New C-nucleoside analogs by dehydration of 1-benzyl-4,5,6,7-tetrahydro-6,6-dimethyl-2-(d-galacto-pentitol-1-yl)-indol-4-one

The reaction between 2-(benzylamino)-2-deoxy-d-glycero-l-gluco-heptose and 5,5-dimethyl-1,3-cyclohexanedione yields 1-benzyl-4,5,6,7-tetrahydro-6,6-dimethyl-2-(d-galacto-pentitol-1-yl)-indol-4-one (2). Acid-catalyzed, intramolecular dehydration of 2 under kinetically controlled conditions gives 1-benzyl-4,5,6,7-tetrahydro-2-α-d-lyxofuranosyl-6,6-dimethylindol-4-one; the anomeric configuration of this compound is only suggested. When the dehydration reaction is conducted under thermodynamically controlled conditions, it produces a 1:1 mixture of the α- and β-d-lyxopyranosyl compounds. The structures of the new compounds were elucidated by chemical and physical methods.     

Peptide syntheses mediated by Bacillus subtilis protease

Bacillus subtilis protease (Amano protease N) was examined as a catalyst for peptide bond formation via both the kinetically and thermodynamically controlled approaches. In general, the latter approach proved to be superior to the former, and a series of dipeptide syntheses and several segment condensations were achieved in good to high yields using the immobilized enzyme on Celite in acetonitrile with low water content.     

Asymmetric synthesis of α-amino acids via homologation of Ni(II) complexes of glycine Schiff bases. Part 2: Aldol, Mannich addition reactions, deracemization and (S) to (R) interconversion of α-amino acids

This review provides a comprehensive treatment of literature data dealing with asymmetric synthesis of α-amino-β-hydroxy and α,β-diamino acids via homologation of chiral Ni(II) complexes of glycine Schiff bases using aldol and Mannich-type reactions. These reactions proceed with synthetically useful chemical yields and thermodynamically controlled stereoselectivity and allow direct introduction of two stereogenic centers in a single operation with predictable stereochemical outcome. Furthermore, new application of Ni(II) complexes of α-amino acids Schiff bases for deracemization of racemic α-amino acids and (S) to (R) interconversion providing additional synthetic opportunities for preparation of enantiomerically pure α-amino acids, is also reviewed. Origin of observed diastereo-/enantioselectivity in the aldol, Mannich-type and deracemization reactions, generality and limitations of these methodologies are critically discussed.     

Determination of the position of linkage of 2-acetamido-2deoxy-D-galactose and 2-acetamido-2-deoxy-D-glucose residues in oligosaccharides and glycoproteins. Synthesis of 2-acetamido-2deoxy-D-xylitol and 2-acetamido-2-deoxy-L-threitol

A method has been studied for the determination of the position of the linkage of the 2-acetamido-2-deoxy-D-galactose and 2-acetamido-2-deoxy-D-glucose residues in oligosaccharides and glycoproteins that is based on the borohydride reduction of the reducing terminal residues to the corresponding alditol derivatives periodate oxidation, borohydride reduction, hydrolysis (eventually followed by borohydride reduction), separation of the fragments as per-O-(trimethylsilyl) or per-O-(trifluoroacetyl) derivatives, and identification of the fragments as derivatives of 2-acetamido-2-deoxyglycerol, 2-acetamido-2-deoxy-L-threitol, 2-acetamido-2-deoxy-L-arabinitol, 2-acetamido-2-deoxy-D-xylitol, 2-acetamido-2-deoxy-D-galactitol, and 2-acetamido-2-deoxy-D-glucitol by gas-liquid chromatography-mass spectrometry. New syntheses for the standard compounds 2-acetamido-2-deoxy-L-threitol and 2-acetamido-2-deoxy-D-xylitol are described.     

Peptide syntheses mediated by Bacillus subtilis protease

Summary Bacillus subtilis protease (Amano protease N) was examined as a catalyst for peptide bond formationvia both the kinetically and thermodynamically controlled approaches. In general, the latter approach proved to be superior to the former, and a series of dipeptide syntheses and several segment condensations were achieved in good to high yields using the immobilized enzyme on Celite in acetonitrile with low water content.     

Total syntheses and stereochemical reassignments of mollenines A and B

Total syntheses of prenylated pyrrolidinoindoline alkaloids, (?)-mollenines A [(?)-1′] and B (2′), were accomplished via three- and four-step sequences including a bioinspired indole prenylation reaction followed by dioxomorpholine ring formation. Then, the stereochemistry of mollenines A and B was reassigned to 3S,6S,14S,16S by analysis of spectroscopic data and chemical syntheses with different approaches along with the comparison of calculated and experimental ECD spectra. In addition, a thermodynamically controlled epimerization reaction on the dioxomorpholine ring was observed in our synthesis.     

Enzymatic peptide synthesis by the recombinant proline-specific endopeptidase from Flavobacterium meningosepticum and its mutationally altered Cys-556 variant

Proline-specific endopeptidase (PSE) (EC 3.4.21.26) was investigated for its potential as a catalyst in peptide synthesis. Using an activated peptide ester or a peptide amide as the acyl component, the enzyme catalyzed kinetically controlled aminolysis and transpeptidation respectively, with various amino acid amides as acyl acceptors. To a certain extent the nucleophile preference reflected the amino acid preference in the S₁-position of the enzyme in peptide hydrolysis: the highest fractions of aminolysis were obtained using amino acid amides with hydrophobic side-chains (e.g. Leu-NH₂, Phe-NH₂). PSE also catalyzed the thermodynamically controlled condensation of short peptides with a free carboxyterminus and various amino acid amides. This enabled us to examine the acceptance of different acyl components in the substrate-binding site of the enzyme with regard to their amino acid composition: In the S₁ position proline was clearly favored, but alanine was also accepted, whereas the S₂ subsite accepted various amino acids rather unspecifically. Since PSE was shown to be extremely sensitive against water-miscible organic solvents, an alternative approach was used to increase yields in enzymatic peptide synthesis: a derivative of PSE in which the catalytic Ser-556 is converted to a Cys was constructed by protein engineering. This mutant (PSE_cys) exhibited a dramatically increased peptide ligase activity in aqueous solution.     

Metabolic flux distribution and thermodynamic analysis of green fluorescent protein production in recombinant Escherichia coli: The effect of carbon source and CO 2 partial pressure

Increasing recombinant protein production yields from bacterial cultures remains an important challenge in biotechnology. Acetate accumulation due to high dissolved carbon dioxide (pCO₂) concentrations in the medium has been identified as a factor that negatively affects such yields. Under appropriate culture conditions, acetate could be re-assimilated by bacterial cells to maintain heterologous proteins production. In this work, we developed a simplified metabolic network aiming to establish a reaction rate analysis for a recombinant Escherichia coli when producing green fluorescent protein (GFP) under controlled pCO₂ concentrations. Because E. coli is able to consume both glucose and acetate, the analysis was performed in two stages. Our results indicated that GFP synthesis is an independent process of cellular growth in some culture phases. Additionally, recombinant protein production is influenced by the available carbon source and the amount of pCO₂ in the culture medium. When growing on glucose, the increase in the pCO₂ concentration produced a down-regulation of central carbon metabolism by directing the carbon flux toward acetate accumulation; as a result, cellular growth and the overall GFP yield decreased. However, the maximum specific rate of GFP synthesis occurred with acetate as the main available carbon source, despite the low activity in the other metabolic pathways. To maintain cellular functions, including GFP synthesis, carbon flux was re-distributed toward the tricarboxylic acid cycle and the pentose phosphate pathway to produce ATP and NADH. The thermodynamic analysis allowed demonstrating the feasibility of the simplified network for describing the metabolic state of a recombinant system.     

Synthesis and biological evaluation of ureido and thioureido derivatives of 2-amino-2-deoxy-D-glucose and related aminoalcohols as N-acetyl-beta-D-hexosaminidase inhibitors

Ureido and thioureido derivatives of 2-acetamido-2-deoxy-beta-D-glucose, 1-amino-1-deoxy-D-glucitol and 2-(2-aminoethoxy)ethanol were prepared as N-acetyl-beta-D-hexosaminidase (NAHase) inhibitors and were evaluated on Trichomonas vaginalis NAHase. Although none showed complete inhibition of the enzyme at 100 microM, 1-amino-1-deoxy-D-glucitol derivatives acted as competitive inhibitors of the NAHase of T. vaginalis.     

Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models

Stoichiometric genome-scale metabolic network models (GEMs) have been widely used to predict metabolic phenotypes. In addition to stoichiometric ratios, other constraints such as enzyme availability and thermodynamic feasibility can also limit the phenotype solution space. Extended GEM models considering either enzymatic or thermodynamic constraints have been shown to improve prediction accuracy. In this paper, we propose a novel method that integrates both enzymatic and thermodynamic constraints in a single Pyomo modeling framework (ETGEMs). We applied this method to construct the EcoETM (E. coli metabolic model with enzymatic and thermodynamic constraints). Using this model, we calculated the optimal pathways for cellular growth and the production of 22 metabolites. When comparing the results with those of iML1515 and models with one of the two constraints, we observed that many thermodynamically unfavorable and/or high enzyme cost pathways were excluded from EcoETM. For example, the synthesis pathway of carbamoyl-phosphate (Cbp) from iML1515 is both thermodynamically unfavorable and enzymatically costly. After introducing the new constraints, the production pathways and yields of several Cbp-derived products (e.g. L-arginine, orotate) calculated using EcoETM were more realistic. The results of this study demonstrate the great application potential of metabolic models with multiple constraints for pathway analysis and phenotype prediction.     

Facile synthesis of 1,2-trans-O-acetyl glycosyl chloride derivatives of cellobiose,lactose, and D-glucose

Solutions of O-acetyl-α-glycosyl bromide derivatives of d-glucose, cellobiose, and lactose in hexamethylphosphoramide were converted into corresponding β-chlorides at room temperature by the action of lithium chloride. At 3:1 mM ratios of chloride ion to glycose, 5–10% w/v solutions of glycosyl bromide formed α- and β-chlorides in ratios of (or greater than) 1:19 within 2–13 min and produced crystalline β-chlorides in 70–80% yields. Anomeric compositions were determined by n.m.r. spectroscopy in hexamethylphosphoramide. Older methods of preparing 1,2-trans-O-acetylgIycosyl chlorides, with aluminum chloride or titanium tetrachloride, gave the α- and β-cellobiosyl and -Iactosyl chlorides in ratios that varied from 2:3 to 1:4 and reached 85–95% levels of β-chloride only with β-d-glucose pentaacetate. When hydrolyzed under conditions that controlled solution acidity, the β-cellobiosyl and -Iactosyl chlorides each gave 2-hydroxy derivatives in yields that could be varied from 16 to 60%. Hepta-O-acetyl-2-O-methyl-α-cellobiose was prepared to demonstrate how these hydrolysis mixtures can be used to synthesize a 2-O-substituted derivative.     

Enantioselective resolution of side-chain modified gem-difluorinated alcohols catalysed by Candida antarctica lipase B and monitored by capillary electrophoresis

An enzymatic alternative to the chemical synthesis of chiral gem-difluorinated alcohols has been developed. The method is highly effective and stereoselective, feasible at laboratory temperature, avoiding the use of toxic heavy metal catalysts which is an important benefit in medicinal chemistry including the synthesis of drugs and drug precursors. Candida antarctica lipases A and B were applied for the enantioselective resolution of side-chain modified gem-difluorinated alcohols, (R)- and (S)-3-benzyloxy-1,1-difluoropropan-2-ols (1a and 1b), compounds serving as chiral building blocks in the synthesis of various bioactive molecules bearing a gem-difluorinated grouping. The catalytic activity of these lipases was investigated for the chiral acetylation of 1a and 1b in non-polar solvents using vinyl acetate as an acetyl donor. The dependence of the reaction course on various substrate and enzyme concentrations, reaction time, and temperature was monitored by chiral capillary electrophoresis (CE) using sulfobutyl ether β-cyclodextrin as a stereoselective additive of the aqueous background electrolyte. The application of CE, NMR, and MS methods has proved that the complex enzyme effect of Candida antarctica lipase B leads to the thermodynamically stable (S)-enantiomer 1b instead of the expected acetylated derivatives. In contrast, the enantioselective acetylation of racemic alcohol 1 was observed as a kinetically controlled process, where (R)-enantiomer 1a was formed as the main product. This process was followed by enzymatic hydrolysis and chiral isomerisation. Finally, single pure enantiomers 1a and 1b were isolated and their absolute configurations were assigned from NMR analysis after esterification with Mosher’s acids.     

Effect of N-Methyl Substituents in 2-Methoxycarbonylphenylsulfamides on Kinetics and Mechanism of Formation of (1H)-2,1,3-Benzothiadiazin-4(3H)-One-2,2-Dioxides

The cyclization reactions of N-methyl-N’-(2-methoxycarbonylphenyl)sulfamide (1a), N-methyl-N-(2-methoxycarbonylphenyl)-sulfamide (2a), and 2-methoxycarbonylphenylsulfamide (3a) were studied in aqueous amine buffers (butylamine, ethanolamine, morpholine, glycinamide). The dependences observed between the rate constants and buffer concentrations show that the reactions are subject to base catalysis in all the three cases, the decomposition of the tetrahedral intermediate being rate limiting. The ratio of the relative rate constants of the base catalyzed cyclizations reactions of the three derivatives is 1a: 2a: 3a = 1: 20000: 100. The logarithm of rate constants of the base catalyzed cyclization reactions was plotted against the pK_a values of conjugated acids of the individual amines used as the buffers in the cyclization of compound 1a, and the value of the Brönsted coefficient obtained was about 0.1, which means that the proton transfer from the intermediate to the basic buffer component is thermodynamically favorable. The intermediate is a much weaker base, and the reaction is controlled by diffusion. The slope of an analogous dependence for compound 2a gradually decreases from values near to 0.5 to values near to zero, which means that the intermediate formed from compound 2a (pK_a ≈ 9.3) has a pK_a value comparable with that of the acid buffer component.     

Biological Control of Meloidogyne incognita by Paecilomyces lilacinus and Pasteuria penetrans

The root-knot nematode Meloidogyne incognita was controlled more effectively and yields of host plants were greater when Paecilomyces lilacinus and Pasteuria penetrans were applied together in field microplots than when either was applied alone. Yields of winter vetch from microplots inoculated with the nematode and with both organisms were not statistically different from yields from uninoculated control plots.     

Stereochemical aspects of the metabolism of the isomeric methylcyclohexanols and methylcyclohexanones

1. The seven isomeric optically inactive forms of methylcyclohexanol (i.e. 1-, and cis- and trans-2-, -3- and -4-) are excreted by rabbits mainly as glucuronides of the thermodynamically more stable forms of the alcohols. The eighth isomer, cyclohexylmethanol, however, undergoes aromatization in vivo, giving rise to benzoic acid and hippuric acid. The (±)-2-, (±-3- and 4-methylcyclohexanones are reduced in the rabbit and excreted mainly as the glucuronides of the thermodynamically more stable forms of the corresponding methylcyclohexanols. 2. Racemic cis- and trans-2-methylcyclohexanol and 2-methylcyclohexanone are all excreted as conjugated trans-2-methylcyclohexanol. However, when the (±)-cis-alcohol or the (±)-ketone is fed, (+)-trans-2-methylcyclohexanol is excreted, whereas when the (±)-trans-alcohol is fed it is excreted as the (±)-trans-alcohol. 3. Racemic cis- and trans-3-methylcyclohexanol and 3-methylcyclohexanone are all excreted as conjugated racemic cis-3-methylcyclohexanol. cis- and trans-4-Methylcyclohexanol and 4-methylcyclohexanone are all excreted as conjugated trans-4-methylcyclohexanol. 4. The metabolic differences between the various methylcyclohexanols are explicable in terms of their conformations and of Vennesland's (1958) hypothesis of the role of NADH in dehydrogenation reactions.     

Effects of Nematicide Placement on Nematode Populations and Soybean Yields

Four methods of placement of DBCP (l,2-dibromo-3-chloropropane) and a single method of application of ethoprop (0-ethyl S,S-dipropyl phosphorodithioate) wexe compared in each of two areas for control of nematodes on soybeans. One area was a Marlboro sand infested with Hoplolaimus columbus. The other area was a Fuquay loamy sand infested with Meloidogne incognita. Soybean yields were increased and numbers of H. columbus in the row 0-20 cm deep were decreased similarly by all methods of DBCP application in Marlboro soil. All DBCP treatments increased the average soybean yields and decreased numbers of M. incognita larvae in the row 0-20 cm deep in the Fuquay soil. Average root-knot indices were reduced by all DBCP treatments except with placement 40 cm deep beneath the row. Similarly, placement of all or part of the DBCP 20 cm deep and 13 cm to either side of the row resulted in greater average yields than placement of the DBCP 40 cm deep. Apparently, control of M. incognita is more critical 0-20 cm deep than 20-40 cm deep for increasing soybean yields. DBCP did not control H. columbus as effectively as it did M. incognita. Control of H. columbus and M. incognita was not obtained at 0-20-cm and 20-40-cm depths 30 cm and 45 cm from the row regardless of the method used to apply DBCP. H. columbus and M. incognita were controlled more effectively and soybean yields were higher with DBCP at 13.6 kg a.i./ha than with ethoprop at 4.5 kg a.i./ha.     

Effects of Phenamiphos,Methyl Bromide,and Fallowing on Pratylenchus Penetrans,Yield of Medicago sativa,and Fusarium Infections

A field study was made of the effects of a residual nematicide (phenamiphos), a fumigant (methyl bromide), and fallowing on the number of root lesion nematodes (Pratylenchus penetrans), forage yields of alfalfa, and the occurrence of Fusarium spp. in plant roots and soil. Fallowing controlled nematodes initially, but by the end of the second growing season, nematode numbers were as high as in plots which had grown a nematode-susceptible crop. Forage yield was greater in fallowed plots only for the first cut in the year after seeding. Fusarium in alfalfa roots and soil was not reduced by fallowing. Phenamiphos reduced nematode numbers, increased forage yields in 2 of 4 years, and reduced Fusarium infections of taproots. Soil fumigation with methyl bromide gave the best control of nematodes and Fusarium and gave significantly higher forage yields for the 4 years of study following fumigation. The 34% increase in alfalfa yield from fumigated plots over the 4 years indicates that the yield of alfalfa is being reduced significantly by microorganisms. The study does not establish the relative contributions of the root lesion nematodes and Fusarium spp. to the reduction.     

Oil extraction from microalgae for biodiesel production

This study examines the performance of supercritical carbon dioxide (SCCO₂) extraction and hexane extraction of lipids from marine Chlorococcum sp. for lab-scale biodiesel production. Even though the strain of Chlorococcum sp. used in this study had a low maximum lipid yield (7.1 wt% to dry biomass), the extracted lipid displayed a suitable fatty acid profile for biodiesel [C18:1 (∼63 wt%), C16:0 (∼19 wt%), C18:2 (∼4 wt%), C16:1 (∼4 wt%), and C18:0 (∼3 wt%)]. For SCCO₂ extraction, decreasing temperature and increasing pressure resulted in increased lipid yields. The mass transfer coefficient (k) for lipid extraction under supercritical conditions was found to increase with fluid dielectric constant as well as fluid density. For hexane extraction, continuous operation with a Soxhlet apparatus and inclusion of isopropanol as a co-solvent enhanced lipid yields. Hexane extraction from either dried microalgal powder or wet microalgal paste obtained comparable lipid yields.     

Production of Hyaluronic Acid by Mutant Strains of Group C Streptococcus

This study addresses the influence of upstream region sequence on the strength of has operon promoter in highly encapsulated S. equi subsp. zooepidemicus (SEZ). For this purpose, seven different strains were constructed. Each strain carries a point mutation in one of the following positions upstream of the has promoter: ?43, ?44, ?49, and ?50 bp. To facilitate measuring of the recombinant promoter relative strength, ß-glucuronidase gene was used as a reporter gene. Three mutations located in positions ?49 and ?50: AT, GT, and AG, positively impacted has promoter strength when compared to the wild type sequence GG. Conversely, two other mutations: TG and TT, exhibited a slight inhibitory effect. Further, three different strains carrying chromosomal mutations in the has promoter region were constructed. In two cases, the has operon is under the control of a stronger promoter and in the third strain the has operon is controlled by a weaker promoter. The laboratory fermenter scale cultivations confirmed the increase of hyaluronan yields for SEZPhasAG and SEZPhas2G, resulting 116 and 105 %, respectively. As expected, the yield of the hyaluronic acid of SEZPhas2B strain fell to 41 %.     

Production of 2-Ketogluconic Acid by Serratia marcescens

Production of 2-ketogluconic acid from glucose by fermentation with Serratia marcescens NRRL B-486 was studied in 20-liter stainless-steel fermentors. Conditions for 2-ketogluconic acid production included the following: glucose-salt medium, aeration rate of 0.75 volumes per volume per minute, agitation rate of 400 rev/min, temperature of 30 C, CaCO₃ to neutralize the acid formed, and a 5% (v/v) inoculum. Foaming was controlled with an antifoam agent added at intervals during the fermentation. When 120 g per liter of glucose were supplied, 95 to 100% yields of 2-ketogluconic acid were obtained in 16 hr. Larger amounts of glucose could be used in the fermentation provided that the carbohydrate was fed continuously. Continuous feeding of glucose to a total amount of 180 g per liter gave 95 to 100% yields of 2-ketogluconic acid in 24 hr; feeding glucose to a total amount of 240 g per liter gave 85 to 90% yields in 32 to 40 hr.