A modification-centric assessment tool for the performance of chemoproteomic probes.

Chemoproteomics has emerged as a key technology to expand the functional space in complex proteomes for probing fundamental biology and for discovering new small-molecule-based therapies. Here we report a modification-centric computational tool termed pChem to provide a streamlined pipeline for unbiased performance assessment of chemoproteomic probes. The pipeline starts with an experimental setting for isotopically coding probe-derived modifications that can be automatically recognized by pChem, with masses accurately calculated and sites precisely localized. pChem exports on-demand reports by scoring the profiling efficiency, modification homogeneity and proteome-wide residue selectivity of a tested probe. The performance and robustness of pChem were benchmarked by applying it to eighteen bioorthogonal probes. These analyses reveal that the formation of unexpected probe-derived modifications can be driven by endogenous reactive metabolites (for example, bioactive aldehydes and glutathione). pChem is a powerful and user-friendly tool that aims to facilitate the development of probes for the ever-growing field of chemoproteomics.

Quantitative assessment of epoxide formation in oil and mayonnaise by 1H-13C HSQC NMR spectroscopy.

Lipid oxidation is detrimental for the quality of oil-based foods. Historically, lipid oxidation research focussed on hydroperoxides and aldehydes, but a third class, the epoxides, have been proposed to resolve observed mechanistic anomalies. Here, we developed a 2D 1H-13C HSQC NMR spectroscopic method to quantify epoxides in food in a reproducible (relative standard deviation ≤11.6 %) and sensitive (LoQ 0.62 mmol/kg oil) manner. Lipid hydroperoxides, aldehydes, and epoxides generated in rapeseed oil and mayonnaise were quantified over time by NMR. Epoxides accounted at most for 10-40 % of the products. They were formed after hydroperoxide accumulation, most likely primarily via alkoxyl radical intermediates, which limits their potential as an early oxidation marker. As 99 % and ∼60 % of the epoxide signal intensities were assigned in a fatty acid and sub-structure specific manner, respectively, our quantitative HSQC method will enable unravelling and quantitative modelling of lipid oxidation mechanisms.

Pot, atom and step economic (PASE) assembly of salicylaldehydes, malononitrile dimer and 4-hydroxypyridine-2(1H)-ones into medicinally relevant 5H-chromeno[2,3-b]pyridine scaffold.

The new multicomponent reaction (MCR) has been found: one-pot selective and efficient formation of the new 5-(4-hydroxy-2-oxo-1,2-dihydropyridin-3-yl)-substituted 5H-chromeno[2,3-b]pyridines in 61-97% yields directly from simple and easily available salicylaldehydes, malononitrile dimer and 4-hydroxypyridine-2(1H)-ones in small amount of pyridine-ethanol catalyst/solvent system. This complex "domino" transformation includes Knoevenagel condensation of salicylaldehyde with malononitrile dimer, Michael addition of 4-hydroxypyridine-2(1H)-one, double Pinner-type reaction cyclization and isomerization with following protonation. This facile multicomponent process opens a new way to 5-(4-hydroxy-2-oxo-1,2-dihydropyridin-3-yl)-substituted 5H-chromeno[2,3-b]pyridine systems, which are promising compounds for the treatment for human inflammatory TNFα-mediated diseases and different biomedical applications.