to investigate their effects on painting degradation. Hence, the use of mobile nuclear magnetic resonance (NMR) as a method of investigation of paintings is gaining increased attention in the world of Heritage Science. In this mini-review, we discuss how this method was used to better understand the stratigraphy of paintings and the effect different factors have on the painting integrity, to analyze the different cleaning techniques suitable for painting conservation, and to show how mobile NMR can be used to identify forgeries. It is also important to keep in mind its limitations and build upon this information to optimize it to extend its applicability to the study of paintings and other precious objects of cultural heritage.     

Evaluating the metabolic perturbations in Mangifera indica (mango) ripened with various ripening agents/practices through gas chromatography ‐ mass spectrometry based metabolomics

Mangifera indica L. (mango) is said to be the king of fruits due to its rich nutritional properties and mainly originates from the Indian sub‐continent. The consumption pattern of the mangoes has increased drastically, due to which, many ripening practices/agents were used to make it ready‐to‐eat fruit or juice for the consumers. The fruit quality and metabolic composition are said to be altered due to different ripening agents/practices. The present communication mainly deals to understand the metabolic perturbations in mango fruits due to different ripening practices/agents (room temperature ripening, ethylene, and calcium carbide) using gas chromatography ‐ mass spectrometry based metabolomics. The partial least square‐discriminant analysis has found 16 differential metabolites for different ripening agents/practices which are belong to the classes of amino acids, fatty acids, sugars, and polyols. Four metabolic pathways were found to alter in the fruit metabolome due to different ripening agents/practices. Fructose, glucose, and galactose were found to be significantly up‐regulated due to calcium carbide ripening in comparison to other ripening agents/practices. Overall findings from the present study advocates that mass spectrometry based metabolomics can be valuable tool to understand the fruit quality and safety with respect to consumer health.     

Data shaving: a focused screening approach

The number of compounds available for evaluation as part of the drug discovery process continues to increase. These compounds may exist physically or be stored electronically allowing screening by either actual or virtual means. This growing number of compounds has generated an increasing need for effective strategies to direct screening efforts. Initial efforts toward this goal led to the development of methods to select diverse sets of compounds for screening, methods to cluster actives into related groups of compounds, and tools to select compounds similar to actives of interest for further screening. In this work we extend these earlier efforts to exploit information about inactive compounds to help make rational decisions about which sets of compounds to include as part of a continuing screening campaign, or as part of a focused follow-up effort. This method uses the information from inactive compounds to "shave" off or deprioritize compounds similar to inactives from further consideration. This methodology can be used in two ways: first, to provide a rational means of deciding when sufficient compounds containing certain structural features have been tested and second as a tool to enhance similarity searching around known actives. Similarity searching is improved by deprioritizing compounds predicted to be inactive, due to the presence of structural features associated with inactivity.     

Addition of some α-halo ethers to unsaturated compounds

Summary The addition was carried out of 2-acetoxyethyl chloromethyl ether and of 2-chloroethyl chloromethyl ether to isobutene, to allyl chloride, to styrene, and to allyl acetate and also of 2-acetoxyethyl chloromethyl ether to butadiene and to ethyl cinnamate.     

Highly effective and enantioselective Phospho-Aldol reaction of diphenyl phosphite with N-alkylated isatins catalyzed by quinine

Cinchona alkaloids were first successfully reported to promote enantioselective Phospho-Aldol reaction of diphenyl phosphite to a variety of N-alkylated isatin derivatives in good to excellent yields (up to 99%) and moderate to good enantioselectivities (up to 73% ee) almost in no time.     

Characterization of diamond surface terminations using electrochemical grafting with diazonium salts

A new characterization technique to identify qualitatively diamond surface terminations and to measure quantitatively the density of hydrogen atoms bonded to the diamond surface is introduced using electrochemical grafting of diamond with diazonium salts. The cathodic peak potentials for the grafting of nitrophenyl layers reveal qualitative information about surface terminations ranging from –H, to –OH to –O–. The charges consumed during the conversion of nitro- to aminophenyl are used to calculate quantitatively the density of hydrogen atoms bonded to the diamond surface. As hydrogen is generally very difficult to detect by other methods like X-ray Photon Spectroscopy, this new method will add significantly to the understanding of surface related properties of transducers.     

Resisting resistance: new chemical strategies for battling superbugs

As microbes become increasingly resistant to antibiotics, and in many cases to several drugs simultaneously, the search is on to find new therapies. One method to combat resistance is to use inhibitors of resistance mechanisms to potentiate existing antibiotics. Recent efforts are encouraging and highlight the importance of research at the chemistry-microbiology interface in developing new approaches to tackle resistance.     

Investigation of isothiocyanate addition to alkylidene derivatives of malononitrile and cyanoacetic acid esters

Addition of arylisothiocyanates to active methylene compounds leads to a variety of compounds depending on the structure of the starting material and conditions used to conduct the addition. Addition of arylisothiocyanate to 1c leads to a pyrido[2,3-d]pyrimidine resulting from addition of a second mole of cyanate to the initial adduct. Addition of arylisothiocyanate to 1b led to a mixture of pyridine and thiopyran adducts, while addition to 1a led to open chain structures.     

Static fatigue fracture of polyethylene: A morphological analysis

The fracture properties of a number of high-density polyethylenes were evaluated and related to their morphology. The resistance to initiation of fracture is related to the resistance to voiding of the materials and the rate of coalescence of voids. The propensity of the materials to void has been shown to be related to the size of the amorphous region. The resistance to propagation of the fracture is also related to the above factors as well as the ease of stretching and rupture of fibrils. The ease of fibril formation has been shown to be related to the degree of perfection of the crystallites.     

Internal quality controls applied in inductively coupled plasma mass spectrometry multi-elemental analysis in the second French Total Diet Study

In 2006, the French Food Safety Agency (AFSSA) started the second French Total Diet Study to assess exposure to essential and non-essential elements through dietary intake by analysing 1352 food samples. A total of 21 elements were analysed to date by Inductively Coupled Plasma Mass Spectrometry after closed vessel microwave digestion, in 660 samples corresponding to at half of the study. This work presents and discusses the results of the various internal quality controls (IQC) applied to ensure that the analytical procedure is correctly carried out, from digestion to analysis, and to enable analytical chemists to validate the results obtained. The whole IQC allows to estimate uncertainties according to elements and to select those that should be discarded from the study or only given as indicative values for elements that were not within defined quality limits.     

Adhesion between graphite and modified polyester surfaces: a theoretical study

This study examines the adhesion of graphite to functionalized polyester surfaces using a range of qualitative and quantitative measures of theoretical adhesion. Modifications to the polyester surfaces include the addition of hydroxyl, carboxyl, or fluorine substituents with coverages of 0.4 and 0.9 groups per nm(2). In each case, the introduction of substituents to the surface of the polyester was calculated to lead to reduced adhesion to graphite. Effects of surface relaxation on adhesion are studied by employing different simulation protocols. The theoretical results suggest one mechanism to reduce adhesion to carbonaceous solids is to increase atomic roughness using strongly hydrophilic or alternatively strongly hydrophobic substituents.     

Modification of Cyclodextrins for Use as Artificial Enzymes

The magical powers of enzymes have been attributed to their ability to bind specific substrates and catalyze reactions of the bound substrate. Artificial enzymes synthetically mimic the binding and the catalytic site to produce molecules that are not only smaller in size but also potentially have similar activity to the real enzymes. The main objective of our research is to create artificial redox enzymes by using cyclodextrins as binding sites and attaching flavin derivatives as the catalytic site. We have developed a strategy to attach a catalytic site to cyclodextrin exclusively at the 2-, 3- or the 6-position. The evaluation of the artificial enzyme in which flavin is attached to the 2-position gives a 647-fold acceleration factor. Although this is modest compared to those of real enzymes (which can have acceleration factors of a trillion), the artificial enzymes allow us to understand the elements that contribute to the incredible catalytic power of enzymes.     

Sodium Hypochlorite Reactions. III. The Catalytic Nakagawa and Related Systems

Mainly through the extensive investigations of Nakagawa and coworkers, nickel peroxide has emerged as a powerful oxidant for organic compounds. For example, it has been used for the oxidation of alcohols to aldehydes or carboxylic acids,^2,3 allylic hydroxyl (selectively) to the carbonyl group,⁴ α-ketols to α-diketones,⁵ α-glycols, α-ketols, α-hydroxyl and α-keto acids to cleavage products,⁶ aldehydes to amides or nitriles in the presence of ammonia,⁷ phenols to quinones,^8,9 certain Schiff bases to benzoxazoles,¹⁰ amines to azo compounds or nitriles,^11,12 diarylamines to hydrazines,¹³ carbazoles to dimers and trimers,¹⁴ hydrazones to diazo compounds,^15,16 1-aminobenzotriazole to benzyne,¹⁷ N-substituted hydroxylamines to azoxy compounds,¹⁸ phenylacetonitrile to dimeric products,¹⁹ a thiouracil to a uracil derivative,²⁰ thiols to disulfides and sulfides to sulfones,²¹ N-substituted phenothiazines to sulfoxides and sulfones,²¹ haloforms to hexahaloethanes.²³     

Gradient Elution Centrifugal Partition Chromatography: Comparison with HPLC Gradients and use of Ternary Diagrams to Build Gradients

Abstract

Just as with HPLC, gradient elution provides to CPC an easy way to fractionate solutes of widely differing polarities and partition coefficients, and to reduce run times. The easiest way to design a gradient for CPC is to refer to ternary diagrams corresponding to the ternary liquid mixtures generally encountered in centrifugal partition chromatography.     

Synthetic, self-assembly ABCD nanoparticles; a structural paradigm for viable synthetic non-viral vectors

Gene therapy research is still in trouble owing to a paucity of acceptable vector systems to deliver nucleic acids to patients for therapy. Viral vectors are efficient but may be too dangerous. Synthetic non-viral vectors are inherently safer but are currently not efficient enough to be clinically viable. The solution for gene therapy lies with improved synthetic non-viral vectors systems. This review is focused on synthetic cationic liposome/micelle-based non-viral vector systems and is a critical review written to illustrate the increasing importance of chemistry in gene therapy research. This review should be of primary interest to synthetic chemists and biomedical researchers keen to appreciate emerging technologies, but also to biological scientists who remain to be convinced about the relevance of chemistry to biology.     

Using one- and two-dimensional NMR techniques to characterize reaction products bound to Chiron SynPhase crowns

Solid-phase MAS techniques have proved to be very useful in characterizing compounds bound to resin; however, little has been reported on using NMR to characterize compounds attached to Chiron SynPhase crowns. We have used proton, carbon, and COSY spectra obtained with a Varian Nano.nmr probe to characterize products from a published reaction sequence attached to MD (methacrylic acid/dimethylacrylamide copolymer) crowns. We have also performed solvent surveys to determine the best solvents for acquiring spectra of materials bound to both MD and PS (polystyrene) crowns.     

Classification of wines from five Spanish origin denominations by aromatic compound analysis

Wine is a complex matrix in which aroma compounds play an important role in the characterization of the flavor pattern of a given wine. Twelve volatile compounds were determined in 244 samples of Spanish red wines from different denominations of origin: Rioja, Navarra, Valdepe?as, La Mancha, and Cari?ena. The samples were analyzed by GC using headspace solid-phase microextraction. The concentration (mg/mL) intervals obtained were 3-methyl-butyl acetate (3.9 to 116), 3-methyl-1-butanol (93 to 724), ethyl hexanoate (0.8 to 39), 1-hexanol (0.3 to 6.7), ethyl octanoate (1.4 to 41), diethyl succinate (0.2 to 13), 2-phenyl ethyl acetate (0 to 5.3), hexanoic acid (0 to 8.3), geraniol (0 to 3.0), 2-phenylethanol (1.5 to 56), octanoic acid (0 to 20), and decanoic acid (0 to 3.3). Wines were classified by multivariate statistical methods: principal component analysis, and lineal discriminant analysis. A correct differentiation among wines according to their origin was obtained by lineal discriminant analysis.     

NMR spectroscopic study of the Murex trunculus dyeing process

It is widely accepted that indigo dyes derived from Murex trunculus were used to produce the biblical dyes tekhelet and argaman. We describe a method of following the debromination of natural leucoindigos and their binding to wool using NMR spectroscopy. Debromination is observed prior to reaction with the wool and prior to oxidation. Binding to the wool is shown to occur prior to oxidation. NMR allows the dyeing process to be followed. This, in principle, could be used to correct problems during dyeing that would increase the reliability of the process.     

Precision of Flash Pyrolysis-GC-MS Analysis: Experimental Evaluation of the Sources of Variability

The present study was carried out to evaluate the precision and to identify significant sources of variability in flash pyrolysis-GC-MS experiments. The analysis of variance has been applied to the example of polyethylene pyrolysis to estimate the impact of several controlled factors: sample handling, flash pyrolysis filament ageing and calibration. It was demonstrated that to get the best precision in experimental results, it is recommended to set the operator to reduce the impact of sample handling procedure and the filament to avoid variability due to changes in filament characteristics. In comparison, filament ageing and filament calibration are shown to influence in a limited extent the experimental results.