Construction of 4D-QSAR Models for Use in the Design of Novel p38-MAPK Inhibitors

The p38-mitogen-activated protein kinase (p38-MAPK) plays a key role in lipopolysaccharide-induced tumor necrosis factor-alpha (TNF-alpha) and interleukin-1 (IL-1) release during the inflammatory process, emerging as an attractive target for new anti-inflammatory agents. Four-dimensional quantitative structure-activity relationship (4D-QSAR) analysis [Hopfinger et al., J. Am. Chem. Soc., 119 (1997) 10509] was applied to a series of 33 (a training set of 28 and a test set of 5) pyridinyl-imidazole and pyrimidinyl-imidazole inhibitors of p38-MAPK, with IC50 ranging from 0.11 to 2100 nM [Liverton et al., J. Med. Chem., 42 (1999) 2180]. Five thousand conformations of each analogue were sampled from a molecular dynamics simulation (MDS) during 50 ps at a constant temperature of 303 K. Each conformation was placed in a 2 angstroms grid cell lattice for each of three trial alignments. 4D-QSAR models were constructed by genetic algorithm (GA) optimization and partial least squares (PLS) fitting, and evaluated by leave-one-out cross-validation technique. In the best models, with three to six terms, the adjusted cross-validated squared correlation coefficients, Q2adj, ranged from 0.67 to 0.85. Model D (Q2adj = 0.84) was identified as the most robust model from alignment 1, and it is representative of the other best models. This model encompasses new molecular regions as containing pharmacophore sites, such as the amino-benzyl moiety of pyrimidine analogs and the N1-substituent in the imidazole ring. These regions of the ligands should be further explored to identify better anti-inflammatory inhibitors of p38-MAPK.     

Synchrotron radiation circular dichroism spectroscopy of ribose and deoxyribose sugars, adenosine, AMP and dAMP nucleotides.

Synchrotron radiation circular dichroism (SRCD) spectra of ribose and deoxyribose sugars, adenosine, AMP and dAMP nucleotides and cyclic derivatives were measured in the vacuum ultraviolet region (down to 168 nm for sugars and 175 nm for adenine derivatives) and at different pH values (3, 6-7, 9-10) and temperatures (between 5 and 45 degrees C). The information content in the VUV region is important since the CD bands strongly depend on the chemical structure of the sugar, the presence and orientation of a phosphate group and the protonation state of adenine. On the other hand, single or double deprotonation of the phosphoric acid group has no influence on the spectra. We assign the vacuum ultraviolet (VUV) CD bands of the nucleoside and nucleotides to be due mainly to n-->pi* transitions in the adenine nucleobase based on a comparison with the absorption spectra. The CD bands of the sugars are due to n(O -->sigma*) transitions and are much smaller than the CD signal from the nucleotides in the VUV region. Bands are assigned to both pyranose and open-chain forms.     

Analysis of phenothiazines in human body fluids using disk solid-phase extraction and liquid chromatography

Seven phenothiazine derivatives, perazine, perphenazine, prochlorperazine, propericiazine, thioproperazine, trifluoperazine, and flupentixol, have been found to be extractable from human plasma and urine samples using disk solid-phase extraction (SPE) with an Empore C18 cartridge. Human plasma and urine (1 mL each) containing the 7 phenothiazine derivatives were mixed with 2 mL of 0.1M NaOH and 7 mL distilled water and then poured into the disk SPE cartridges. The drugs were eluted with 1 mL chloroform- acetonitrile (8 + 2) and determined by liquid chromatography with ammonium formate/formic acid-acetonitrile gradient elution. The detection was performed by ultraviolet absorption at 250 nm. The separation of the 7 phenothiazine derivatives from each other and from impurities was generally satisfactory using a SymmetryShield RP8 column (150 x 2.1 mm id, 3.5 microm particle size). The recoveries of the 7 phenothiazine derivatives spiked into plasma and urine samples were 64.0-89.9% and 65.1-92.1%, respectively. Regression equations for the 7 phenothiazine derivatives showed excellent linearity, with detection limits of 0.021-0.30 microg/mL for plasma and 0.017-0.30 microg/mL for urine. The within-day and day-to-day coefficients of variation for both samples were commonly below 9.0 and 14.9%, respectively.     

Electron transfer dissociation of peptide anions

Ion/ion reactions of multiply deprotonated peptide anions with xenon radical cations result in electron abstraction to generate charge-reduced peptide anions containing a free-radical site. Peptide backbone cleavage then occurs by hydrogen radical abstraction from a backbone amide N to facilitate cleavage of the adjacent C-C bond, thereby producing a- and x-type product ions. Introduction of free-radical sites to multiply charged peptides allows access to new fragmentation pathways that are otherwise too costly (e. g., lowers activation energies). Further, ion/ion chemistry, namely electron transfer reactions, presents a rapid and efficient means of generating odd-electron multiply charged peptides; these reactions can be used for studying gas-phase chemistries and for peptide sequence analysis.     

A kinetic stability study of <Emphasis Type="Italic">M</Emphasis>N<Subscript>5</Subscript> (<Emphasis Type="Italic">M</Emphasis>=Li,Na, K,and Rb)

A structure and kinetic stability study on some complexes with the general formula MN₅, where M are the alkali-metal atoms, Li, Na, K, and Rb, has been carried by using hybrid density functional methods. Complex B (C_2v) with two points of attachment to the N₅ ring is the most energetically favored for all metals considered here. Pyramidal structures A (C_5v) are kinetically unstable and they rapidly rearrange to the most stable planar structures B. At the QCISD(T)/6-311 + G*//B3LYP/6-311 + G* + ZPE (B3LYP/6-311 + G*) level, the decomposition barrier heights of LiN₅-B, NaN₅–B, KN₅-B, and RbN₅-B are predicted to be 19.9, 22.0, 22.5, and 23.0 kcal/mol, respectively. In addition, the rate constants of the decomposition reaction MN₅-B MN₃ + N₂ (M + Li, Na, K, and Rb) are also predicted using conventional transition state theory and canonical variational transition state theory, respectively.     

The performance of density functional theory for LnF (Ln=Nd,Eu, Gd,Yb) and YbH

Different density functional theory (DFT) functionals have been evaluated by studying geometries and bond strengths of YbH, YbF, EuF, GdF, and NdF and compared with accurate CCSD(T) results and, when available, experiment. The agreement between the CCSD(T) results and experiment, when available, is good. The agreement is also good between bond strengths calculated at the DFT level using relativistic effective core potentials and the CCSD(T) results. However, the all-electron ADF calculations systematically overestimate binding energies. The geometries obtained by both the all-electron and the effective-core-potential-based DFT calculations are generally in good agreement with the CCSD(T) results.Contribution to the Björn Roos Honorary Issue     

Monolithic octadecylsilyl-silica gel column for the high-speed ion chromatographic determination of acidity

A monolithic ODS-silica gel column modified by saturating it with lithium dodecylsulfate (Li-DS) was used to demonstrate the high-speed separation of H+ from other mono- and divalent cations, such as Na+, NH4+, K+, Mg2+ and Ca2+ using ion chromatography (IC). Using a 5 mM EDTA-2K solution containing 0.10 mM Li-DS (pH 4.80) as eluent, H+ was eluted with a sharp and symmetrical peak within 1.0 min before other cations at a flow-rate of 1.5 ml min(-1). The rapid elution of H+ and its conductimetric detection could be attributed to the presence of EDTA (HY2-), which can convert H+ ions as anions. i.e. H(+) + H2Y(2-) --> H3Y(-). The acidity of rainwater and deionized water samples was determined using this IC system with satisfactory results.     

Substituent control in the diastereoselectivity of dipolar cycloadditions of nitrones and their Zn(II) complexes with N-arylmaleimides

The π-π stacking interactions between maleimide's and nitrone's aromatic rings during the 1,3-dipolar cycloaddition were assumed to control the exo-endo selectivity of the reaction. The exo-endo ratios change during the reactions until they reach a constant value, which depends on the substituent. Electron-withdrawing groups favour the exo adduct while electron-donating groups favour the endo adduct. The nitrone ZnBr₂ complexes react much more slowly than the free nitrone and the cycloaddition is exo selective in all cases independent of the substituents on the maleimide's aromatic ring. Thermal retrocycloaddition of the cycloadducts produce the corresponding nitrones. The ring opening in the presence of secondary amines did not induce imine formation. endo Adducts were shown for the first time to be the stable paramagnetic compounds.     

Excess Molar Volumes and Liquid–Liquid Equilibria of the Ionic Liquid 1-Methyl-3Octyl-Imidazolium Tetrafluoroborate Mixed with Butan-1-ol and Pentan-1-ol

Experimental densities were measured for the system 1-methyl-3-octyl-imidazolium tetrafluoroborate [OMIM][BF₄] + butan-1-ol, + pentan-1-ol at 298.15 K and ambient pressure using a vibrating tube densimeter, taking into account the influence of the viscosity correction. Excess molar volumes V^E have been determined. V^E is quite small and negative in the alcohol-rich range of the mixture composition and positive in the alcohol-poor range. LLE data of [OMIM][BF₄] + pentan-1-ol have been measured using a laser light scattering cell for detecting cloud points at different compositions in the temperature range of 282–292 K. A miscibility gap with an upper critical solution temperature (UCST) of 292 K has been found.     

Synthesis and characterization of new strontium 4-carboxyphenylphosphonates

Several new strontium 4-carboxyphenylphosphonates, i.e., two modifications of Sr(HOOCC₆H₄PO₃H)₂, SrH(OOCC₆H₄PO₃)·H₂O, Sr₃(OOCC₆H₄PO₃)₂·4H₂O and Sr₃(OOCC₆H₄PO₃)₂·5.7H₂O were prepared and characterized by elemental analysis, thermogravimetry, X-ray powder diffraction and infrared spectroscopy. It was found that the compositions of these compounds depend on the acidity of the reaction medium. In addition, the presented compounds are interconvertible in dependence on pH. The position of the acid hydrogen atom in SrH(OOCC₆H₄PO₃)·H₂O was determined from the IR spectra of the studied compounds.The structure of the β modification of Sr(HOOCC₆H₄PO₃H)₂ was solved from its X-ray powder diffraction pattern using an ab initio method (the FOX program) with subsequent Rietveld refinement in the FULLPROF program. The compound is monoclinic, with the space group P2₁/c (No. 14), a=49.88(2), b=7.867(2), c=5.602(3) Å, β=128.68(2)°, and Z=4. It has a one-dimensional structure with an inorganic part built of SrO₈ distorted tetragonal antiprisms.