A method for C(alpha) direct-detection in protonless NMR

Attempts are made to efficiently decouple (13)C nuclei without significant loss of coherence during the application of the decoupling package. Such attempts are based on the S(3)E spin-state selection method. A newly developed double S(3)E (DS(3)E) is particularly efficient for C(alpha) detection for proteins as large as 480 kDa.     

Integration of quantitative DCE-MRI and ADC mapping to monitor treatment response in human breast cancer: initial results

PURPOSE: The objective of this study was to assess changes in the water apparent diffusion coefficient (ADC) and in pharmacokinetic parameters obtained from the fast-exchange regime (FXR) modeling of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) during neoadjuvant chemotherapy in breast cancer. MATERIALS AND METHODS: Eleven patients with locally advanced breast cancer underwent MRI examination prior to and after chemotherapy but prior to surgery. A 1.5-T scanner was used to obtain T1, ADC and DCE-MRI data. DCE-MRI data were analyzed by the FXR model returning estimates of K(trans) (volume transfer constant), v(e) (extravascular extracellular volume fraction) and tau(i) (average intracellular water lifetime). Histogram and correlation analyses assessed parameter changes post-treatment. RESULTS: Significant (P < .05) changes or trends towards significance (P < .10) were seen in all parameters except tau(i), although there was qualitative reduction in tau(i) values post-treatment. In particular, there was reduction (P < .035) in voxels with K(trans) values in the range 0.2-0.5 min(-1) and a decrease (P < .05) in voxels with ADC values in the range 0.99 x 10(-3) to 1.35 x 10(-3) mm2/s. ADC and v(e) were negatively correlated (r = -.60, P < .02). Parameters sensitive to water distribution and geometry (T(1), v(e), tau(i) and ADC) correlated with a multivariable linear regression model. CONCLUSION: The analysis presented here is sensitive to longitudinal changes in breast tumor status; K(trans) and ADC are most sensitive to these changes. Relationships between parameters provide information on water distribution and geometry in the tumor environment.     

Capillary electrophoresis method for analysis of inorganic and organic anions related to habitability and the search for life

In situ missions of exploration require analytical methods that are capable of detecting a wide range of molecular targets in complex matrices without a priori assumptions of sample composition. Furthermore, these methods should minimize the number of reagents needed and any sample preparation steps. We have developed a method for the detection of metabolically relevant inorganic and organic anions that is suitable for implementation on in situ spaceflight missions. Using 55 mM acetic acid, 50 mM triethylamine, and 5% glycerol, more than 21 relevant anions are separated in less than 20 min. The method is robust to sample ionic strength, tolerating high concentrations of background salts (up to 900 mM NaCl and 300 mM MgSO₄). This is an important feature for future missions to ocean worlds. The method was validated using a culture of Escherichia coli and with high salinity natural samples collected from Mono Lake, California.     

Characterization of multiple fragmentation pathways initiated by collision‐induced dissociation of multifunctional anions formed by deprotonation of 2‐nitrobenzenesulfonylglycine

The correlation of anion structure with the fragmentation behavior of deprotonated nitrobenzenesulfonylamino acids was investigated using tandem mass spectrometry, isotopic labeling and computational methods. Four distinct fragmentation pathways resulting from the collision‐induced dissociation (CID) of deprotonated 2‐nitrobenzenesulfonylglycine (NsGly) were characterized. The unusual loss of the aryl nitro substituent as HONO was the lowest energy process. Subsequent successive losses of CO, HCN and SO₂ indicated that an ortho cyclization reaction had accompanied loss of HONO. Other pathways involving rearrangement of the ionized sulfonamide group, dual bond cleavage and intramolecular nucleophilic displacement were proposed to account for the formation of phenoxide, arylsulfinate and arylsulfonamide product ions at higher collision energies. The four distinct fragmentation pathways were consistent with precursor–product relationships established by CID experiments, isotopic labeling results and the formation of analogous product ions from 2,4‐dinitrobenzenesulfonylglycine and the Ns derivatives of alanine and 2‐aminoisobutyric acid. The computations confirmed a low barrier for ortho cyclization with loss of HONO and feasible energetics for each reaction step in the four pathways. Computations also indicated that three of the fragmentation pathways started from NsGly ionized at the carboxyl group. Overall, the pathways identified for the fragmentation of the NsGly anion differed from processes reported for anions containing a single functional group, demonstrating the importance of functional group interactions in the fragmentation pathways of multifunctional anions. Copyright © 2014 John Wiley & Sons, Ltd.     

Mixed solvents for cellulose derivatization under homogeneous conditions: kinetic,spectroscopic, and theoretical studies on the acetylation of the biopolymer in binary mixtures of an ionic liquid and molecular solvents

Rate constants for the acetylation of microcrystalline cellulose (MCC), by ethanoic anhydride in the presence of increasing concentrations of the ionic liquid (IL), 1-allyl-3-methylimidazolium chloride in dipolar aprotic solvents (DAS), N,N-dimethylacetamide (DMAC), and acetonitrile (MeCN), have been calculated from conductivity data. The third order rate constants showed a linear dependence on [IL]. We explain this result by assuming that the reacting cellulose is hydrogen-bonded to the IL. This is corroborated by kinetic data of the acetylation of cyclohexylmethanol, FTIR of the latter compound and of cellobiose in mixtures of IL/DAS, and conductivity of the binary solvent mixtures in absence, and presence of MCC. Cellulose acetylation is faster in IL/DMAC than in IL/MeCN; this difference is explained based on solvatochromic data (empirical polarity and basicity) and molecular dynamics simulations. Results of the latter indicate hydrogen-bond formation between the hydroxyl groups of the anhydroglucose unit of MCC, (Cl^?) of the IL, and the dipole of the DMAC. Under identical experimental conditions, acetylation in IL/DMAC is faster than that in LiCl/DMAC (2.7–8 times), due to differences in the enthalpies and entropies of activation.     

Advances in Modeling Sorption and Diffusion of Moisture in Porous Reactive Materials

Water‐vapor‐uptake experiments were performed on a silica‐filled poly(dimethylsiloxane) (PDMS) network and modeled by using two different approaches. The data was modeled by using established methods and the model parameters were used to predict moisture uptake in a sample. The predictions are reasonably good, but not outstanding; many of the shortcomings of the modeling are discussed. A high‐fidelity modeling approach is derived and used to improve the modeling of moisture uptake and diffusion. Our modeling approach captures the physics and kinetics of diffusion and adsorption/desorption, simultaneously. It predicts uptake better than the established method; more importantly, it is also able to predict outgassing. The material used for these studies is a filled‐PDMS network; physical interpretations concerning the sorption and diffusion of moisture in this network are discussed.     

Scaffold mining of kinase hinge binders in crystal structure database

Protein kinases are the second most prominent group of drug targets, after G-protein-coupled receptors. Despite their distinct inhibition mechanisms, the majority of kinase inhibitors engage the conserved hydrogen bond interactions with the backbone of hinge residues. We mined Pfizer internal crystal structure database (CSDb) comprising of several thousand of public as well as internal X-ray binary complexes to compile an inclusive list of hinge binding scaffolds. The minimum ring scaffolds with directly attached hetero-atoms and functional groups were extracted from the full compounds by applying a rule-based filtering procedure employing a comprehensive annotation of ATP-binding site of the human kinase complements. The results indicated large number of kinase inhibitors of diverse chemical structures are derived from a relatively small number of common scaffolds, which serve as the critical recognition elements for protein kinase interaction. Out of the nearly 4,000 kinase-inhibitor complexes in the CSDb we identified approximately 600 unique scaffolds. Hinge scaffolds are overwhelmingly flat with very little sp3 characteristics, and are less lipophilic than their corresponding parent compounds. Examples of the most common as well as the uncommon hinge scaffolds are presented. Although the most common scaffolds are found in complex with multiple kinase targets, a large number of them are uniquely bound to a specific kinase, suggesting certain scaffolds could be more promiscuous than the others. The compiled collection of hinge scaffolds along with their three-dimensional binding coordinates could serve as basis set for hinge hopping, a practice frequently employed to generate novel invention as well as to optimize existing leads in medicinal chemistry.