A Classification Model to Predict the Rate of Decline of Kidney Function.

The African American Study of Kidney Disease and Hypertension (AASK), a randomized double-blinded treatment trial, was motivated by the high rate of hypertension-related renal disease in the African-American population and the scarcity of effective therapies. This study describes a pattern-based classification approach to predict the rate of decline of kidney function using surface-enhanced laser desorption ionization/time of flight proteomic data from rapid and slow progressors classified by rate of change in glomerular filtration rate. An accurate classification model consisting of 7 out of 5,751 serum proteomic features is constructed by applying the logical analysis of data (LAD) methodology. On cross-validation by 10-folding, the model was shown to have an accuracy of 80.6 ± 0.11%, sensitivity of 78.4 ± 0.17%, and specificity of 78.5 ± 0.16%. The LAD discriminant is used to identify the patients in different risk groups. The LAD risk scores assigned to 116 AASK patients generated a receiver operating curves curve with AUC 0.899 (CI 0.845-0.953) and outperforms the risk scores assigned by proteinuria, one of the best predictors of chronic kidney disease progression.

Discovery of novel cyclophilin A ligands using an H/D exchange- and mass spectrometry-based strategy.

Cyclophilin A (CypA) is an overexpressed protein in lung cancer tumors and as a result is a potential therapeutic and diagnostic target. Described here is use of an H/D exchange- and a matrix assisted laser desorption/ionization (MALDI) mass spectrometry-based assay, termed single-point SUPREX (Stability of Unpurified Proteins from Rates of H/D Exchange), to screen 2 chemical libraries, including the 1280-compound LOPAC library and the 9600-compound DIVERSet library, for binding to CypA. This work represents the first application of single-point SUPREX using a pooled ligand approach, which is demonstrated here to yield screening rates as fast as 6 s/ligand. The false-positive and false-negative rates determined in the current work using a set of control samples were 0% and 9%, respectively. A false-positive rate of 20% was found in screening the actual libraries. Eight novel ligands to CypA were discovered, including 2-(α-naphthoyl)ethyltrimethyl-ammonium iodide, (E)-3-(4-t-Butylphenylsulfonyl)-2-propenenitrile, 3-(N-benzyl-N-isopropyl)amino-1-(naphthalen-2-yl)propan-1-one, cis-diammineplatinum (II) chloride, 1-(3,5-dichlorophenyl)-1H-pyrrole-2,5-dione, N-(3-chloro-1, 4-dioxo-1,4-dihydro-2-naphthalenyl)-N-cyclohexylacetamide, 1-[2-(3,4-dimethoxyphenyl)ethyl]-1H-pyrrole-2,5-dione, and 4-(2-methoxy-4-nitrophenyl)-1-methyl-10-oxa-4-azatricyclo[5.2.1.0~2,6~]dec-8-ene-3,5-dione. These compounds, which had moderate binding affinities to CypA (i.e., K(d) values in the low micromolar range), provide new molecular scaffolds that might be useful in the development of CypA-targeted diagnostic imaging or therapeutic agents for lung cancer.

Investigation of intramolecular proton migration in a series of model, metal-cationized tripeptides using in situ generation of an isotope label.

In this study we used an isotope label, generated in situ, to investigate intramolecular proton migration or scrambling during formation of [b(2)+17+Li](+) products by collision-induced dissociation (CID) of Li(+)-cationized tripeptides. To generate the isotope label, we used a McLafferty-type rearrangement of N-terminally acetylated, C-terminal peptide tert-butyl esters in which all amide positions were exchanged with deuterium. Using a set of small, model peptides, we show that intramolecular proton scrambling occurs during CID, particularly amongst adjacent sites along a peptide backbone, on the time scales employed for low-energy collisional activation in an ion-trap mass spectrometer.

Production and collision-induced dissociation of gas-phase, water- and alcohol-coordinated uranyl complexes containing halide or perchlorate anions.

Electrospray ionization was used to generate mono-positive gas-phase complexes of the general formula [UO2A(S)n]+ where A = OH, Cl, Br, I or ClO4, S = H2O, CH3OH or CH3CH2OH, and n = 1-3. The multiple-stage dissociation pathways of the complexes were then studied using ion-trap mass spectrometry. For H2O-coordinated cations, the dissociation reactions observed included the elimination of H2O ligands and the loss of HA (where A = Cl, Br or I). Only for the Br and ClO4 versions did collision-induced dissociation (CID) of the hydrated species generate the bare, uranyl-anion complexes. CID of the chloride and iodide versions led instead to the production of uranyl hydroxide and hydrated UO2+. Replacement of H2O ligands by alcohol increased the tendency to eliminate HA, consistent with the higher intrinsic acidity of the alcohols compared to water and potentially stronger UO2-O interactions within the alkoxide complexes compared to the hydroxide version.

Intrinsic hydration of monopositive uranyl hydroxide, nitrate, and acetate cations.

The intrinsic hydration of three monopositive uranyl-anion complexes (UO(2)A)(+) (where A = acetate, nitrate, or hydroxide) was investigated using ion-trap mass spectrometry (IT-MS). The relative rates for the formation of the monohydrates [(UO(2)A)(H(2)O)](+), with respect to the anion, followed the trend: Acetate > or = nitrate >> hydroxide. This finding was rationalized in terms of the donation of electron density by the strongly basic OH(-) to the uranyl metal center, thereby reducing the Lewis acidity of U and its propensity to react with incoming nucleophiles, viz., H(2)O. An alternative explanation is that the more complex acetate and nitrate anions provide increased degrees of freedom that could accommodate excess energy from the hydration reaction. The monohydrates also reacted with water, forming dihydrates and then trihydrates. The rates for formation of the nitrate and acetate dihydrates [(UO(2)A)(H(2)O)(2)](+) were very similar to the rates for formation of the monohydrates; the presence of the first H(2)O ligand had no influence on the addition of the second. In contrast, formation of the [(UO(2)OH)(H(2)O)(2)](+) was nearly three times faster than the formation of the monohydrate.

Elucidation of the collision induced dissociation pathways of water and alcohol coordinated complexes containing the uranyl cation.

Multiple-stage tandem mass spectrometry was used to characterize the dissociation pathways for complexes composed of (1) the uranyl ion, (2) nitrate or hydroxide, and (3) water or alcohol. The complex ions were derived from electrospray ionization (ESI) of solutions of uranyl nitrate in H2O or mixtures of H2O and alcohol. In general, collisional induced dissociation (CID) of the uranyl complexes resulted in elimination of coordinating water and alcohol ligands. For undercoordinated complexes containing nitrate and one or two coordinating alcohol molecules, the elimination of nitric acid was observed, leaving an ion pair composed of the uranyl cation and an alkoxide. For complexes with coordinating water molecules, MS(n) led to the generation of either [UO2(2+)OH-] or [UO2(2+)NO3(-)]. Subsequent CID of [UO2(2+)OH-] produced UO2(+). The base peak in the spectrum generated by the dissociation of [UO2(2+)NO3(-)], however, was an H2O adduct to UO2(+). The abundance of the species was greater than expected based on previous experimental measurements of the (slow) hydration rate for UO2(+) when stored in the ion trap. To account for the production of the hydrated product, a reductive elimination reaction involving reactive collisions with water in the ion trap is proposed.