Protein-reactive natural products

Researchers in the post-genome era are confronted with the daunting task of assigning structure and function to tens of thousands of encoded proteins. To realize this goal, new technologies are emerging for the analysis of protein function on a global scale, such as activity-based protein profiling (ABPP), which aims to develop active site-directed chemical probes for enzyme analysis in whole proteomes. For the pursuit of such chemical proteomic technologies, it is helpful to derive inspiration from protein-reactive natural products. Natural products use a remarkably diverse set of mechanisms to covalently modify enzymes from distinct mechanistic classes, thus providing a wellspring of chemical concepts that can be exploited for the design of active-site-directed proteomic probes. Herein, we highlight several examples of protein-reactive natural products and illustrate how their mechanisms of action have influenced and continue to shape the progression of chemical proteomic technologies like ABPP.     

Bia-amperometric quantification of salbutamol in pharmaceutical products

This paper presents a simple, rapid and reproducible method of analysis of salbutamol in pharmaceutical products, utilizing batch injection analysis (BIA) associated with amperometric detection. A study of salbutamol oxidation demonstrated a strong dependence between electrode fouling and pH. All determinations were done utilizing a glassy carbon electrode in presence of 3.0 mol l⁻¹ NaOH. A large linear dynamic range from 8×10⁻⁷ to 2×10⁻⁴ mol l⁻¹ was obtained by using an injected volume of 100 μl with a detection limit of 2.5×10⁻⁷ mol l⁻¹. R.S.D. of 0.92% for 50 successive injections of 4×10⁻⁶ mol l⁻¹ of salbutamol and a sample throughput of 60 samples per hour were achieved. The method was applied for salbutamol quantification in syrups.     

On-probe pyrolysis desorption electrospray ionization (DESI) mass spectrometry for the analysis of non-volatile pyrolysis products

An on-probe pyrolyzer has been constructed and interfaced with desorption electrospray ionization (DESI) mass spectrometry (MS) for the rapid analysis of non-volatile pyrolysis products. The detection and analysis of non-volatile pyrolysis products of peptides, proteins and the synthetic polymer poly(ethylene glycol) were demonstrated with this instrument. The on-probe pyrolyzer can be operated off-line or on-line with the DESI source and was interfaced with a tandem MS (MS/MS) instrument, which allowed for structure characterization of the non-volatile pyrolytic products. Advantages of this system are its simplicity and speed of analysis since the pyrolysis is performed in situ on the DESI source probe and hence, it avoids extraction steps and/or the use of matrices (e.g., as in MALDI–MS analyses).     

Synthesis and structural revision of naturally occurring ayapin derivatives

The synthesis of three highly oxygenated naturally occurring coumarins, 8-methoxy-6,7-methylenedioxycoumarin, 5-methoxy-6,7-methylenedioxycoumarin and 5,8-dimethoxy-6,7-methylenedioxycoumarin is described for the first time, together with a new method for the preparation of ayapin (6,7-methylenedioxycoumarin). Comparison of the spectroscopic data of the synthetic tetraoxygenated coumarin 5,8-dimethoxy-6,7-methylenedioxycoumarin with literature reports resulted in the structural revision of several natural coumarins. Two coumarins, both identified as 5,8-dimethoxy-6,7-methylenedioxycoumarin must have other structures, while the structure of another coumarin, described as the isomeric 7,8-dimethoxy-5,6-methylenedioxycoumarin has to be revised to 5,8-dimethoxy-6,7-methylenedioxycoumarin.     

QSAR models for biocides: The example of the prediction of Daphnia magna acute toxicity

ABSTRACT

Biocides are multi-component products used to control undesired and harmful organisms able to affect human or animal health or to damage natural and manufactured products. Because of their widespread use, aquatic and terrestrial ecosystems could be contaminated by biocides. The environmental impact of biocides is evaluated through eco-toxicological studies with model organisms of terrestrial and aquatic ecosystems. We focused on the development of in silico models for the evaluation of the acute toxicity (EC₅₀) of a set of biocides collected from different sources on the freshwater crustacean Daphnia magna, one of the most widely used model organisms in aquatic toxicology. Toxicological data specific for biocides are limited, so we developed three models for daphnid toxicity using different strategies (linear regression, random forest, Monte Carlo (CORAL)) to overcome this limitation. All models gave satisfactory results in our datasets: the random forest model showed the best results with a determination coefficient r² = 0.97 and 0.89, respectively, for the training (TS) and the validation sets (VS) while linear regression model and the CORAL model had similar but lower performance (r² = 0.83 and 0.75, respectively, for TS and VS in the linear regression model and r² = 0.74 and 0.75 for the CORAL model).     

Quantitative determination of several mono- and oligosaccarides in food products by means of high-pressure liquid chromatography replacement of the toxic eluent 'acetonitrile/water' by a mixture of harmless solvents

Summary The toxic eluent mixture acetonitrile/water frequently used for separation of mono- and oligosaccarides is replaced by the harmless temary mixture acetone/ethyl acetate/water. By various techniques — degassing of the eluent, parallel connection of two columns and temperature control of the columns, of the eluate and RI-detector — the method is made suitable for the determination of lower saccharide concentrations than usual. Methods for rational preparation of samples — extraction of the saccarides, deionizing of the sample solution — are suggested. Based on examples, the efficiency of the method is demonstrated.     

Simultaneous screening and determination eight phthalates in plastic products for food use by sonication-assisted extraction/GC-MS methods

Studies on determination of eight kinds of phthalates, e.g. di-ethyl phthalate (DEP), di-propyl phthalate (DPP), di-isobutyl phthalate (DIBP), di-butyl phthalate (DBP), benzyl butyl phthalate (BBP), di-cyclohexyl phthalate (DCHP), di-(2-ethylhexyl) phthalate (DEHP), di-octyl phthalate (DOP), in 25 kinds of plastic products for food use, including packaging bags, packaging film, containers, boxes for microwave oven use, sucking tubes, spoons, cups, plates, etc. by gas chromatography in combination with mass spectrometry detector (GC-MS) in electronic ionisation mode (EI) with selected-ion monitoring (SIM) acquisition method (GC-MS (EI-SIM)) have been carried out. Methods have been developed for both qualitative and quantitative analysis of phthalates. Extraction, clean-up and analysis procedure have been optimized. Determination of samples were performed after frozen in liquid nitrogen and sonication-assisted extraction with hexane, clean-up with LC-C18 SPE and analyzed by GC-MS methods. The base peak (m/z = 149) of all the phthalates was selected for the screening studies. The characteristic ions, 121, 177, 222 for DEP; 191, 209 for DPP; 57, 223 for DIBP; 104 for DBP; 91, 132, 206 for BBP; 55, 167 for DCHP; 113, 167, 279 for DEHP; 279 for DOP were chosen for quantitative studies. These techniques are possible to detect phthalates at the level of 10.0 μg/kg. Overall recoveries were 82-106% with R.S.D. values at 3.8-10.2%. Only one of the 25 examined samples was free from phthalates. The rest 24 samples were found to contain at least three or more of these phthalates. The predominant phthalate detected in the studied samples was DEHP.     

Determination of iodide by detection of iodine using gas-diffusion flow injection and chemiluminescence

This work describes development of a flow injection (FI) system for determination of iodide, based on the chemiluminescence (CL) reaction between iodine and luminol. Iodide in the sample zone is oxidized to iodine. Employment of a gas-diffusion (GD) unit allows for selective detection of the generated CL (425 nm). Preliminary results showed for concentrations of less than 2 mg L⁻¹, that signals were irreproducible and that the calibration was not linear.In order to solve these problems, a method of ‘membrane conditioning’ was investigated, in which iodide stream was continuously merged with oxidant to generate I₂ that conditioned the GD membrane and tubing. This minimized surface interaction between the active surface and the I₂ generated from the samples, thus improving both precision and sensitivity. By employing membrane conditioning, it has been possible to reliably detect concentrations down to 0.1 mg L⁻¹.At the optimized condition, an excellent linear calibration (r² = 0.999) was obtained from 0.1 to 1.0 mg L⁻¹. The method was successfully applied to determine iodide in some pharmaceutical products such as potassium iodide tablets and a liquid patent medicine. However, for vitamin tablets, ascorbic acid was found to interfere seriously by causing a negative signal.     

Solid-phase ultraviolet absorbance spectrophotometric multisensor for the simultaneous determination of butylated hydroxytoluene and co-existing antioxidants

Continuous flow injection and UV spectrophotometric detection have been proposed for simultaneous determination of the two binary mixtures, butylated hydroxytoluene (BHT)/n-propyl gallate (n-PG) and butylated hydroxytoluene (BHT)/butylated hydroxyanisole (BHA), in food and cosmetics samples. The method is based on the different residence times of each antioxidant when the flow cell is packed to a height of 25 mm with silica C₁₈ using methanol-water 50:50% (v/v) as a carrier with a flow rate of 1.25 and 1.10 ml min⁻¹, respectively. The determination of each antioxidant is based on the measurement of its absorbance at its maximum wavelengths using a DAD detector at 30 and 180 s for the mixture n-PG-BHT and 90 and 220 s for BHA-BHT. Calibration graphs were linear over the range 10.0-300.0 μg ml⁻¹ for each antioxidant in both mixtures. The relative standard deviations were 2.5% for BHT and 2.0% for the co-existing antioxidant. Resolution of the n-PG-BHT mixture in ratios between 1:8 and 8:1 and the BHA-BHT mixture in ratios between 1:10 and 10:1 is possible. The method was applied to the determination of both antioxidants in fat foods and cosmetics samples with recoveries ranging between 101 and 105%.     

Physico-chemical aspects of polyethylene processing in an open mixer. Part 25: Mechanisms of aldehyde and carboxylic acid formation

Aldehydes and acids can be formed in numerous reactions in oxidizing polyethylene melts. Significant amounts of aldehydes result from β-scission of alkoxy radicals that are formed on bimolecular hydroperoxide decomposition. There are also large amounts of aldehydes expected from acid-catalyzed decomposition of allylic hydroperoxides as soon as enough acids have accumulated for efficient catalysis. There are difficulties in explaining the formation of aldehydes at a constant rate in sufficient amount for explaining the experimental data. There are much less difficulties with the constant rate of carboxylic acid formation. The α,γ-keto-hydroperoxides that are formed on chain propagation might account for the bulk of the acids formed at a constant rate.The foremost problems with the acids pertain to their formation at increasing rates in the initial as well as in the advanced stages. Formation and decomposition of α,β-di-hydroperoxides and α,γ-di-hydroperoxides is a possibility in this respect. Similarly, α,β-keto-hydroperoxides might be formed on peroxidation in the α-position to ketone groups in the advanced stages. There are considerable difficulties in elucidating the exact role of the aldehydes that are usually seen as the main precursors of the acids. Although there are many possibilities for transformation of aldehydes into acids, the free radical mechanisms envisaged usually have considerable disadvantages. These disadvantages result essentially from fast decarbonylation of acyl radicals and even faster decarboxylation of acyl-oxy radicals. Direct transformation of peracids into acids on reaction with double bonds is always a possibility. Moreover, in the low temperature range (150-160 °C) where hydroperoxides are accumulating, direct reaction of aldehydes with primary and/or secondary hydroperoxides will also yield acids.