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.     

Intramolecular 1,3-dipolar cycloaddition of cyclo-1,3-diene-tethered nitrile oxides

Intramolecular 1,3-dipolar cycloaddition of cyclo-1,3-diene- and -1,3,5-triene-tethered nitrile oxides gave tricyclic isoxazolines as a single stereoisomer in most cases. The relative stereochemistry of tricycle-fused isoxazolines resulting from 1,3-dipolar cycloaddition of cyclo-1,3-diene-tethered nitrile oxides is cis-cis, whereas from cyclohepta-1,3,5-triene-tethered nitrile oxides the cis-trans isomer predominates.     

Synthesis of peptides employing Fmoc-amino acid chlorides and commercial zinc dust

Coupling of Fmoc-amino acid chlorides mediated by activated commercial zinc dust for the synthesis of peptides is described. The reaction is carried out in an organic medium. The necessity of using an inorganic base like NaHCO₃/Na₂CO₃ or an organic base like DIEA/NMM/TEA/pyridine is circumvented. The coupling is reasonably fast, clean, racemization free and high yielding.     

In vitro and in vivo investigations on the photodynamic activity of core-modified expanded porphyrin--ammonium salt of 5,10,15,20-tetrakis-(meso-p-sulfonato phenyl)-25,27,29-trithia sapphyrin

The core modification of expanded porphyrins has been proved to have better photochemical properties, which are favorable for photodynamic therapy (PDT) applications. In this context, this study was aimed to investigate the in vitro and in vivo photodynamic activity of one such core-modified expanded porphyrin, namely, ammonium salt of 5,10,15,20-tetrakis-(meso-p-sulfonato phenyl)-25,27,29-trithia sapphyrin. For the in vitro studies, human erythrocytes were used as a membrane semimodel system to investigate the partitioning ability and drug-uptake characteristics. The partition studies on the membrane semimodel system revealed that maximum partitioning occurs at 12 microgm/mL concentration, and from the drug-uptake studies it is observed that maximum amount of the sensitizer is bound to the erythrocyte membranes during a 45 min incubation period. Photohemolysis studies at different concentrations of the sensitizer and exposure time showed maximum damage at 5 microgm/mL and 30 min exposure time. In vivo studies were performed on 7,12-dimethylbenz(a)nthracene-induced superficial squamous cell carcinoma on mouse skin. The sensitizer at a concentration of 2.5% in 2.0% dimethyl sulfoxide was applied topically on the tumor spot. After 1 h incubation the tumor spot was exposed to laser irradiation from Nd-YAG laser at its second harmonic wavelength of 532 nm. The photodynamic efficacy was estimated by tumor volume measurements at regular intervals after the treatment. One month after PDT exposure a 3.9-fold decrease in the tumor volume was observed with respect to the tumor volume before treatment. The treatment efficacy was further confirmed by histological and fluorescence spectroscopic evaluations of the tissue biopsy sample from the treated area. The results of our study suggest that the ammonium salt of 5,10,15,20-tetrakis-(meso-p-sulfonato phenyl)-25,27,29-trithia sapphyrin may find possible applications in the new modality of cancer treatment.     

Locking effects in the finite element approximation of elasticity problems

Summary We consider the finite element approximation of the 2D elasticity problem when the Poisson ratiov is close to 0.5. It is well-known that the performance of certain commonly used finite elements deteriorates asv0, a phenomenon calledlocking. We analyze this phenomenon and characterize the strength of the locking androbustness of varioush-version schemes using triangular and rectangular elements. We prove that thep-andh-p versions are free of locking with respect to the error in the energy norm. A generalization of our theory to the 3D problem is also discussed.The work of this author was supported in part by the Office of Naval Research under Naval Research Grant N00014-90-J-1030The work of this author was supported in part by the Air Force Office of Scientific Research, Air Force Systems Command, U.S. Air Force, under grant AFOSR 89-0252     

Triphase catalysis. I. Kinetics and mechanism of alkylation of phenylacetonitrile with alkyl halides catalyzed by aqueous naoh and polymer-supported benzyltriethylammonium chloride

The alkylation and cycloalkylation of phenylacetonitrile (PAN) with excess of 1-bromobutane and 1,4-dibromobutane respectively catalyzed by aqueous NaOH and insoluble polystyrene-bound benzyltriethylammonium chloride were studied and the rates depend upon several experimental parameters. The rate of cycloalkylation of PAN is five times faster than the alkylation and the former proceeds even in the absence of the solid catalyst. Both alkylation and cycloalkylation gave higher rates in reverse addition method than in direct addition. Deprotonation of PAN by hydroxide ion takes place without participation of the polymeric catalyst. The electrostatic force between the positive charge on the nitrogen atom of catalyst and carbanion is responsible for alkylation of active nitrile with polystyrene-bound phase-transfer catalyst. The rates of both the reactions increase with increased stirring speed, ring substitution, hydroxide ion concentration and catalyst amount and decrease with increased particle size and the degree of cross-linking of the polymer. Apparent activation energies for the reactions were calculated. The kinetic results are discussed in terms of mass transfer and a combination of intraparticle diffusion and intrinsic reactivity limitations of the rates.