Sugar-to-base correlation in nucleic acids with a 5D APSY-HCNCH or two 3D APSY-HCN experiments

A five-dimensional (5D) APSY (automated projection spectroscopy) HCNCH experiment is presented, which allows unambiguous correlation of sugar to base nuclei in nucleic acids. The pulse sequence uses multiple quantum (MQ) evolution which enables long constant-time evolution periods in all dimensions, an improvement that can also benefit non-APSY applications. Applied with an RNA with 23 nucleotides the 5D APSY-HCNCH experiment produced a complete and highly precise 5D chemical shift list within 1.5 h. Alternatively, and for molecules where the out-and-stay 5D experiment sensitivity is not sufficient, a set of out-and-back 3D APSY-HCN experiments is proposed: an intra-base (3D APSY-b-HCN) experiment in an MQ or in a TROSY version, and an MQ sugar-to-base (3D APSY-s-HCN) experiment. The two 3D peak lists require subsequent matching via the N1/9 chemical shift values to one 5D peak list. Optimization of the 3D APSY experiments for maximal precision in the N1/9 dimension allowed matching of all ¹⁵N chemical shift values contained in both 3D peak lists. The precise 5D chemical shift correlation lists resulting from the 5D experiment or a pair of 3D experiments also provide a valuable basis for subsequent connection to chemical shifts derived with other experiments.     

细微短足软珊瑚的化学成分研究

本文对采自广西涠洲岛海域细微短足软珊瑚（Cladiellasubtilis）的化学成分进行研究,经理化常数和波谱数据分析,分别鉴定为（20R,24S）-5-烯-21羧基-麦角甾-3β-醇（1）、柳珊瑚甾醇（2）、鲨肝醇（3）及麦角甾-5-烯-3β-醇（4）。对细微短足软珊瑚（Cladiella subtilis）化学成分的研究尚属首次。     

Fragment library screening reveals remarkable similarities between the G protein-coupled receptor histamine H₄ and the ion channel serotonin 5-HT₃A

A fragment library was screened against the G protein-coupled histamine H(4) receptor (H(4)R) and the ligand-gated ion channel serotonin 5-HT(3A) (5-HT(3A)R). Interestingly, significant overlap was found between H(4)R and 5-HT(3A)R hit sets. The data indicates that dual active H(4)R and 5 HT(3A)R fragments have a higher complexity than the selective compounds which has important implications for chemical genomics approaches. The results of our fragment-based library screening study illustrate similarities in ligand recognition between H(4)R and 5-HT(3A)R and have important consequences for selectivity profiling in ongoing drug discovery efforts on H(4)R and 5-HT(3A)R. The affinity profiles of our fragment screening studies furthermore match the chemical properties of the H(4)R and 5-HT(3A)R binding sites and can be used to define molecular interaction fingerprints to guide the in silico prediction of protein-ligand interactions and structure.     

Nucleotide and AP5A complexes of porcine adenylate kinase: A 1H and 19F NMR study

Proton and fluorine nuclear magnetic resonance spectroscopies (NMR) were used as methods to investigate binary complexes between porcine adenylate kinase (AK1) and its substrates. We also studied the interaction of fluorinated substrate analogues and the supposed bisubstrate analogue P1,P5-bis(5'-adenosyl) pentaphosphate (AP5A) with AK1 in the presence of Mg2+. The chemical shifts of the C8-H, C2-H, and ribose C1'-H resonances of both adenosine units in stoichiometric complexes of AK1 with AP5A in the presence of Mg2+ could be determined. The C2-H resonance of one of the adenine bases experiences a downfield shift of about 0.8 ppm on binding to the enzyme. The chemical shift of the His36 imidazole C2-H was changed in the downfield direction on ATP-Mg2+ and, to a lesser extent, AMP binding. 19F NMR chemical shifts of 9-(3-fluoro-3-deoxy-beta-D-xylofuranosyl)adenine triphosphate (3'-F-X-ATP)-Mg2+ and 9-(3-fluoro-3-deoxy-beta-D-xylofuranosyl)adenine monophosphate (3'-F-X-AMP) bound to porcine adenylate kinase could be determined. The different chemical shifts of the bound nucleotides suggest that their mode of binding is different. Free and bound 3'-F-X-AMP are in fast exchange with respect to their 19F chemical shifts, whereas free and bound 3'-F-X-ATP are in slow exchange on the NMR time scale in the absence as well as in the presence of Mg2+. This information could be used to determine the apparent dissociation constants of the nucleotides and the 3'-F-X analogues in the binary complexes.(ABSTRACT TRUNCATED AT 250 WORDS)     

Backbone structure confirmation and side chain conformation refinement of a bradykinin mimic BKM-824 by comparing calculated (1)H, (13)C and (19)F chemical shifts with experiment

Calculated and experimental (1)H, (13)C and (19)F chemical shifts were compared in BKM-824, a cyclic bradykinin antagonist mimic, c[Ava(1)-Igl(2)-Ser(3)-DF5F(4)-Oic(5)-Arg(6)] (Ava=5-aminovaleric acid, Igl=alpha-(2-indanyl)glycine, DF5F=pentafluorophenylalanine, Oic=(2S,3aS,7aS)-octahydroindole-2-carboxylic acid). The conformation of BKM-824 has been studied earlier by NMR spectroscopy (M. Miskolzie et al., J. Biomolec. Struct. Dyn. 17, 947-955 (2000)). All NMR structures have qualitatively the same backbone structure but there is considerable variation in the side chain conformations. We have carried out quantum mechanical optimization for three representative NMR structures at the B3LYP/6-31G* level, constraining the backbone dihedral angles at their NMR structure values, followed by NMR chemical shift calculations at the optimized structures with the 6-311G** basis set. There is an intramolecular hydrogen bond at Ser(3) in the optimized structures. The experimental (13)C chemical shifts at five C(alpha) positions as well as at the Cbeta, Cgamma and Cdelta position of Ava(1), which forms part of the backbone, are well reproduced by the calculations, confirming the NMR backbone structure. A comparison between the calculated and experimental H(beta) chemical shifts in Igl(2) shows that the dominant conformation at this residue is gauche. Changes of proton chemical shifts with the scan of the chi(1) angle in DF5F(4) suggest that chi(1)180 degrees. The calculated (1)H and (13)C chemical shifts are in good agreement with experiment at the rigid residue Oic(5). None of the models gives accurate results for Arg(6), presumably because of its positive charge. Our study indicates that calculated NMR shifts can be used as additional constraints in conjunction with NMR data to determine protein conformations. However, to be computationally effective, a database of chemical shifts in small peptide fragments should be precalculated.     

Further studies on the inhibition of sterol biosynthesis in animal cells by 15-oxygenated sterols

The chemical syntheses of a number of C27 15-oxygenated sterols and their derivatives have been pursued to permit evaluation of their activity in the inhibition of sterol biosynthesis in animal cells in culture. Described herein are chemical syntheses of 3 alpha-benzoyloxy-5 alpha-cholest-8(14)-en-15-one, 5 alpha-cholest-8(14)-en-3 alpha-ol-15-one, 5 alpha-cholest-8(14)-en-15-one-3 beta-yl pyridinium sulfate, 5 alpha-cholest-8(14)-en-15-one-3 beta-yl potassium sulfate (monohydrate), 5 alpha-cholest-8(14)-en-15-one-3 alpha-yl pyridinium sulfate, 5 alpha-cholest-8(14)-en-3 alpha-yl potassium sulfate (monohydrate), 5 alpha-cholest-8(14)-en3,7,15-trione, 5 alpha-cholest-8(14)-en-15 alpha-ol-3-one, 5 alpha, 14 alpha-cholestan-3 beta, 15 beta-diol diacetate, 5 alpha, 14 beta-cholestan-3 beta, 15 beta-diol diacetate, 5 alpha, 14 alpha-cholestan-3 beta, 15 alpha-diol, 5 alpha, 14 alpha-cholestan-15 alpha-ol-3-one, 5 alpha, 14 beta-cholestan-3 beta, 15 beta-diol, 5 alpha, 14 alpha-cholestan-3,15-dione, and 5 alpha, 14 beta-cholestan-3,5-dione. The effects of 8 of the above compounds and of 5 alpha-cholesta-6,8(14)-dien-3 beta-ol-15-one, 3 beta-he misuccinoyloxy-5 alpha-cholest-8(14)-en-15 one, 3 beta-hexadecanoyloxy-5 alpha-cholest-8(14)-en-15-one, 5 alpha-cholest-8(14)-en-3,15-dione, 5 alpha-cholesta-6,8(14)-dien-3,15-dione, 5 alpha-cholest-8-en-3 beta, 15 alpha-diol, 5 alpha-cholest-7-en-3 beta, 15 alpha-diol, 5 alpha-cholest-8(14)-en-15 alpha-ol-3-one, 5 alpha-cholest-8-en-15 alpha-ol-3-one, and 5 alpha-cholest-7-en-15 alpha-ol-3-one on the synthesis of digitonin-precipitable sterols and on levels of HMG-CoA reductase activity have been investigated and compared with previously published data on 7 other C27 15-oxygenated sterols.     

Detection and classification of neurotoxins using a novel short-term plasticity quantification method

A tissue-based biosensor is described for screening chemical compounds that rapidly affect the nervous system. The proposed sensor is an extension of a previous work on cultured hippocampal slices [Biosens. Bioelectron. 16 (2001) 491]. The detection of the chemical compounds is based on a novel quantification method of short-term plasticity (STP) of the CA1 system in acute hippocampal slices, using random electrical impulse sequences as inputs and population spike (PS) amplitudes as outputs. STP is quantified by the first and the second order kernels using a variant of the Volterra modeling approach. This approach is more specific and time-efficient than the conventional paired pulse and fixed frequency train methods [J. Neurosci. Methods 2 (2002) 111]. Describing the functional state of the biosensor, the kernels changed accordingly as chemical compounds were added. The second order kernel was decomposed into nine Laguerre functions. The corresponding Laguerre coefficients along with the first order kernel were used as features for classification purposes. The biosensor was tested using picrotoxin (100 μM), trimethylopropane phosphate (10 μM), tetraethylammonium (4 mM), valproate (5 mM), carbachol (5 mM), DAP5 (25 μM), CNQX (3 μM), and DNQX (0.15, 1.5, 3, 5 and 10 μM). Each chemical compound gave a different feature profile corresponding to its pharmacological class. The first order kernel and the Laguerre coefficients formed the input to an artificial neural network (ANN) comprised of a single layer of perceptrons. The ANN was able to classify each tested compound into its respective class.     

Metabolism of sitosterol by a Pseudomonas species.

Fermentation of sitosterol by a Pseudomonas species (SK-25) resulted in the formation of 5-stigmastene-3 beta, 7 alpha-diol; 5,6 alpha-epoxy-5 alpha-stigmastan-3 beta-ol; 5,6 beta-epoxy-5 beta-stigmastan-3 beta-ol and 5 alpha-stigmastan-3 beta, 5,6 beta-triol. The metabolites were characterized by a variety of conventional chemical and spectrometric techniques.     

The Chemical Constituents of Elsholtzia densa Benth.

Ten compounds were isolated from Elsholtzia densa Benth. and their structures were identified by spectral and chemical methods as following: n-nonacosane (1), succinic acid (2), 5- ( 3 ”, 3 ”-dimethylallyl ) -8-methoxyfurocoumarin (3), 5- ( 3 ”-methylbutyl) -8- methoxyfurocoumarin (4), 5- (3”-hydroxy-3”-methylbutyl) -8-methoxyfurocoumarin (5), 3, 4-dihydroxycinnamic acid ( 6 ), 5-hydroxy-3’-methoxyflavanone-7-O-rutinoside ( 7 ), quercetin-3-O-β-D-glucoside ( 8 ), kaempferol-3-O-β-D-glucoside ( 9 ), 5-hydroxy-4’- methoxyflavone-7-O-rutinoside (10). Among them, compounds 4 and 5 are new naturally occurring furocoumarins.     

Discovery of 2-substituted benzoxazole carboxamides as 5-HT3 receptor antagonists

A new class of 2-substituted benzoxazole carboxamides are presented as potent functional 5-HT(3) receptor antagonists. The chemical series possesses nanomolar in vitro activity against human 5-HT(3)A receptors. A chemistry optimization program was conducted and identified 2-aminobenzoxazoles as orally active 5-HT(3) receptor antagonists with good metabolic stability. These novel analogues possess drug-like characteristics and have potential utility for the treatment of diseases attributable to improper 5-HT(3) receptor function, especially diarrhea predominant irritable bowel syndrome (IBS-D).     

Resonance assignments of non-exchangeable protons in B type DNA oligomers, an overview.

The chemical shifts of 1H resonances of non exchangeable protons (except H5', H5" and adenine H2) of over six hundred nucleotides have been collected. The influence which the base of the nucleotide itself as well as the bases on its 5' and 3' side exert on the chemical shifts of the various resonances has been investigated. Most of the resonances appear to be predominantly influenced by only one base. For H2', H2", H3', H4' and H6/H8 this is the base of the central nucleotide, for H5(C) and CH3(T) it is the one on the 5' side and for H1' it is the one on the 3' side. Chemical shift distribution profiles are presented which allow an estimation of the probability of finding a particular resonance at a particular position in the spectrum.     

New pregnane steroids from Turraea pubescens

Three new pregnane steroids, 2beta,3beta,5beta-trihydroxy-pregn-20-en-6-one (1), 3beta-hydroxy-5alpha-pregn-7,20-dien-6-one (2), and 3beta-acetoxy-5alpha-pregn-7,20-dien-6-one (3) were isolated from the twigs and leaves of Turraea pubescens, and were structurally elucidated on the basis of spectroscopic data and chemical method.     

Three New Steroidal Alkaloids from Pachysandra axillaris

This paper describes the chemical structure elucidation of the three new alkaloids isolated from Pachysandra axillarls Franch. They are pachysamine G (20α-dimethylamino-3β-tigloylamino-5α-pregnane), pachysamine H (20α-dimethylamino-3α-N-methyl, benzoylamino-5α-pregnane) and pachysanaximine A (20 α-dimethylamino-3β-methylamino-4β-benzoxyl-5α-pregnane) respectively. Other two compounds were identified as Pachysamine A, B.     

广东冬青中的三萜及三萜皂甙成分

从广东冬青（Ｉｌｅｘ ｋｗａｎｇｔｕｎｇｅｎｓｉｓ）的叶中分离得到四个三萜皂甙和三个三萜成分,通过光谱解析及化学方法,三个三萜成分分别鉴定为齐墩果酸（１）、熊果酸（２）和常春藤皂甙元（３）;四个三萜皂甙成分分别鉴定为齐墩果酸３－Ｏ－β－Ｄ－吡喃葡萄糖基－（１→３）－α－Ｌ－吡喃阿拉伯糖甙（４）、齐墩果酸３－Ｏ－β－Ｄ－吡喃葡萄糖基－（１→２）－α－Ｌ－吡喃阿拉伯糖甙（５）、齐墩果酸３－Ｏ－β－Ｄ－     

Eudesmane and megastigmane glucosides from Laggera alata

Four eudesmane glucosides, alatosides A-D (1-4), and one megastigmane glucoside, alatoside E (5), were isolated from the BuOH fraction of Laggera alata along with six known compounds. Structures of the new compounds were elucidated by a combination of chemical and spectroscopic methods. Alatosides A-E were characterized as: 1alpha-O-(beta-D-glucopyranosyloxyl)-7-epi-eudesma-11-en-2beta,4alpha-diol (1), 2beta-O-(beta-D-glucopyranosyloxyl)-eudesma-4alpha-hydroxyl-11(13)-en-12-oic-acid (2), 5beta-O-(beta-D-glucopyranosyloxyl)-eudesma-4(15),11(13)-dien-12-oic-acid (3), 5alpha-O-(beta-D-glucopyranosyloxyl)-eudesma-3,11(13)-dien-12-oic acid (4) and 3beta-O-(beta-D-glucopyranosyloxyl)-megastigma-9-one (5), respectively. Based on the chemical characteristics of eudesmane derivatives isolated from the Laggera genus, it was suggested that there are probably two different biogenetic pathways for these secondary metabolites in this genus.     

Synthesis and properties of oligodeoxyribonucleotides containing a mutagenic base, N4-aminocytosine.

Oligodeoxyribonucleotides containing a mutagenic base analog, N4-aminocytosine, 5'-AATTGC(am)AATT-3' and 5'-AATTAC(am)AATT-3' (C(am); N4-aminocytosine) were prepared by chemical modification of 5'-AATTGCAATT-3' and 5'-AATTACAATT-3', respectively. The values of Tm were 29 degrees C for 5'-AATTGC(am)AATT-3' and 32 degrees C for 5'-AATTGCAATT-3'. In contrast, no melting was observed for 5'-AATTAC(am)AATT-3' and 5'-AATTACAATT-3'. These data show that the stability of C(am)-purine paris is C(am)-G > C(am)-A and that C(am)-G is less stable than C-G. This property is consistent with the incorporation specificity of N4-amino-dCTP during DNA synthesis in vitro.     

Anthocyanins in callus induced from purple storage root of Ipomoea batatas L

Two anthocyanins were isolated from the highly pigmented callus derived from the storage root of purple sweet potato (Ipomoea batatas L.) cultivar 'Ayamurasaki'. One was identified as cyanidin 3-O-sophoroside-5-O-glucoside, and the other as cyanidin 3-O-(2-O-(6-O-(E)-p-coumaroyl-beta-D-glucopyranosyl)-beta-D-glucop yranoside)-5-O-beta-D-glucopyranoside, by chemical and spectroscopic analysis.     

Chemical interactions with herpes simplex type 2 virus: Enhancement of transformation by hydrazine and 1,2-dimethylhydrazine

Quantitative assays for the morphological transformation of 3T3 Swiss mouse cells by herpes simplex type 2 virus (HSV-2) were employed to examine the effect on cell transformation of chemical carcinogens and suspected carcinogens. Exposure of the cells to the chemical compound, followed by virus infection, resulted in enhancement of transformation when compared to that observed with chemical or virus alone. Enhancement occurred in tests utilizing either UV light-inactivated HSV-2 (strain 333) or a temperature-sensitive (ts) mutant of HSV-2 [A₈(293)]. A series of seven ts-mutants were tested and exhibited varying degrees of transformation. Enhancement of transformation occurred in cells treated with hydrazine (HZ) and 1,2-dimethylhydrazine (SDMH). No enhancement occurred when cells were treated with monomethylhydrazine, 1,1-dimethylhydrazine and the jet fuels JP-5, JP-10, RJ-4 and RJ-5. A strong time dependence after treatment was demonstrated with some enhancement seen at 6 h after chemical treatment but the greatest enhancement appeared when virus infection began after 24 h of chemical exposure.     

海南长须果化学成分的研究

从海南长须果（ＴａｃｃａｃｈａｎｔｒｉｅｒｉＡｎｄｒｅ）中分离得到了３个结晶性成分,经过理化常数和光谱分析,分别鉴定为箭根酮内酯Ａ（Ｉ）、１,７－二对苯羟墓－３,５－二羟基－庚烷（Ⅱ）和α－单棕桐酸甘油酯（Ⅲ）。它们均属首次从该植物中分得。其中箭根酮内酯Ａ有抗癌活性。