The NCI Drug Information System. 3. The DIS Chemistry Module

The Chemistry Module of the Drug Information System (DIS) handles a database of 400,000 structures. New or modified records are created in this database on a daily basis and are merged into the file promptly. The Chemistry database is searchable in a wide variety of ways and provides novel methods for both input and output of chemical structures.     

Conformational studies of free and Li+ complexed jasplakinolide, a cyclic depsipeptide from the Fijian marine sponge Jaspis splendens

The complexation of Li+ to jasplakinolide, a marine sponge derived cyclic depsipeptide showed preferential binding to two out of four carbonyl oxygens (C-10, C-14) and the electrons of the aromatic system of the beta-tyrosine amino acid residue. This is in contrast to previous results obtained by others who proposed complexation to three out of four available carbonyl oxygens (C-1, C-10, C-14). The structure of the complex in CD3CN was determined by NOE restrained molecular dynamic calculations. Structures of the uncomplexed jasplakinolide were calculated in CDCl3 and CD3CN for comparison.     

A conversational mass spectral search and retrieval system—II: Combined search options

An interactive, conversational mass spectral search system based on 8782 uncertified electron-impact mass spectra and accessible over ordinary telephone lines, is described. Compounds whose mass spectra are in the file can be immediately identified and very useful structural inferences can be obtained for compounds that are not represented in the file. The file may be searched in a number of ways, including by peaks and intensities, molecular weight, complete and partial molecular formula, molecular weight plus peaks/intensities, molecular formula plus peaks/intensities and molecular weight plus molecular formula. Lastly, the complete spectrum of any compound in the file can be printed out.     

ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature

Background  

We describe the database ExplorEnz, which is the primary repository for EC numbers and enzyme data that are being curated on behalf of the IUBMB. The enzyme nomenclature is incorporated into many other resources, including the ExPASy-ENZYME, BRENDA and KEGG bioinformatics databases.     

Identification of intact oxidation products of glycerophospholipids in vitro and in vivo using negative ion electrospray iontrap mass spectrometry

Free radical‐induced oxidation products of polyunsaturated fatty acids esterified to phospholipids have been implicated in a number of human diseases including atherosclerosis and neurodegenerative diseases. Some of these phospholipid oxidation products have potent biological activities and likely contribute to human pathophysiological conditions. Oxidation products have also been used as markers of oxidative stress in vivo. Identification and quantification of phospholipid oxidation products are often performed by analyzing the oxidized free fatty acid moieties after hydrolysis from the phospholipids head groups by gas chromatography–mass spectrometry (GC–MS) or liquid chromatography–mass spectrometry (LC–MS). We now describe the definitive identification of intact oxidized products of glycerophospholipids including glycerophosphatidylcholine (GPC), glycerophosphatidylethanolamine (GPE), and glycerophosphatidylserine (GPS) in vitro and in vivo using iontrap MS. For these analyses, the negative ions of the oxidation products of phospholipids are fragmented to MSⁿ and unequivocal structural characterization is obtained based on collision‐induced dissociation (CID) of the sn‐2 carboxylate ion. This technique overcomes the need to hydrolyze fatty acids from phospholipids in the analysis. The method has been used to identify a number of oxidation products of glycerophospholipids including hydroxyeicosatetraenoates (HETEs) and isoprostanes (IsoPs) esterified to different classes of glycerophospholipids in vitro and in vivo. These studies thus provide a new approach to identify the intact oxidation products of glycerolphospholipids. Copyright © 2009 John Wiley & Sons, Ltd.     

2-Amino-2-thiazoline. V. phenylthioureido and phenylureido derivatives of 2-thiazoline

The reaction of 2-amino-2-thiazoline (I) with phenylisothiocyanate has been reported to give 2-imino-3-phenylthiocarbamoylthiazolidine (II) at low temperatures and l-phenyl-3-(2-thiazolin-2-yl)-2-thiourea (III) at ca. 100°. When performed by us, however, this reaction gave only a single mono-adduct regardless of the temperature. Nmr and chemical evidence indicates that structure III is the correct one. Treatment of I with phenylisocyanate also gave a mono-adduct which was established to be l-phenyl-3-(2-thiazolin-2-yl)urea (V). Compound I does not form a simple di-adduct with excess phenylisothiocyanate but does so with phenylisocyanate to give 2-phenylcarbamoylimino-3-phenylcarbamoylthiazolidine (VI). The reaction of III with phenylisocyanate gives 2-phenylthiocarbamoylimino-3-phenylcarbamoylthiazolidine (VII), however, the corresponding reaction of V with phenylisothiocyanate does not give the anticipated product but a mixture of compounds which includes VI and VII.