Dynamic characteristics of a peptide-binding groove of human HLA-A2 class I MHC molecules: normal mode analysis of the antigen peptide-class I MHC complex

Class I major histocompatibility complex (MHC) binds antigen peptides with various sequences. We performed a normal mode analysis of HLA-A2 MHC that binds three peptides with different affinity. HLA-A2 MHC has a peptide-binding groove composed of two alpha-helices (residue 49-84, residue 140-179). Some residues in the center of the groove showed an increase in fluctuations and some residue pairs between two helix groups showed a negative change in correlations by removing the antigen peptide. The extent of the fluctuation and correlation changes correlated well with the experimental ranking of the three peptides in binding affinity. Some definite anti-correlative motions were found between two helix groups in low frequency modes (<50 cm(-1)) by removing the antigen peptide. We propose that the above anti-correlative motions play an important role to bind the antigen peptide, especially in obtaining a "dynamic fit."     

Vibrational spectra and density functional study of propylgermane

Raman and infrared spectra of propylgermane, CH₃CH₂CH₂GeH₃, and its Ge-deuterated analog, CH₃CH₂CH₂GeD₃, were investigated in their gaseous, liquid and solid states. The normal coordinate treatment was carried out by density functional theory (DFT) calculation, using B3LYP/6-31G^* and 6-311++G^** basis sets, and the corresponding fundamental vibrations were assigned. The trans (T) and gauche (G) forms around the central C–C bond coexisted in the gaseous and liquid states and only the T form existed in the solid state. From the temperature dependent measurements of the Raman spectra in the liquid state, the enthalpy difference was found to be ΔH(T−G)=−0.36±0.02 kcalmol⁻¹ with the T form being more stable. The energy differences between the isomers obtained by DFT calculations were ΔE(T−G)=−0.46 kcalmol⁻¹ and ΔE(T−G)=−0.87 kcalmol⁻¹ by the 6-31G^* basis set and 6-311++G^** basis set, respectively.     

Novel superstructure of nondiscoid mesogens: uneven-parallel association of half-disk molecules, 3,4,5-trialkoxybenzoic anhydrides, to a columnar structure and its one-directionally geared interdigitation

Compact and simple nondiscoid mesogens, trialkoxybenzoic anhydrides 2-11 ((RO)(3)C(6)H(2)-CO-O-CO-C(6)H(2)(OR)(3), R = C(2)H(5), n-C(3)H(7), n-C(4)H(9), n-C(6)H(13), n-C(8)H(17), n-C(10)H(21), n-C(12)H(25), n-C(14)H(29), n-C(16)H(33), and (S)- and (R)-3,7-dimethyloctyl) were designed and synthesized, and their superstructures were investigated by polarized light microscopy, differential scanning calorimetry, calculation (MM2 and AM1), circular dichroism spectroscopy, and X-ray diffraction. As the result, in the cases of 5-9 and 11, the half-disk molecules in the liquid crystal phases were self-assembled by the dipole-dipole interaction between their carbonyl groups to a column in which the molecules were piled up in an alternately antiparallel manner, and the columns were interdigitated each other. The observed interdigitations were highly directional in the perpendicular direction to the column axis. In the case of compound 11 which has (S)- or (R)-3,7-dimethyloctyl groups, a helical organization of the molecules in the column was estimated from the peaks in the circular dichroism spectra. This is the first report of a one-directionally interdigitated columnar phase, and these compounds are the first liquid crystalline acid anhydrides. It was demonstrated that a -CO-O-CO- moiety is useful as a polar junction in liquid crystalline compounds.     

Synthesis of C-nor-4,6-secocamptothecin and related compounds

C-nor-4,6-Secocamptothecin 2 , 4-ethyl-4-hydroxy-6-(2-quinolinyl)-1H-pyrano[3,4-c]pyridine-3,8(4H,7H)-dione, lacking the C-ring of camptothecin 1 , and its related compounds 3 and 4 were prepared from ethyl quinoline-2-carboxylate 7 . By an analogous reaction sequences, synthesis of 6-(2-pyridinyl)-1H-pyrano[3,4-c]-pyridine-3,8(4H7H)-dione derivatives 5 and 6 , which contain the B, D, and E ring of 1 , were achieved.     

Further studies on the anti-ulcerogenic effects of compound, 2-(E-2-decenoylamino)ethyl 2-(cyclohexylethyl) sulfide.

Tha anti-ulcerogenic mechanism of 2-(E-2-decenoylamino)ethyl 2-(cyclohexylethyl) sulfide (compd. III-1a) was investigated in various gastric defensive factors. Compound III-1a maintained the high molecular glycoprotein (relative content of Fr. I hexose) and accelerated hexosamine synthesis which were reduced by water immersion stress. But plaunotol did not have these actions. The lipid peroxide level in the gastric mucosa from water immersion stressed rat was lowered by the administration of compd. III-1a. Compound III-1a maintained prostaglandin E2 (PGE2) and PGI2 contents which were reduced in the early phase of the stress and accelerated PGs synthesis in the late phase of the stress. Furthermore, compd. III-1a maintained phospholipase A2 (PLA2) activity which was reduced by the stress. The plaunotol treated group showed the same tendency as the compd. III-1a treated group on the lipid peroxide level, PGE2 and PGI2 contents, and PLA2 activity, but the potency of plaunotol was less than that of compd. III-1a. Compound III-1a accelerated gastric cell proliferation in pyloric glands of hydrocortisone treated rats. Tetragastrin accelerated significantly the cell proliferation in fundic glands. The sucralfate treated group showed the same tendency as the compd. III-1a treated group but the potency of sucralfate was less than that of compd. III-1a. The results in the present study suggest that compd. III-1a has a protective action on gastric mucosa.     

Deoxyribonucleic acid (DNA) damage induced by bleomycin-Fe(II) in vitro: formation of 8-hydroxyguanine residues in DNA

Treatment of calf thymus deoxyribonucleic acid (DNA) with bleomycin-Fe(II) at 0 degree C for 5 min resulted in the formation of 8-hydroxyguanine (8-OH-Gua) residues in DNA in a dose dependent manner, in addition to the formation of base propenal, a DNA-degradation product. The amount of 8-OH-Gua was about one-hundredth of that of base propenal. Treatment of cellular DNA with bleomycin did not result in any increase of 8-OH-Gua even under conditions of 100% cell killing.     

Continuous flotation of trace amounts of nitrite ion in water

A flotation method in which sample is continuously fed at flow rates of 2–3 1 h^-1 into a separation tube is described. The nitrite (3–40 μg l^-1) is continuously converted to an azo dye for spectrophotometric measurement at 15-min intervals.     

A simple chromatographic method for determining norfloxacin and enoxacin in pharmacokinetic study assessing CYP1A2 inhibition

We developed a simple assay method for the determination of serum and urine norfloxacin and enoxacin using reversed‐phase high‐performance liquid chromatography and perchloric acid precipitation for sample pre‐treatment. Optimized conditions can permit detection of norfloxacin and enoxacin in the same chromatogram, so either compound can be used as an internal standard for another determinant. Supernatants of the precipitated samples were analyzed by the octadecylsilyl silica‐gel column under ambient temperature and an ultraviolet wavelength of 272 nm. A mobile phase solvent consisting of 20 mm sodium dihydrogenphosphate (pH 3.0) and acetonitrile (85:15, v/v) was pumped at a flow rate of 1.0 mL/min. The calibration curves for norfloxacin and enoxacin at a concentration of 62.5–1000 ng/mL for serum and 250–4000 ng/mL for urine were linear (r > 0.9997). The recoveries of norfloxacin and enoxacin from serum and urine were >94% with the coefficient of variations (CV) <5%. The CVs for intra‐ and inter‐day assay of norfloxacin and enoxacin were <4.2 and <5.5%, respectively. This method can be applied to the pharmacokinetic study of norfloxacin and enoxacin after repeated administration to assess changes in CYP1A2 activity in healthy subjects. Copyright © 2010 John Wiley & Sons, Ltd.