Alpha-oxo semicarbazone peptide or oligodeoxynucleotide microarrays

We describe in this paper the preparation and characterization of semicarbazide glass slides and their use for the fabrication of microarrays using site-specific alpha-oxo semicarbazone ligation. The functional density and homogeneity of the semicarbazide glass slides were optimized by analyzing the reactivity of the layer toward a synthetic glyoxylyl fluorescent probe. Oligonucleotide microarrays were prepared by site-specific immobilization of glyoxylyl oligodeoxynucleotides. The slides were directly used in the hybridization assays using fluorescence detection and displayed a significant gain in sensibility as compared to the aldehyde glass slide/amino oligodeoxynucleotide chemistry. Semicarbazide slides were also used for the immobilization of a biotinylated peptide alpha-oxo aldehyde. The peptide microarrays allowed model interaction studies with streptavidin or an anti-biotin antibody.     

Transamination of glutamate to tricarboxylic acid-cycle intermediates in cultured neurons correlates with the ability of oxo acids to support neuronal survival in vitro.

Cultures of central-nervous-system neurons at low densities require for their survival exogenous pyruvate, alpha-oxoglutarate or oxaloacetate, even in the presence of high glucose concentrations. Most other alpha-oxo acids support cell survival only in the presence of alpha-amino acids which transaminate to alpha-oxoglutarate, oxaloacetate or pyruvate. The alpha-oxo acids therefore operate as acceptors of amino groups from appropriate donors to generate tricarboxylic acid-cycle-relevant substrates, and these alpha-oxo acids provide for neuronal support only insofar as they make it possible for exogenously supplied alpha-amino acid precursors to generate intracellularly one of the three critical metabolites. To examine more closely the relationship between transamination activity and neuronal survival, we measured 14CO2 production from [14C]glutamate in the presence of appropriate alpha-oxo acid partners by using 8-day-embryonic chick forebrain, dorsal-root-ganglion and ciliary-ganglion neurons. Neuronal survival was measured concurrently in monolayer neuronal cultures maintained with the corresponding amino acid/oxo acid pairs. Forebrain and ganglionic cell suspensions both produced 14CO2 from [14C]glutamate, which accurately correlated with 24 h neuronal survival. Concentrations of glutamate or alpha-oxo acid which provide for maximal neuronal survival also produced maximal amounts of 14CO2. The same ability to generate CO2 from glutamate (in the presence of the appropriate alpha-oxo acids) can ensure neuronal survival in 24 h cultures and therefore must meet energy or other metabolic needs of those neurons which glucose itself is unable to satisfy.     

The oxidation of oxyhaemoglobin by glyceraldehyde and other simple monosaccharides.

Glyceraldehyde and other simple monosaccharides oxidize oxyhaemoglobin to methaemoglobin in phosphate buffer at pH 7.4 and 37 degrees C, with the concomitant production of H2O2 and an alpha-oxo aldehyde derivative of the monosaccharide. Simple monosaccharides also reduce methaemoglobin to ferrohaemichromes (non-intact haemoglobin) at pH 7.4 and 37 degrees C. Carbonmonoxyhaemoglobin is unreactive towards oxidation by autoxidizing glyceraldehyde. Free-radical production from autoxidizing monosaccharides with haemoglobins was observed by the e.s.r. technique of spin trapping with the spin trap 5,5-dimethyl-l-pyrroline N-oxide. Hydroxyl and l-hydroxyalkyl radical production observed from monosaccharide autoxidation was quenched in the presence of oxyhaemoglobin and methaemoglobin. The haemoglobins appear to quench the free radicals by reaction with the free radicals and/or the ene-diol precursor of the free radical.     

The mechanism of disulphide reduction by mitochondria

1. Cystamine was reduced to the corresponding thiol by rat liver mitochondria, even in the presence of rotenone or antimycin A. 2. The reduction of disulphides was stimulated by the accumulation of NADH or by the addition of NADH to osmotically ;shocked' mitochondria. 3. Energy made available by oxidative phosphorylation was not essential for the reduction of disulphides. 4. Cystamine was not reduced during the oxidation of NADH by ultrasonically treated particles, which had lost their capacity for oxidation of alpha-oxo acids. 5. In intact mitochondria, arsenite and other inhibitors of vicinal dithiols caused a decrease in the capacity for reduction of disulphides concomitantly with an inhibition of the oxidation of alpha-oxo acids. 6. Isolated lipoamide dehydrogenase reduced cystamine at the expense of NADH, provided that lipoic acid was also present. 7. It is concluded that in mitochondria the reduction of cystamine and related disulphides is probably brought about by interaction with reduced lipoic acid, generated by the alpha-oxo acid dehydrogenase complexes during the oxidation of alpha-oxo acids or by reaction of lipoamide dehydrogenase with NADH.     

Crystal structure of an aldehyde reductase Y50F mutant-NADP complex and its implications for substrate binding

Pig aldehyde reductase containing the active site mutation tyrosine(50) to phenylalanine has been crystallized in the presence of the cofactor NADP(H) to a resolution of 2.2 A. This structure clearly shows loss of the tyrosine hydroxyl group and no other significant perturbations compared with previously determined structures. The mutant binds cofactor (both oxidized and reduced) more tightly than the wild-type enzyme but shows a complete lack of binding of the aldehyde reductase inhibitor barbitone, as determined by fluorescence titrations. Numerous attempts at preparing a ternary complex with a range of small aldehyde substrates were unsuccessful. This result, in addition to the inability of the mutant protein to bind the inhibitor, provides strong evidence for the proposal that the tyrosine hydroxyl group is essential for substrate binding in addition to catalysis.     

Acid-base chemical mechanism of homocitrate synthase from Saccharomyces cerevisiae

Homocitrate synthase (acetyl-coenzyme A:2-ketoglutarate C-transferase; E.C. 2.3.3.14) catalyzes the condensation of AcCoA and alpha-ketoglutarate to give homocitrate and CoA. The enzyme was found to be a Zn-containing metalloenzyme using inductively coupled plasma mass spectrometry. Dead-end analogues of alpha-ketoglutarate were used to obtain information on the topography of the alpha-ketoglutarate binding site. The alpha-carboxylate and alpha-oxo groups of alpha-ketoglutarate are required for optimum binding to coordinate to the active site Zn. Optimum positioning of the alpha-carboxylate, alpha-oxo, and gamma-carboxylate of alpha-ketoglutarate is likely mimicked by the location in space of the 2-carboxylate, pyridine nitrogen, and 4 carboxylate of pyridine 2,4-dicarboxylate. The pH dependence of the kinetic parameters was determined to obtain information on the chemical mechanism of homocitrate synthase. The V profile is bell shaped with slopes of 1 and -1, giving pKa values of 6.7 and 8.0, while V/K(AcCoA) exhibits a slope of 2 on the acidic side with an average pKa value of 6.6 and a slope of -2 on basic side of the profile with an average pKa value of 8.2. The V/K(alpha-Kg) pH-rate profile exhibits a single pKa of 6.9 on the acidic side and two on the basic side with an average value of 7.8. The pH dependence of the Ki for glyoxylate, a competitive inhibitor vs alpha-ketoglutarate, gives a pKa of 7.1 for a group, required to be protonated for optimum binding. Data suggest a chemical mechanism for the enzyme in which alpha-ketoglutarate first binds to the active site Zn via its alpha-carboxylate and alpha-oxo groups, followed by acetyl-CoA. A general base then accepts a proton from the methyl of acetyl-CoA, and a general acid protonates the carbonyl of alpha-ketoglutarate in the formation of homocitryl-CoA. The general acid then acts as a base in deprotonating Zn-OH2 in the hydrolysis of homocitryl-CoA to give homocitrate and CoA. A solvent deuterium kinetic isotope effect of 1 is measured for homocitrate synthase, while a small pH-independent primary kinetic deuterium isotope effect (approximately 1.3) is observed using deuterioacetyl-CoA. Data suggest rate-limiting condensation to form the alkoxide of homocitryl-CoA, followed by hydrolysis to give products.     

Radioiodination of proteins by reductive alkylation

The use of the aliphatic aldehyde, para-hydroxyphenylacetaldehyde as the reactive moiety in the radioiodination of proteins by reductive alkylation is described. The para-hydroxyphenyl group is radiolabeled with 125I, reacted through its aliphatic aldehyde group with primary amino groups on proteins to form a reversible Schiff base linkage which can then be stabilized with the mild reducing agent NaCNBH3. The introduction of the methylene group between the benzene ring and the aldehyde group increases its reactivity with protein amino groups permitting efficient labeling at low aldehyde concentrations. Using this method, radioiodinated proteins with high specific activity can be produced. The reductive alkylation procedure is advantageous in that the labeling conditions are mild, the reaction is specific for lysyl residues, and the modification of the epsilon-ammonium group of lysine results in ionizable secondary amino groups avoiding major changes in protein charge.     

Backbone amide linker (BAL) strategy for Nalpha-9-fluorenylmethoxycarbonyl (Fmoc) solid-phase synthesis of peptide aldehydes.

A rapid and efficient strategy has been developed for the general synthesis of complex peptide aldehydes. N(alpha)-Benzyloxycarbonylamino acids were converted to protected aldehyde building blocks for solid-phase synthesis in four steps and moderate overall yields. The aldehydes were protected as 1,3-dioxolanes except for one case where a dimethyl acetal was used. These protected amino aldehyde monomers were then incorporated onto 5-[(2 or 4)-formyl-3,5-dimethoxyphenoxy]butyryl-resin (BAL-PEG-PS) by reductive amination, following which the penultimate residue was introduced by HATU-mediated acylation. The resultant resin-bound dipeptide unit, anchored by a backbone amide linkage (BAL), was extended further by routine Fmoc chemistry procedures. Several model peptide aldehydes were prepared in good yields and purities. Some epimerization of the C-terminal residue occurred (10% to 25%), due to the intrinsic stereolability conferred by the aldehyde functional group, rather than any drawbacks to the synthesis procedure.     

The preparation of α-oxo acid derivatives suitable for specific-radioactivity determination

1. Conditions favouring the condensation of o-phenylenediamine with alpha-oxo acids to form substituted quinoxalines have been investigated. The best yields (85-100%) are obtained by incubation of the reagents in 2m-hydrochloric acid. Substitution of acetic acid for hydrochloric acid, or of halogen-substituted 1,2-diaminobenzenes for phenylenediamine, increases the initial rate of reaction, but not the yield of quinoxalines. 2. The quinoxaline derivatives are insoluble in water and can be readily purified. They are very suitable for determination of the specific radioactivities of radioactively labelled alpha-oxo acids because they are colourless, soluble in dioxan-based scintillators, and their strong absorption of u.v. light facilitates their chemical determination. As little as 1 nmol can be accurately determined by means of the blue fluorescence produced by absorption of light at 340-360nm. 3. Optimum conditions for preparation, purification and separation by paper and thin-layer chromatography are described.     

On-plate digestion of proteins using novel trypsin-immobilized magnetic nanospheres for MALDI-TOF-MS analysis

In this study, a novel method of on-plate digestion using trypsin-immobilized magnetic nanospheres was developed followed by MALDI-TOF-MS for rapid and effective analysis and identification of proteins. We utilized a facile one-pot method for the direct preparation of amine-functionalized magnetic nanospheres with highly magnetic properties and the amino groups on the outer surface. Through the reaction of the aldehyde groups with amine groups, trypsin was simply and stably immobilized onto the magnetic nanospheres. The obtained trypsin-linked magnetic nanospheres were then applied for on-plate digestion of sample proteins (myoglobin and Cytochrome c). Moreover, after digestion, the trypsin-linked nanospheres could be easily removed from the plate due to their magnetic property, which would avoid causing contamination on the ion source chamber in MS. The effects of the temperature and incubation time on the digestion efficiency were characterized. Within only 5 min, proteins could be efficiently digested with the peptide sequence coverage higher than or equal to that of the traditional in-solution digestion for 12 h. Furthermore, RPLC fractions of rat liver extract were also successfully processed using this novel method. These results suggested that our improved on-plate digestion protocol for MALDI-MS may find further application in automated analysis of large sets of proteins.     

The dimerization of Δ1-piperidine-2-carboxylic acid

The l-amino acid oxidase of Mytilus edulis has been used to oxidize l-lysine on a large scale in the presence of catalase. The alpha-oxo acid derived from lysine cyclizes to a Schiff base, which readily dimerizes. The dimer undergoes spontaneous dehydration and decarboxylation to form 1,2,3,4,5,6,7,8-octahydropyrido[3,2-a]-indolizin-10(4bH)-one. This structure was established by a study of its molecular weight and infrared, nuclear-magnetic-resonance and mass spectra.     

Preparation of 2,6-anhydro-aldose acylhydrazones, -semicarbazones and -oximes from 2,6-anhydro-aldononitriles (glycosyl cyanides)

Reductive transformation of per-O-acylated 2,6-anhydro-aldononitriles (glycopyranosyl cyanides of the D-galacto, D-gluco, D-xylo, and D-arabino configuration) with Raney-nickel-NaH(2)PO(2) in pyridine-AcOH-water solvent mixture in the presence of benzoylhydrazine, ethyl carbazate, and semicarbazide gave the corresponding anhydro-aldose benzoylhydrazones, -ethoxycarbonylhydrazones, and -semicarbazones, respectively. Acid catalyzed transimination of the semicarbazones with thiosemicarbazide, hydroxylamine, and O-benzylhydroxylamine, resulted in the formation of anhydro-aldose thiosemicarbazones, and E/Z mixtures of anhydro-aldose oximes, and O-benzyl-(anhydro-aldose)-oximes, respectively.     

Synthesis of betulonic aldehyde derivatives

Selective functionalization of betulonic aldehyde (the oxidation product of betulin) was studied with the aim of obtaining new physiologically active substances. We developed a method for the synthesis of azomethine derivatives at the C-28 aldehyde group and benzylidene derivatives at the 2-methylene group of the A ring. The structure of the synthesized products was proved by ¹H NMR.     

Analysis of positional isomers of monounsaturated fatty acids by high performance liquid chromatography of 2,4-dinitrophenylhydrazones of reduced ozonides

A method is described for quantifying the positional isomers in monounsaturated fatty acid methyl ester (FAME) fractions. The procedure involves the preparation of 2,4-dinitrophenylhydrazones (DNPH) of the fragments generated during reductive ozonolysis of FAME, class isolation of the aldehyde and aldehyde ester DNPH, and separation of the aldehyde ester derivatives by high performance liquid chromatography (HPLC). The high extinction coefficient of the DNPH provides for a sensitive assay which is linear for a large range of components over a concentration range of 0.075-5 nmol/component, and the stability of the DNPH permits the independent analysis of the aldehyde and aldehyde ester fragments generated during reductive ozonolysis. The reductive ozonolysis-DNPH-HPLC method developed is as sensitive, reproducible, and accurate as reductive ozonolysis-gas-liquid chromatography and does not suffer from some of the drawbacks of the classical procedure.     

Liquid chromatography-tandem mass spectrometry analysis of protocatechuic aldehyde and its phase I and II metabolites in rat

A method using liquid chromatography-electrospray ionization tandem mass spectrometry (LC-MS/MS) analysis was established for the identification of metabolites in rat after oral administration of protocatechuic aldehyde, a major bioactive phenolic acid in the roots of Salvia miltiorrhiza. Eleven metabolites in rat plasma and urine were firstly identified as protocatechuic aldehyde, protocatechuic acid and their methylated, glucuronized or glycine conjugates on the basis of their MS fragmentation behaviors, while nine of these metabolites (except protocatechuic aldehyde and protocatechuic acid) were detected in rat bile. In addition, the possible metabolic pathway was proposed for the first time. In the phase I metabolism, protocatechuic aldehyde could be oxidized to protocatechuic acid. The conjugates would be formed in rat intestine, liver and kidney and excreted from rat urine and bile. Enthrohepatic circulation played an important role in the metabolism of protocatechuic aldehyde. The results proved that the established method was simple, reliable and sensitive, revealing that it could be used to rapid screen and identify the structures of active components responsible for pharmacological effects of protocatechuic aldehyde and to better understand its in vivo metabolism.     

Reduction of α-oxo carboxyylic acids by pigeon liver `malic'' enzyme

1. Pigeon liver ;malic' enzyme [l-malate-NADP(+) oxidoreductase (decarboxylating); EC 1.1.1.40] was shown to catalyse the reductase reaction: [Formula: see text] l-Malate was identified as the reaction product, and was formed in stoicheiometric amount. 2. In addition to oxaloacetate and pyruvate, a number of other alpha-oxo carboxylic acids were also reduced.     

Design, synthesis and properties of synthetic chlorophyll proteins.

A chemoselective method is described for coupling chlorophyll derivatives with an aldehyde group to synthetic peptides or proteins modified with an aminoxyacetyl group at the epsilon-amino group of a lysine residue. Three template-assembled antiparallel four-helix bundles were synthesized for the ligation of one or two chlorophylls. This was achieved by coupling unprotected peptides to cysteine residues of a cyclic decapeptide by thioether formation. The amphiphilic helices were designed to form a hydrophobic pocket for the chlorophyll derivatives. Chlorophyll derivatives Zn-methyl-pheophorbide b and Zn-methyl-pyropheophorbide d were used. The aldehyde group of these chlorophyll derivatives was ligated to the modified lysine group to form an oxime bond. The peptide-chlorophyll conjugates were characterized by electrospray mass spectrometry, analytical HPLC, and UV/visible spectroscopy. Two four-helix bundle chlorophyll conjugates were further characterized by size-exclusion chromatography, circular dichroism, and resonance Raman spectroscopy.     

Reaction‐based probe for hydrogen sulfite: dual‐channel and good ratiometric response

We designed and synthesized a new series of intramolecular charge transfer (ICT) molecules (compounds T1, T2 and T3) by attaching various electron‐donating thiophene groups to the triphenylamine backbone with aldehyde group as the electron acceptor. Based on the nucleophilic addition reaction between hydrogen sulfite and aldehyde, all compounds could act as ratiometric optical probe for hydrogen sulfite and displayed efficient chromogenic and fluorogenic signaling. Upon the addition of hydrogen sulfite anions, probe T3 displayed apparent fluorescent color changes from yellowish‐green to blue, with a large emission wavelength shift (Δλ = 120 nm). T3 responded to hydrogen sulfite with high sensitivity and the detection limit was determined to be as low as 0.9 μM. At the same time, apparent changes in UV–vis spectra could also be observed. By virtue of the special nucleophilic addition reaction with aldehyde, T3 displayed high selectivity over other anions. Copyright © 2016 John Wiley & Sons, Ltd.     

Experimental researches on the role of phosphoinositide-specific phospholipase C in 4-hydroxynonenal induced exocytosis

The action of 4-hydroxynonenal (HNE), a chemotactic aldehyde produced by lipid peroxidation, was analysed on exocytosis in parallel with its effects on phosphoinositide-specific phospholipase C (PLC) both in undifferentiated HL-60 cells and in cells induced to differentiate toward the granulocytic cell line by 1.25% DMSO. Exocytosis was evaluated by the secretion of beta-glucuronidase from cells incubated at 37 degrees C for 10 min in the presence of various aldehyde concentrations. HNE action was more pronounced in DMSO-differentiated cells, where concentrations between 10(-8) and 10(-6) m were able both to trigger exocytosis and to strongly activate PLC; in both processes maximal stimulation was given by 10(-7) m. HNE-induced exocytosis was completely prevented by pertussis toxin and by the PLC inhibitor U73122. The comparison between HNE and formyl-methionyl-leucyl-phenylalanine (fMLP), used as a positive control, showed that the tripeptide produced an higher stimulation of exocytosis than the aldehyde; by contrast HNE induced a stronger increase of PLC activity. Wortmannin, an inhibitor of phosphatidylinositol-3-kinase (PI3K), strongly inhibited the exocytosis induced by fMLP, while it failed to induce a statistically significant inhibition of HNE action. We conclude that both compounds trigger exocytosis through a Ptx-sensitive G protein; the present data support the hypothesis that the lower ability of the aldehyde to trigger exocytosis as compared to fMLP might depend upon a low ability to activate PI3K, while PLC activation appears to play a key role in HNE-induced exocytosis.     

Human aldehyde dehydrogenases: potential pathological,pharmacological, and toxicological impact

Aldehyde dehydrogenases catalyze the pyridine nucleotide-dependent oxidation of aldehydes to acids. Seventeen enzymes are currently viewed as belonging to the human aldehyde dehydrogenase superfamily. Summarized herein, insofar as the information is available, are the structural composition, physical properties, tissue distribution, subcellular location, substrate specificity, and cofactor preference of each member of this superfamily. Also summarized are the chromosomal locations and organization of the genes that encode these enzymes and the biological consequences when enzyme activity is lost or substantially diminished. Broadly, aldehyde dehydrogenases can be categorized as critical for normal development and/or physiological homeostasis (1). even when the organism is in a friendly environment or (2). only when the organism finds itself in a hostile environment. The primary, if not sole, evolved raison d'être of first category aldehyde dehydrogenases appears to be to catalyze the biotransformation of a single endobiotic for which they are relatively specific and of which the resultant metabolite is essential to the organism. Most of the human aldehyde dehydrogenases for which the relevant information is available fall into this category. Second category aldehyde dehydrogenases are relatively substrate nonspecific and their evolved raison d'être seems to be to protect the organism from potentially harmful xenobiotics, specifically aldehydes or xenobiotics that give rise to aldehydes, by catalyzing their detoxification. Thus, the lack of a fully functional first category aldehyde dehydrogenase results in a gross pathological phenotype in the absence of any insult, whereas the lack of a functional second category aldehyde dehydrogenase is ordinarily of no consequence with respect to gross phenotype, but is of consequence in that regard when the organism is subjected to a relevant insult.