The Role of Intramolecular Reactions and Chemical Degradation in the Apparent Biotransformation Pathways of a Series of SYK Inhibitors.

In vitro metabolism studies of the spleen tyrosine kinase inhibitors AZ-A and AZ-B identified four unusual metabolites. M1 (mass-to-charge ratio 411) was formed by both molecules and was common to several analogs (AZ-C to AZ-H) sharing the same core structure, appearing to derive from the complete loss of a pendent 3,4-diaminotetrahydropyran ring and pyrazole ring cleavage resulting in a nonobvious metabolite. M2-M4 were formed by AZ-A and a subset of the other compounds only and apparently resulted from a sequential loss of H2 from parent. Initial attempts to isolate M3 for identification were unsuccessful due to sample degradation, and it was subsequently found that M2 and M3 underwent sequential chemical degradation steps to M4. M4 was successfully isolated and shown by mass spectrometry and NMR spectroscopy to be a tricyclic species incorporating the pyrazole and the 3,4-diaminotetrahydropyran groups. We propose that this arises from an intramolecular reaction between the primary amine on the tetrahydropyran and a putative epoxide intermediate on the adjacent pyrazole ring, evidence for which was generated in a ß-mercaptoethanol-trapping experiment. The loss of the tetrahydropyran moiety observed in M1 was found to be enhanced in an analog that was unable to undergo the intramolecular reaction step, leading us to propose two possible reaction pathways originating from the reactive intermediate. Ultimately, we conclude that the apparently complex and unusual metabolism of this series of compounds likely resulted from a single metabolic activation step forming an epoxide intermediate, which subsequently underwent intramolecular rearrangement and/or chemical degradation to form the final observed products. SIGNIFICANCE STATEMENT: The current work provides an unusual biotransformation example showing the potential for intramolecular reactions and chemical degradation to give the appearance of complex metabolism arising from a single primary route of metabolism.

Upregulation of GALNT7 in prostate cancer modifies O-glycosylation and promotes tumour growth.

Prostate cancer is the most common cancer in men and it is estimated that over 350,000 men worldwide die of prostate cancer every year. There remains an unmet clinical need to improve how clinically significant prostate cancer is diagnosed and develop new treatments for advanced disease. Aberrant glycosylation is a hallmark of cancer implicated in tumour growth, metastasis, and immune evasion. One of the key drivers of aberrant glycosylation is the dysregulated expression of glycosylation enzymes within the cancer cell. Here, we demonstrate using multiple independent clinical cohorts that the glycosyltransferase enzyme GALNT7 is upregulated in prostate cancer tissue. We show GALNT7 can identify men with prostate cancer, using urine and blood samples, with improved diagnostic accuracy than serum PSA alone. We also show that GALNT7 levels remain high in progression to castrate-resistant disease, and using in vitro and in vivo models, reveal that GALNT7 promotes prostate tumour growth. Mechanistically, GALNT7 can modify O-glycosylation in prostate cancer cells and correlates with cell cycle and immune signalling pathways. Our study provides a new biomarker to aid the diagnosis of clinically significant disease and cements GALNT7-mediated O-glycosylation as an important driver of prostate cancer progression.

Bump-and-hole engineering of human polypeptide N-acetylgalactosamine transferases to dissect their protein substrates and glycosylation sites in cells.

Despite the known disease relevance of glycans, the biological function and substrate specificities of individual glycosyltransferases are often ill-defined. Here, we describe a protocol to develop chemical, bioorthogonal reporters for the activity of the GalNAc-T family of glycosyltransferases using a tactic termed bump-and-hole engineering. This allows identification of the protein substrates and glycosylation sites of single GalNAc-Ts. Despite requiring transfection of cells with the engineered transferases and enzymes for biosynthesis of bioorthogonal substrates, the tactic complements methods in molecular biology. For complete details on the use and execution of this protocol, please refer to Schumann et al. (2020)1, Cioce et al. (2021)2, and Cioce et al. (2022)3.

Cell-specific bioorthogonal tagging of glycoproteins.

Altered glycoprotein expression is an undisputed corollary of cancer development. Understanding these alterations is paramount but hampered by limitations underlying cellular model systems. For instance, the intricate interactions between tumour and host cannot be adequately recapitulated in monoculture of tumour-derived cell lines. More complex co-culture models usually rely on sorting procedures for proteome analyses and rarely capture the details of protein glycosylation. Here, we report a strategy termed Bio-Orthogonal Cell line-specific Tagging of Glycoproteins (BOCTAG). Cells are equipped by transfection with an artificial biosynthetic pathway that transforms bioorthogonally tagged sugars into the corresponding nucleotide-sugars. Only transfected cells incorporate bioorthogonal tags into glycoproteins in the presence of non-transfected cells. We employ BOCTAG as an imaging technique and to annotate cell-specific glycosylation sites in mass spectrometry-glycoproteomics. We demonstrate application in co-culture and mouse models, allowing for profiling of the glycoproteome as an important modulator of cellular function.

Benefits of Chemical Sugar Modifications Introduced by Click Chemistry for Glycoproteomic Analyses.

Mucin-type O-glycosylation is among the most complex post-translational modifications. Despite mediating many physiological processes, O-glycosylation remains understudied compared to other modifications, simply because the right analytical tools are lacking. In particular, analysis of intact O-glycopeptides by mass spectrometry is challenging for several reasons; O-glycosylation lacks a consensus motif, glycopeptides have low charge density which impairs ETD fragmentation, and the glycan structures modifying the peptides are unpredictable. Recently, we introduced chemically modified monosaccharide analogues that allowed selective tracking and characterization of mucin-type O-glycans after bioorthogonal derivatization with biotin-based enrichment handles. In doing so, we realized that the chemical modifications used in these studies have additional benefits that allow for improved analysis by tandem mass spectrometry. In this work, we built on this discovery by generating a series of new GalNAc analogue glycopeptides. We characterized the mass spectrometric signatures of these modified glycopeptides and their signature residues left by bioorthogonal reporter reagents. Our data indicate that chemical methods for glycopeptide profiling offer opportunities to optimize attributes such as increased charge state, higher charge density, and predictable fragmentation behavior.

State of the art in the determination of trace elements in seawater: a worldwide proficiency test.

This manuscript presents the results of the International Measurement Evaluation Programme 40 (IMEP-40) study, a proficiency test (PT) which was organised to assess the worldwide performance of laboratories for the determination of trace elements in seawater. This PT supports the implementation of the European Union Water Framework Directive 2000/60/EC, which aims at achieving a long-term high level protection of the aquatic environment, covering lakes, ground water and coastal waters. Forty-six participants reported results. The test item was seawater containing the trace elements As, Cd, Co, Cr, Cu, Fe, Mn, Mo, Ni, Pb, Se and Zn. The trace elements in the test item were present in very low concentrations to mimic natural levels. The results of the participants were rated with z and zeta (ζ) scores in accordance with ISO 13528 and ISO 17043. The standard deviation for proficiency assessment, σ̂, was set at 25% of the respective assigned values for the 12 measured elements based on previous experience with similar PTs. The low levels of the trace elements combined with the high salt concentration of the seawater made the measurements challenging. Many laboratories were unable to detect or quantify the elements and reported "lower than X" values. The percentage of satisfactory performances (expressed as z scores) ranged from 41% (Cr, Fe) to 86% (Mo). The PT study showed that the use of proper standard methods, like ISO 17294-2, and sensitive techniques, like inductively coupled plasma mass spectrometry (ICP-MS), contributed to performing well in this PT round.

Proficiency test on the determination of pesticide residues in grapes with multi-residue methods.

This manuscript presents the results of the International Measurement Evaluation Programme 37 (IMEP-37) study, a proficiency test (PT) which was organised to assess the world-wide performance of food control laboratories on the determination of pesticide residues in grapes. This PT supports the implementation of Regulation (EC) No 396/2005 on maximum residue levels of pesticides in or on food and feed of plant and animal origin. Eighty-one participants reported results, forty from EU Member States and forty-one from outside the EU. The test item was a grape sample spiked with 20 selected pesticides. The results of the participants were rated with z- and zeta (ζ-) scores in accordance with ISO 13528 and ISO 17043. The standard deviation for the proficiency assessment, σˆ, of this PT was set at 25% for the 20 measured pesticides based on previous experience with similar measurands. The results reported to IMEP-37 showed that the participants performed satisfactorily, ranging from 81% (carbendazim) to 97% (azoxystrobin, penconazole, pyrimethanil) of the participating laboratories. However, only 30% of the participants managed to analyze all pesticides satisfactorily. Overall, the performance of the participants in this PT was good but there is room for improvement in the development of multi-residue methods for the simultaneous analysis of a large number of pesticides with an increased accuracy.

Feed premix: a difficult matrix for the accurate determination of trace elements - the outcome of IMEP-114 and IMEP-36.

This paper presents the outcome of two proficiency tests (IMEP-114/36) running in parallel, which focused on the determination of total As, Cd, Pb, Hg and Sn in feed premixes. Both exercises aimed to test the performance of laboratories measuring trace elements in feed, in compliance with Directive 2002/32/EC of the European Parliament and of the Council on undesirable substances in animal feed. IMEP-114 was run for the European Union National Reference Laboratories, while IMEP-36 was open to all food control laboratories that wished to participate. In total 80 laboratories from 37 countries registered to both proficiency tests, from which 75 laboratories reported results. The test material used in this exercise was commercially available feed premix, which was processed, bottled, labelled and dispatched to participants. The performance of the participating laboratories was similar in both proficiency tests and was very good in the case of total Cd and less satisfactory for total As and total Pb. For total Sn only one-third of the participants reported results, from which 33% performed satisfactorily. Thirty-four participants reported results for total Hg, although the expert laboratories stated that the mass fraction for that measurand was below the limit of detection of the method used. An evaluation of the reasons that could be at the basis of unsatisfactory results has been carried out and is presented here.

3-MCPD in food other than soy sauce or hydrolysed vegetable protein (HVP).

This review gives an overview of current knowledge about 3-monochloropropane-1,2-diol (3-MCPD) formation and detection. Although 3-MCPD is often mentioned with regard to soy sauce and acid-hydrolysed vegetable protein (HVP), and much research has been done in that area, the emphasis here is placed on other foods. This contaminant can be found in a great variety of foodstuffs and is difficult to avoid in our daily nutrition. Despite its low concentration in most foods, its carcinogenic properties are of general concern. Its formation is a multivariate problem influenced by factors such as heat, moisture and sugar/lipid content, depending on the type of food and respective processing employed. Understanding the formation of this contaminant in food is fundamental to not only preventing or reducing it, but also developing efficient analytical methods of detecting it. Considering the differences between 3-MCPD-containing foods, and the need to test for the contaminant at different levels of food processing, one would expect a variety of analytical approaches. In this review, an attempt is made to provide an up-to-date list of available analytical methods and to highlight the differences among these techniques. Finally, the emergence of 3-MCPD esters and analytical techniques for them are also discussed here, although they are not the main focus of this review.

Investigation of the correlation of the acrylamide content and the antioxidant activity of model cookies.

The purpose of this study was to evaluate the correlation between the acrylamide (AA) content and the antioxidant activity (AOA) of self-prepared cookies. Cookies were baked in the laboratory under defined conditions following four different recipes. The parameters of investigation were the influence of the type and relative content of sugar (glucose and fructose) and the baking time on the AA content as well as AOA of the final products. Parameters depending on the recipe and baking conditions such as the moisture content, the total nitrogen concentration, and the color of the products were evaluated for all samples as well. To prove the transferability of the findings gained with model cookies to samples from industry, the same measurements were performed on seven different types/brands of cookies that were purchased in local markets. A direct correlation was found between the concentration of AA and the AOA. With increasing baking time, the moisture content of the cookies decreased. The latter parameter correlated well with the AA concentration and AOA. The use of fructose enhanced the concentration of AA and the AOA of the final products, when compared with the use of sucrose. However, a simple model for the prediction of acrylamide contents and the AOA of samples from the baking time, color, protein, or moisture content of the samples was not found.

Development and validation of an analytical method for the determination of semicarbazide in fresh egg and in egg powder based on the use of liquid chromatography tandem mass spectrometry.

In this work the development of a method to determine semicarbazide (SEM) in fresh whole egg and in whole egg and egg white powders as those used in the food industry, by using LC-MS/MS is described. The method is based on a recently validated one for the determination of SEM in baby food. SEM is extracted from egg with 0.2 mol L(-1) hydrochloric acid and derivatised with 2-nitrobenzaldehyde. The extract is neutralised and purified by passing through a solid phase extraction (SPE) cartridge. The 2-nitrobenzaldehyde derivative is eluted with ethyl acetate. The eluate is evaporated to dryness and the residue re-dissolved in methanol:water mobile phase. SEM is determined by reversed-phase LC-MS/MS. The "in-house" validation of this method has been performed taking into account the "Harmonized guidelines for single-laboratory validation of methods of analysis" (IUPAC Technical report) and the Commission Decision (2002/657/EC). The performance characteristics of the method were established by in-house validation procedures employing assays with standard solutions, sample blanks and spiked samples. Linearity, matrix effect, trueness, precision, selectivity, limits of detection and of quantification were determined. The fitness for purpose of this method was assessed based on its performance characteristics. LOD's of 0.15 and 0.4 microg kg(-1) for whole fresh egg and industrial egg powders, respectively, were obtained. The LOQ for fresh whole egg was 0.2 microg kg(-1) and for industrial egg powders 0.8 microg kg(-1). Linear calibration curves were obtained in the ranges 1-100 and 0.8-400 microg kg(-1) for fresh whole egg and the egg powders, respectively.

Composition and analysis of liquid smoke flavouring primary products.

Smoke flavourings are produced on a large scale and have been applied to a variety of food products for more than 30 years. The use of them has many advantages compared to traditional smoking techniques. Among others, the amount of (known) toxic compounds deriving from combustion processes can be more easily controlled in smoke flavourings. In order to ensure safe products, a new European Regulation requests data on the composition and lays down, in particular, the maximum permitted concentrations for selected polycyclic aromatic hydrocarbons (PAHs). This review compiles results published on the chemical composition of liquid smoke flavouring primary products, partly in relation to production process parameters, and the analytical methods involved. The methods cover chromatographic techniques for analysis of specific compounds including extraction methods and clean-up procedures. Analysis of sensorial and bulk parameters such as acidity and total phenolic compounds are described as well as they are used as standard methods for analysis of liquid smoke flavourings. A special section is devoted to discussing the analysis of PAHs.

Overview of acrylamide monitoring databases.

Since high acrylamide levels in carbohydrate-rich food were reported in 2002, many research activities were started in order to gain knowledge on occurrence, formation, and prevention of this compound in food products. Among them, monitoring programs were conducted in many countries worldwide by official bodies as well as by the food industry. National and international bodies set up monitoring databases. In 2003, both the European Commission and the World Health Organization posted calls for data and placed their spreadsheets for the submission of data on the Web. The goal of the databases is to collect data for a reliable estimation of the exposure of consumers to acrylamide via the food chain. This paper describes the assessment of the data quality and outlines the composition of the data in the 2 databases, to date.

Evaluation of the results from an inter-laboratory comparison study of the determination of acrylamide in crispbread and butter cookies.

Analytical methods currently employed for determination of acrylamide (AA) in two carbohydrate-rich food samples, crispbread and butter cookies, obtained commercially, and native and spiked bread extract samples have been evaluated in a collaborative study. The objective of the study was to obtain information about the performance of the participating laboratories when analysing samples with an AA content close to the limit of quantification ( LOQ) and at a higher AA level, and to investigate the influence of sample-preparation procedures on the results of the analysis. For this purpose an aqueous native extract of white bread crumb, a fortified extract, and AA standard solutions, the analyte content of which were not disclosed to the participants, were included in the study. A total of 62 laboratories, applying seven different measurement techniques and a broad spectrum of analyte extraction and sample-preparation procedures reported their analytical results. Because the measurement data were not normally distributed, they were evaluated by application of robust statistics. The relative performance of the laboratories was highlighted by calculation of z-scores. For the crispbread sample, especially, a large percentage of the calculated z-scores were outside the satisfactory range. From their distribution it became obvious that one of the analytical techniques might be biased, if not applied correctly. Consequently, the impact of the applied methods was examined in more detail. Information about the analytical technique, extraction solvent, quantity weighed, calibration method, clean-up, and the experience of the participating laboratories were extracted from the analytical protocols and transcribed into a data matrix which was evaluated by multifactor analysis of variance. The applied measurement technique seems to have a statistically significant influence on the analytical results.