天然产物中五元杂环生物合成过程的研究进展

五元杂环是指一类含有除碳以外的杂原子的五元环有机化合物,可分为含有一个杂原子的杂环和含有两个杂原子的五元杂环。杂原子通常为氮原子、氧原子或硫原子,在成环时符合休克尔(Hückel)规则,具有芳香性。五元杂环以独特的生物学特性和参与氢键相互作用的能力,成为天然化合物发挥活性功能的重要基团。五元杂环在不同的生物合成途径中有多种环化过程,其前体可以是天然氨基酸、乙酸及乙酰辅酶A等多种形式。将从吡咯、恶唑和噻唑三种五元杂环入手,以代表性化合物为例,对其在生命体中生物合成过程的成环过程进行探讨,为组合生物合成和未知化合物中五元杂环成环过程的研究提供参考。     

Volatile cephalic substances of the stingless bees, Trigona mexicana and Trigona pectoralis

Extracts of the heads of the stingless bees, Trigona mexicana and T. pectoralis, contain mixtures of compounds that are identifiable by gas chromatography and mass spectrometry. These compounds form homologous series of aliphatic alcohols and ketones with an odd number of carbon atoms and functional groups at the 2-position. The alcohols and the ketones range from 7 to 17 carbon atoms. Benzaldehyde and a nitrogen containing compound are also present in the mixtures. The series of compounds from the two species are nearly identical qualitatively. They differ in the absence of 2-undecanol and 2-pentadecanol from the extracts of T. mexicana and T. pectoralis, respectively. The highest concentration of material is found in the 7-carbon fraction in T. mexicana and in the 13 to 15 carbon range in T. pectoralis. There is a major difference in the relative concentration of 2-heptanol and 2-heptanone in the two species with the concentration of the alcohol being one-fourth that of 2-heptanone in T. mexicana and ten times greater than the ketones in T. pectoralis.Both the alcohols and ketones are alarm pheromones. The alcohols are more active in inducing attack by the bees than are the ketones, but a mixture of the ketones and benzaldehyde was very active.     

Degradation of Ovalbumin by L-Ascorbic Acid in the Presence of Cupric Ion

Ovalbumin, L-ascorbic acid and cupric sulfate were allowed to react at pH 3.0, 6.0, 6.8 and 7.5. Non-proteinous nitrogen compounds were formed from ovalbumin coupled with autoxidation of ascorbic acid, and a pronounced increase in their formation was observed in the reactions of neutral pH ranges. Non-proteinous nitrogen compounds contained peptides, free amino acids and ammonia. In the reactions of ovalbumin with triose reductone similar results to those with ascorbic acid were obtained. In the ovalbumin degraded with ascorbic acid at pH 6.8 was found an increase of N-terminal amino acid, which could react with carbonyl compounds resulting in browning.     

Kinetics of Organic Transformations under Mild Aqueous Conditions: Implications for the Origin of Life and its Metabolism

The rates of thermal transformation of organic molecules containing carbon, hydrogen, and oxygen were systematically examined in order to identify the kinetic constraints that governed origin-of-life organic chemistry under mild aqueous conditions. Arrhenius plots of the kinetic data were used to estimate the reaction of half-lifes at 50 degrees C. This survey showed that hydrocarbons and organic substances containing a single oxygenated group were kinetically the most stable; whereas organic substances containing two oxygenated groups in which one group was an alpha- or beta-positioned carbonyl group were the most reactive. Compounds with an alpha- or beta-positioned carbonyl group (aldehyde or ketone) had rates of reaction that were up to 10(24)-times faster than rates of similar molecules lacking the carbonyl group. This survey of organic reactivity, together with estimates of the molecular containment properties of lipid vesicles and liquid spherules, indicates that an origins process in a small domain that used C,H,O-intermediates had to be catalytic and use the most reactive organic molecules to prevent escape of its reaction intermediates.     

Addition of amines and carbon nucleophiles to vinyl sulfone-modified 6-deoxy-hex-3-enopyranoside: a case of nucleophile dependent diastereoselectivity

Reactions of amines and carbon nucleophiles with 4-sulfonyl-hex-3-enopyranoside generate a range of C-3 amino- and C-3 branched-chain sugars, which are analogues of 3-amino-3,6-dideoxy sugars and 3-C-branched-chain-3,6-dideoxy sugars. The diastereoselectivity of addition reaction is nucleophile dependent; while both nitrogen and carbon nucleophiles added in cis-fashion, amines generated C3-C4 trans-diaxial products (gulo-derivatives), and carbon nucleophiles afforded C3-C4 trans-diequatorial products (gluco-analogues).     

Novel [Ru(polypyridine)(CO)2Cl2] and [Ru(polypyridine)2(CO)Cl]-type complexes: Characterizing the effects of introducing azopyridyl ligands by electrochemical, spectroscopic and crystallographic measurements

The reaction of ruthenium carbonyl polymer ([Ru(CO)₂Cl₂]_n) with azopyridyl compounds (2,2′-azobispyridine; apy or 2-phenylazopyridine; pap) generated new complexes, [Ru(azo)(CO)₂Cl₂] (azo = apy, pap). [Ru(apy)(CO)₂Cl₂] underwent photodecarbonylation to give a chloro-bridged dimer complex, whereas the corresponding pap complex ([Ru(pap)(CO)₂Cl₂]) was not converted to a dimer. The reactions of the chloro-bridged dimer containing the bpy ligand (bpy = 2,2′-bipyridine) with either apy or pap resulted in the formation of mixed polypyridyl complexes, [Ru(azo)(bpy)(CO)Cl]⁺. The novel complexes containing azo ligands were characterized by various spectroscopic measurements including the determination of X-ray crystallographic structures. Both [Ru(azo)(CO)₂Cl₂] complexes have two CO groups in a cis position to each other and two chlorides in a trans position. The azo groups are situated cis to the CO ligand in [Ru(azo)(bpy)(CO)Cl]⁺. All complexes have azo N-N bond lengths of 1.26-1.29 Å. The complexes exhibited azo-based two-electron reduction processes in electrochemical measurements. The effects of introducing azopyridyl ligands to the ruthenium carbonyl complexes were examined by ligand-based redox potentials, stretching frequencies and force constants of CO groups and bond parameters around Ru-CO moieties.     

Use of carbonyl group addition--elimination reactions for synthesis of nucleic acid conjugates

This review outlines the synthesis of covalent conjugates of oligonucleotides and their analogues that are obtained by reactions of carbonyl compounds with various nucleophiles such as primary amines, N-alkoxyamines, hydrazines, and hydrazides. The products linked by imino, oxime, hydrazone, or thiazolidine groups are shown to be useful intermediates for a wide range of chemical biology applications. Methods for their preparation, isolation, purification, and analysis are highlighted, and the comparative stabilities of the respective linkages are evaluated. The relative merits of incorporation of a carbonyl group, particularly an aldehyde group, into either the oligonucleotide or the ligand parts are considered. Examples of harnessing of aldehyde-nucleophile coupling for the labeling of nucleic acids are given, as well as their conjugation to various biomolecules (e.g. peptides and small molecule ligands), site-specific cross-linking of oligonucleotides to nucleic acid-binding proteins, assembly of multibranched supramolecular structures, and immobilization on functionalized surfaces. Future perspectives of bioconjugation and complex molecular engineering via carbonyl group addition-elimination reactions in nucleic acids chemistry are discussed.     

Nucleophilic Substitution Reactions of 5-Bromo-6-methyluridines

Abstract

The reactions of the 5-bromo-6-methyl-2′,3′-O-isopropylideneuridines 9 and 10 with a number of nucleophiles in hot DMF have been investigated. With acetate ion as the nucleophile, either the 5-acetoxy- (11,12) or the 6-acetoxymethyl- (15) products can be obtained in modest yield depending upon the exact reaction conditions. With nitrogen nucleophiles (aniline or p-methoxybenzylamine) reaction takes place at the 6-methyl carbon, whereas with sulfur nucleophiles (thiophenol, thioacetate) only the 5-substituted products are obtained.     

Reaction of l-halogenoses with nitrogen nucleophiles in the presence of tert-amine. Synthesis of 2'-deoxyribofuranosyl and arabinofuranosyl pyrimidines

Selective introduction of 2'-deoxyribofuranosyl and arabinofuranosyl moieties onto one of two nitrogen atoms in the pyrimidine ring was demonstrated by the reaction of 1-glycosyl chlorides with pyrimidines protected by the (octylthio)carbonyl group in the presence of tert-amine. Replacing pyrimidines by imidazole derivatives such as benzimidazole and theophylline as nucleophiles gave no nucleosides but orthoamide derivatives.     

Torsional strain considerations in the mechanism of the proteolytic enzymes,with particular application to carboxypeptidase A

Torsional deformation of the peptide linkage by anti distortion of cis substituents (i.e., forcing groups attached to one side of an amide partial π bond out of plane in opposite directions) leads to rehybridization of the constituent atoms (nitrogen and carbonyl carbon) toward tetrahedral geometry. In consequence the partial π bond is uniquely activated toward trans (antarafacial) addition with defined steric orientation of addends. Application of these considerations to the known structure of an enzyme-substrate complex of carboxypeptidase A leads to a unique mechanistic hypothesis for proteolytic cleavage by this enzyme. Extant evidence concerning the mode of catalysis is considered in light of a mechanism involving electrostatically induced torsional activation of the scissile peptide bond, Lewis acid coordination of zinc to amide carbonyl, proton donation from Glu 270 to the amide nitrogen of the scissile bond, with concerted attack upon the amide carbonyl by solvent water.     

Synthesis and biological evaluation of antitumour-active betulin derivatives

The reaction of betulinic aldehydes with various carbon nucleophiles gave a series of new betulin derivatives, among them epoxides, glycidic derivatives and β-hydroxy carbonyl compounds. Subsequent transformations of the β-hydroxy carbonyls lead to 1,3-diketo- and α,β-unsaturated betulin derivatives. These compounds were assayed for cytotoxicity using 15 human cancer cell lines and a colorimetric SRB-assay. Several compounds revealed significant antitumour activity.     

The Effect of Storage in Various Gaseous Atmospheres on the Microflora of Lamb Chops Held at—1°C

The effect of different gaseous atmospheres on the development of the bacterial flora on lamb chops stored at –1°C was examined. The atmospheres were air, nitrogen, hydrogen, and mixtures of air + carbon dioxide, oxygen + nitrogen, oxygen + carbon dioxide, nitrogen + carbon dioxide and hydrogen + carbon dioxide (gas ratio = 80:20, v/v). Storage life of chops ranged from two weeks in air to eight weeks in oxygen-free atmospheres. At the end of storage life Microbacterium thermosphactum was present as a major constituent of the bacterial flora in all atmospheres. In oxygen + carbon dioxide it was the predominant organism. In all other oxygen containing atmospheres, Pseudomonas spp. made up a large proportion of the flora. Strains of Enterobacteriaceae occurred in low-oxygen and oxygen-free atmospheres, and Lactobacillus spp. occurred in oxygen-free atmospheres.     

Pd-mediated functionalization of polysubstituted pyrroles: Their evaluation as potential inhibitors of PDE4

Novel polysubstituted pyrroles have been designed and accessed via a one-pot multicomponent reaction followed by Pd-mediated C-C bond forming reactions. All the compounds synthesized were tested for their PDE4B inhibitory properties in vitro and two of them obtained via Heck reaction showed significant inhibition. The docking results suggested that these alkenyl derivatives containing ester moiety interact well with the PDE4B protein in silico where the ester carbonyl oxygen played a key role. The pyrrole framework presented here could be a new template for the identification of small molecule based novel inhibitors of PDE4. The single crystal X-ray data of a representative compound is presented.     

Structural reassignment of the peroxide oxidation product of 5-methyl-5,6,7,8-tetrahydrofolate

Oxidation of 5-methyl-5,6,7,8-tetrahydrofolate with hydrogen peroxide at pH 6 gives a derivative containing an extra oxygen atom, which can then be reduced with the uptake of two hydrogen atoms by borohydride or by catalytic hydrogenation. The two compounds were previously suggested to be 4a-hydroxylated pteridines [G. R. Gapski, J. M. Whiteley and F. M. Huennekens, $\text{Biochemistry}\text{10}$: 2390 (1971)]. In this report ¹³C NMR studies show the disappearance of the clearly defined C-4a resonance of the folate derivative (?33 ppm relative to p-doxane) during oxidation, with the emergence, in the oxygenated product, of a new downfield resonance in the characteristic carbonyl region of the spectrum. After the reduction step this transposed resonance is in turn replaced by a resonance which corresponds to that of a secondary hydroxyl substituted carbon atom. The results suggest rearrangement of the pteridine nucleus has occurred during oxidation. Comparison with similar oxidation reactions in the simple lumazine and pterin series supports this occurrence. Of several possible isomeric structures 2-amino-8-methyl-4,9-dioxo-7-methyl-p-aminobenzoylglutamate-6,7,8,9-tetrahydro-4H-pyrazino (1,2-a)-s-triazine and its 9-hydroxyl analog have been assigned to the isolated products. Reevaluation of the previous experimental findings is in accordance with these assignments.     

Physiological studies on nitrogen fixation in the blue-green alga anabaena cylindrica

Summary Short-term manometric experiments with bacteria-free cultures of Anabaena cylindrica showed that the close dependency of nitrogen fixation upon photosynthesis could be temporarily eliminated in nitrogen-starved cells. Initial rates of nitrogen uptake by these cells in the absence of carbon dioxide were equally rapid in the light and dark, decreasing and finally ceasing after two hours. Continued steady nitrogen uptake was only maintained for long periods in the presence of carbon dioxide in the light. In the dark, nitrogen uptake was accompanied by carbon dioxide evolution.More oxygen was evolved in the light by cells fixing nitrogen than by those incubated under argon. This additional oxygen evolution could be accounted for by extra carbon dioxide fixation in the presence of nitrogen.Of a number of organic compounds tested, only sodium pyruvate stimulated nitrogen fixation. This stimulation was achieved both in the light and dark and in the presence and absence of carbon dioxide, showing that the role of pyruvate was other than acting as a carbon skeleton.Three metabolic inhibitors, cyanide and chlorpromazine (chiefly respiratory) and phenylurethane (photosynthetic) differentially inhibited photosynthesis and nitrogen fixation. The latter inhibitor had a more marked effect on photosynthesis while the two chiefly respiratory inhibitors had a stronger effect on nitrogen fixation.     

Characterization of bio-oil from induction-heating pyrolysis of food-processing sewage sludges using chromatographic analysis

In this study, gas chromatography–mass spectrometry (GC–MS) was used to analyze the pyrolytic bio-oils and gas fractions derived from the pyrolysis of industrial sewage sludges using induction-heating technique. The liquid products were obtained from the cryogenic condensation of the devolatilization fraction in a nitrogen atmosphere using a heating rate of 300 °C/min ranging from 25 to 500 °C. The analytical results showed that the pyrolysis bio-oils were very complex mixtures of organic compounds and contained a lot of nitrogenated and/or oxygenated compounds such as aliphatic hydrocarbons, phenols, pyridines, pyrroles, amines, ketones, and so on. These organic hydrocarbons containing nitrogen and/or oxygen should originate from the protein and nucleic acid textures of the microbial organisms present in the sewage sludge. The non-condensable devolatilization fractions were also composed of nitrogenated and oxygenated compounds, but contained small fractions of phenols, 1H-indoles, and fatty carboxylic acids. On the other hand, the compositions in the non-condensable gas products were principally carbon dioxide, carbon monoxide and methane analyzed by gas chromatography–thermal conductivity detector (GC–TCD).     

Structural Basis of the Divergent Oxygenation Reactions Catalyzed by the Rieske Nonheme Iron Oxygenase Carbazole 1,9a-Dioxygenase

Carbazole 1,9a-dioxygenase (CARDO), a Rieske nonheme iron oxygenase (RO), is a three-component system composed of a terminal oxygenase (Oxy), ferredoxin, and a ferredoxin reductase. Oxy has angular dioxygenation activity against carbazole. Previously, site-directed mutagenesis of the Oxy-encoding gene from Janthinobacterium sp. strain J3 generated the I262V, F275W, Q282N, and Q282Y Oxy derivatives, which showed oxygenation capabilities different from those of the wild-type enzyme. To understand the structural features resulting in the different oxidation reactions, we determined the crystal structures of the derivatives, both free and complexed with substrates. The I262V, F275W, and Q282Y derivatives catalyze the lateral dioxygenation of carbazole with higher yields than the wild type. A previous study determined the crystal structure of Oxy complexed with carbazole and revealed that the carbonyl oxygen of Gly178 hydrogen bonds with the imino nitrogen of carbazole. In these derivatives, the carbazole was rotated approximately 15, 25, and 25°, respectively, compared to the wild type, creating space for a water molecule, which hydrogen bonds with the carbonyl oxygen of Gly178 and the imino nitrogen of carbazole. In the crystal structure of the F275W derivative complexed with fluorene, C-9 of fluorene, which corresponds to the imino nitrogen of carbazole, was oriented close to the mutated residue Trp275, which is on the opposite side of the binding pocket from the carbonyl oxygen of Gly178. Our structural analyses demonstrate that the fine-tuning of hydrophobic residues on the surface of the substrate-binding pocket in ROs causes a slight shift in the substrate-binding position that, in turn, favors specific oxygenation reactions toward various substrates.     

Hatch opening and closing on oxygenation and deoxygenation of C60 bathysphere

The structures and stabilities of C₆₀O_n, where n=1-6, 9, have been calculated using the AM1 Hamiltonian and the program mopac 6.0, and by the density functional technique B3LYP/6-31G* at the AM1 geometry using Gaussian 98. Modes of oxygen addition considered were ethers, epoxides, ketones and ketenes. It is confirmed that in C₆₀O a carbon-carbon bond on a pent-hex edge is replaced by an ether linkage. For higher levels of oxygen addition the replacement of a carbon-carbon bond by two ketone groups becomes important. Particularly stable structures are formed if the additions are on the same, or adjacent, C₆ rings of the C₆₀ structure where the oxygen atoms cooperate in opening up large holes in the molecule. Molecules of greatest stability have a mixture of ether oxygen atoms on pent-hex edges and diketone additions on hex-hex edges. A particularly important stable structure is the mixed ether/ketone isomer of C₆₀O₆ in which a hinged C₅O₂ hatch lid containing two ketone oxygen atoms is opened revealing a hatch 4-5 Å in diameter. An even larger hole of approximately 6 Å in diameter is opened up in a particularly stable isomer of C₆₀O₉ which contains three ether and six ketone groups. Removal of the oxygen atoms from these structures and reoptimisation leads to hatch closing and C₆₀ is reformed.     

Relative strengths of Se?N,O interactions: Implications for glutathione peroxidase activity

Natural bond orbital (NBO) studies of model compounds of glutathione peroxidase and its mimics are used to examine the relative strengths of nitrogen and oxygen donor groups in simple models and ω-substituted selenenic acids. Nitrogen-containing groups are generally better donors, but the weak Lewis basicity of the amide nitrogen allows for preferential interaction with the carbonyl oxygen which suggests that the glutamine of the GPX catalytic triad influences activity through an Se?O interaction.     

Bioremediation of volatile oil hydrocarbons by epiphytic bacteria associated with American grass (Cynodon sp.) and broad bean (Vicia faba) leaves

Fresh leaves of American grass and broad beans grown in pristine soil were naturally colonized with cultivable volatile oil hydrocarbon-utilizing bacteria, whose numbers increased significantly in plants grown in oily soil. According to their 16S rRNA gene sequences those bacteria were affiliated to various species of the genera Rhodococcus and Pseudomonas. Qualitative growth studies revealed that pure cultures of these phyllospheric bacteria could grow successfully on a solid mineral medium containing individual alkanes with chain lengths of C₉ through C₄₀ and the aromatics phenanthrene, naphthalene, and biphenyl as sole sources of carbon and energy. Quantitative measurements showed that the individual pure bacterial isolates degraded between about 20 and 30% of crude oil, n-hexadecane, or phenanthrene in batch culture after a one-week incubation. These results reflect the high hydrocarbon degradation potential of those bacteria. The isolates were diazotrophic (nitrogen fixers), meaning that they were self-dependent in covering their nitrogen requirements. Incubating fresh leaves in closed microcosms containing volatile oil hydrocarbons resulted in up to more than 80% attenuation of these compounds after two weeks. Experimental evidence was provided that the leaf tissues did not contribute to this attenuation, which was exclusively due to the bacterial activity.