Synthesis of a trigalacturonic acid analogue mimicking the expected transition state in the glycosidases

A trigalacturonic acid analogue carrying a cyclohexene framework in place of the central pyranose ring was synthesized as a molecular probe for the mechanistic investigation of endo-polygalacturonase 1 (endo-PG 1). Preliminary enzymatic studies revealed that this analogue inhibited endo-PG 1 activity by about 30% at 0.3 mM concentration.     

Chiral metal complexes. 25. Cobalt(III) complexes of some linear mesomeric tetramine ligands

The complexes of Λ-α-[Co(R,S-picbn)Cl₂] ClO₄ (where R,S-picbn is 3R,4S-dimethyl-1,6-di(2-pyridyl)-2,5-diazahexane) together with its Δ-Λ-α and Δ,Λ-β exo congeners,Δ-Λ-β-exo-[Co(picchmn)Cl₂] ClO₄ (where picchmn is N,N'-di(2-picolyl)-1R, 2S-diaminocyclohexane) as well as Δ,Λ-β-endo-[Co(R,S-picstien)Cl₂] ClO₄·2H₂O, [Co(R,S-picstien)(ox)] ClO₄·0.5H₂O and [Co(R,S-picstien)(mal)] ClO₄·3H₂O (where picstien is 3R,4S-diphenyl-1,6-di(2-pyridyl)-2,5-diazahexane, ox is the oxalate dianion and mal is the malonate dianion) have been synthesised. The nature of the compounds was determined using a combination of ¹H NMR and, for certain chiral species, chiroptical techniques. In the various β complexes, the tetradentate is observed to adopt either the exo or endo geometry, specifically. Factors which influence coordination geometry include steric interactions and hydrophobic bonding effects.A number of chemical transformations between dinitro and dichloro complexes of Co(III) with R,S- picbn have been examined, as has the reaction of Δ,Λ-β-exo-[Co(R,S-picbn)Cl₂]⁺ with S-alanine in aqueous solution. The resulting product mixture contains eight of the sixteen possible β diastereoisomers, of which three have been isolated and characterised. The eight are composed of four β₁ and four β₂ isomers, however, and it is noted that isomerisation at the inplane amine nitrogen atom is restricted by the overall geometry of the complexes formed. Discriminatory forces in these complexes are small in magnitude, and exo/endo isomerisation is somewhat dependent upon the choice of ligand(s) used to complete the coordination sphere.     

A Simple Method for Resolution of Endo‐/Exo‐Monoesters of Trans‐Norborn‐5‐Ene‐2,3‐Dicarboxylic Acids Into Their Enantiomers

Separation of optical isomers obtainable from trans‐norborn‐5‐ene‐2,3‐dicarboxylic acid methyl and tert‐butyl monoesters was performed by crystallization of the respective salts prepared with (R)‐ and (S)‐1‐phenylethylamine. Starting from racemic endo‐monomethyl ester of trans‐norborn‐5‐ene‐2,3‐dicarboxylic acid, prepared by partial hydrolysis of the cyclopentadiene‐dimethyl fumarate adduct, the corresponding (2R,3R)‐endo‐monoester was isolated in 97% enantiomeric excess (ee) yield after seven repeated crystallizations from tetrachloromethane. Starting from exo‐mono‐tert‐butyl ester of the same acid, prepared by alcoholysis of the cyclopentadiene‐maleic anhydride adduct followed by isomerization, (2R,3R)‐exo‐monoester was isolated in >98% ee yield after four repeated crystallizations from ethanol. Crystallization of the acids from the mother liquor containing (S)‐1‐phenylethylamine yielded products with inverse stereochemical configuration. Chirality 27:151–155, 2015. © 2014 Wiley Periodicals, Inc.     

Highly selective biotransformation of (+)-(1S)- and (−)-(1R)-camphorquinone by Aspergillus wentii

Abstract

To clarify the structures of biotransformation products and metabolic pathways, the biotransformation of monoterpenoids, (+)- and (?)-camphorquinone (1a and b), has been investigated using Aspergillus wentii as a biocatalyst. Compound 1a was converted to (?)-(2S)-exo-hydroxycamphor (2a), (?)-(2S)-endo-hydroxycamphor (3a), (?)-(3S)-exo-hydroxycamphor (4a), (?)-(3S)-endo-hydroxycamphor (5a), and (+)-camphoric acid (6a). Compound 1b was converted to (+)-(2R)-exo-hydroxycamphor (2b), (+)-(2R)-endo-hydroxycamphor (3b), (+)-(3R)-exo-hydroxycamphor (4b), (+)-(3R)-endo-hydroxycamphor (5b), and (?)-camphoric acid (6b). Compound 1a mainly produced 2a (65.0%) with stereoselectivity, whereas 1b afforded 3b (84.3%) with high stereoselectivity. These structures were confirmed by gas chromatography–mass spectrometry, infrared, ¹H nuclear magnetic resonance (NMR), and ¹³C NMR spectral data. The products illustrate the marked ability of A. wentii for enzymatic oxidation and ketone reduction.     

Ab initio and DFT study on the electrophilic addition of bromine to endo-tricyclo[3.2.1.02,4]oct-6-ene

Full geometric optimization of endo-tricyclo[3.2.1.0^2,4]oct-6-ene (endo-TCO) by ab initio and DFT methods allowed us to investigate the structure of the molecule. The double bond is endo-pyramidalized and its two faces are no longer found to be equivalent. The exo face of the double bond has regions with far more electron density (q_i,HOMO) and more negative electrostatic potential. The endo-TCO-Br₂ system was investigated at the B3LYP/6-311+G** level and the endo-TCO···Br₂(exo) molecular complex was found to be relatively more stable than the endo-TCO···Br₂(endo) complex. The cationic intermediates of the reaction were studied by ab initio and DFT methods. The bridged exo-bromonium cation(I) is relatively more stable than the endo-bromonium cation(II). An absolute exo-facial selectivity should be observed in the addition reaction of Br₂ to endo-TCO, which is caused by steric and electronic factors. The nonclassical rearranged cation IV was found to be the most stable ion among the cationic intermediates and the ionic addition occurs via the formation of this cation. The mechanism of the addition reaction is also discussed.     

Purification and characterization of an exo-polygalacturonase from Pycnoporus sanguineus

The present work describes the purification and characterization of a novel extracellular polygalacturonase, PGase I, produced by Pycnoporus sanguineus when grown on citrus fruit pectin. This substrate gave enhanced enzyme production as compared to sucrose and lactose. PGase I is an exocellular enzyme releasing galacturonic acid as its principal hydrolysis product as determined by TLC and orcinol-sulphuric acid staining. Its capacity to hydrolyze digalacturonate identified PGase I as an exo-polygalacturonase. SDS-PAGE showed that PGase I is an N-glycosidated monomer. The enzyme has a molecular mass of 42 kDa, optimum pH 4.8 and stability between pH 3.8 and 8.0. A temperature optimum was observed at 50–60 °C, with some enzyme activity retained up to 80 °C. Its activation energy was 5.352 cal mol⁻¹. PGase I showed a higher affinity towards PGA than citric pectin (Km = 0.55 ± 0.02 and 0.72 ± 0.02 mg ml⁻¹, respectively). Consequently, PGase I is an exo-PGase, EC 3.2.1.82.     

Bacillus megaterium, KM beta-galactosidase: purification by affinity chromatography and characterization of the active species

The enzyme β-galactosidase from Bacillus megaterium, strain KM has been purified by affinity chromatography. The enzyme was found to have a dimeric subunit structure, with the monomer having a molecular weight of 120,000. The K_eq of the monomer-dimer equilibrium was strongly shifted towards dissociation in the isolated state. Inclusion of 5% sucrose in the buffer (and maintenance of the temperature at 5 °) minimized this dissociation. Molecularly homogeneous monomer and dimer could be prepared on sucrose gradients. The dimer was determined to have an S_20,w of 8, while the monomer had an S_20,w of 3. The amino acid composition was found to be similar to that of the E. coli β-galactosidase although significant differences occur. The activity of the monomer was studied by both urea-denaturation experiments and by immobilization of the monomer on Sepharose-4B. The monomer, bound to Sepharose-4B, was found to be inactive but still capable of binding the inhibitor thio-methyl galactoside. Activity was reconstituted by adding free monomer, in 8 M urea, to the Sepharose-bound monomer, followed by removal of the urea by dialysis. In addition, free monomers from E. coli β-galactosidase were found to form active hybrids with Sepharose-bound B. megaterium β-galactosidase monomers. We conclude on the basis of these studies that the free monomer is inactive, and that the dimer is the active species, in marked contrast to E. coli β-galactosidase where only the tetrameric form is active.     

Synthesis of enantiomers of exo‐2‐norbornyl‐N‐n‐butylcarbamate and endo‐2‐norbornyl‐N‐n‐butylcarbamate for stereoselective inhibition of acetylcholinesterase

The acetylcholinesterase inhibition by enantiomers of exo‐ and endo‐2‐norbornyl‐N‐n‐butylcarbamates shows high stereoselelectivity. For the acetylcholinesterase inhibitions by (R)‐(+)‐ and (S)‐(?)‐exo‐2‐norbornyl‐N‐n‐butylcarbamates, the R‐enantiomer is more potent than the S‐enantiomer. But, for the acetylcholinesterase inhibitions by (R)‐(+)‐ and (S)‐(?)‐endo‐2‐norbornyl‐N‐n‐butylcarbamates, the S‐enantiomer is more potent than the R‐enantiomer. Optically pure (R)‐(+)‐exo‐, (S)‐(?)‐exo‐, (R)‐(+)‐endo‐, and (S)‐(?)‐endo‐2‐norbornyl‐N‐n‐butylcarbamates are synthesized from condensations of optically pure (R)‐(+)‐exo‐, (S)‐(?)‐exo‐, (R)‐(+)‐endo‐, and (S)‐(?)‐endo‐2‐norborneols with n‐butyl isocyanate, respectively. Optically pure norborneols are obtained from kinetic resolutions of their racemic esters by lipase catalysis in organic solvent. Chirality 2010. © 2009 Wiley‐Liss, Inc.     

Polygalacturonic acid trans-eliminase of Xanthomonas campestris

Polygalacturonic acid trans-eliminase from the culture fluid of Xanthomonas campestris was purified 66-fold by acetone precipitation, citrate extraction and chromatography on diethylaminoethyl- and carboxymethyl-cellulose. The optimum pH is 9·5 in glycine–sodium hydroxide buffer. Up to 1mm-calcium chloride brings about a remarkable stimulation of the enzyme activity and, at this concentration, no other cations promote or inhibit enzyme action except Ba²⁺ ions, which cause complete inhibition. The enzyme degrades polygalacturonic acid in a random manner; it does not act upon polygalacturonate methyl glycoside, although it can cleave partially (68%) esterified pectin. The end products from polygalacturonic acid at 46% breakdown are unsaturated di- and tri-galacturonic acids, in addition to saturated mono-, di- and tri-galacturonic acids. Pentagalacturonic acid is split preferentially into saturated dimer plus unsaturated trimer, or into saturated trimer plus unsaturated dimer; at a lower rate, it is also split into monomer and unsaturated tetramer. Unsaturated pentamer is split into unsaturated dimer plus unsaturated trimer. Tetragalacturonic acid is split some-what preferentially at the central bond to form dimer and unsaturated dimer, but it is also split into monomer and unsaturated trimer. Unsaturated tetramer is split only at the central bond to yield only unsaturated dimer. Trigalacturonic acid is split into monomer and unsaturated dimer. Unsaturated trimer is cleaved into saturated dimer and probably 4-deoxy-l-5-threo-hexoseulose uronic acid, which has not yet been directly identified. Neither saturated nor unsaturated digalacturonic acid is attacked. The unsaturated digalacturonic acid was isolated and proved to be O-(4-deoxy-β-l-5-threo-hexopyranos-4-enyluronic acid)-(1→4)-d-galacturonic acid.     

De(side chain) model of epothilone: bioconformer interconversions DFT study

Using ab initio methods, we have studied conformations of the de(sidechain)de(dioxy)difluoroepothilone model to quantify the effect of stability change between the exo and endo conformers of the epoxy ring. The DFT minimization of the macrolactone ring reveals four low energy conformers, although MP2 predicted five stable structures. The model tested with DFT hybride functional (B3LYP/6–31+G(d,p)) exhibits the global minimum for one of the exo forms (C), experimentally observed in the solid state, but unexpectedly with the MP2 electron correlation method for the virtual endo form (W). Using the QST3 technique, several pathways were found for the conversion of the low energy conformers to the other low energy exo representatives, as well as within the endo analog subset. The potential energy relationships obtained for several exo forms suggest a high conformational mobility between three, experimentally observed, conformers. The high rotational barrier, however, excludes direct equilibrium with experimental EC-derived endo form S. The highest calculated transition state for the conversion of the most stable exo M interligand to the endo S form is approximately a 28 kcal/mol above the energy of the former. The two-step interconversion of the exo H conformer to the endo S requires at least 28 kcal/mol. Surprisingly, we found that the transition state energy of the H form to the virtual endo W has the acceptable value of about 9 kcal/mol and the next energy barrier for free interconversion of endo W to endo S is 13 kcal/mol. Figure DFT Model of Epothilone Interconversions Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The dual exo/endo-type mode and the effect of ionic strength on the mode of catalysis of chitinase 60 (CHI60) from Serratia sp. TU09 and its mutants

Mutations of the tryptophan residues in the tryptophan-track of the N-terminal domain (W33F/Y and W69F/Y) and in the catalytic domain (W245F/Y) of Serratia sp. TU09 Chitinase 60 (CHI60) were constructed, as single and double point substitutions to either phenylalanine or tyrosine. The enzyme-substrate interaction and mode of catalysis, exo/endo-type, of wild type CHI60 and mutant enzymes on soluble (partially N-acetylated chitin), amorphous (colloidal chitin), and crystalline (β-chitin) substrates were studied. All CHI60 mutants exhibited a reduced substrate binding activity on colloidal chitin. CHI60 possesses a dual mode of catalysis with both exo- and endo-type activities allowing the enzyme to work efficiently on various substrate types. CHI60 preferentially uses the endo-type mode on soluble and amorphous substrates and the exo-type mode on crystalline substrate. However, the prevalent mode of hydrolysis mediated by CHI60 is regulated by ionic strength. Slightly elevated ionic strength, 0.1-0.2 M NaCl, which promotes enzyme-substrate interactions, enhances CHI60 hydrolytic activity on amorphous substrate and, interestingly, on partially N-acetylated chitin. High ionic strength, 0.5-2.0 M NaCl, prevents the enzyme from dissociating from amorphous substrate, occupying the enzyme in an enzyme-substrate non-productive complex. However, on crystalline substrates, the activity of CHI60 was only inhibited approximately 50% at high ionic strength, suggesting that the enzyme hydrolyzes crystalline substrates with an exo-type mode processively while remaining tightly bound to the substrate. Moreover, substitution of Trp-33 to either phenylalanine or tyrosine reduced the activity of the enzyme at high ionic strength, suggesting an important role of Trp-33 on enzyme processivity.     

Liquid-chromatographic analysis of the depolymerization of (1→4)-β-d-mannuronan by an extracellular alginate lyase from a marine bacterium

The extracellular alginate lyase activity from a fermentative marine bacterium isolated from actively growing tissues of Sargassum fluitans has been purified and studied with respect to substrate specificity and mechanism. The enzyme endolytically depolymerizes (1→4)-β-d-mannuronan derived from alginate to oligomeric products possessing 4,5-unsaturated, nonreducing termini. Reversed-phase liquid chromatography has established that early in the reaction the tri-, tetra-, and pentameric oligomers are the predominant species. The pentamer and larger products that at first accumulate in the reaction are later degraded to smaller products. The trimer is the major product late in the reaction, at which time the dimer and tetramer are also present in significant amounts. By incubating purified oligomers with enzyme, the trimer is shown to be completely refractory to further depolymerization and therefore represents a limit product of the reaction catalyzed by this enzyme. The tetramer is slowly converted into trimer and monomer, whereas the pentamer is readily converted into trimer and dimer.     

The active site of yeast endo-polygalacturonase contains seven subsites

The rate of hydrolysis of oligomers by the endopolygalacturonase of yeast is in the order: heptamer > hexamer > pentamer > tetramer. This suggests that the active site accommodates at least 7 units. Since the heptamer disappears concurrently with the bulk of larger oligomers, the maximum number of units appears to be 7. The release of labelled (unsaturated, or ³H labelled and reduced) end units from larger substrate is interpreted to indicate that the enzyme interacts with 3 saccharide units toward the reducing end from the bond to be broken, and with 4 units toward the non-reducing end. The relative affinities for the enzyme of saccharide units in various positions are unequal, as indicated by the very low relative rate of monomer production from the hydrolysis of hexamer and pentamer, and the apparently unequal probability of two other modes of hexamer hydrolysis [(tetramer + dimer) = 2.5 (trimer + trimer)].     

A New Sialidase Mechanism: BACTERIOPHAGE K1F ENDO-SIALIDASE IS AN INVERTING GLYCOSIDASE

Bacteriophages specific for Escherichia coli K1 express a tailspike protein that degrades the polysialic acid coat of E. coli K1 that is essential for bacteriophage infection. This enzyme is specific for polysialic acid and is a member of a family of endo-sialidases. This family is unusual because all other previously reported sialidases outside of this family are exo- or trans-sialidases. The recently determined structure of an endo-sialidase derived from bacteriophage K1F (endoNF) revealed an active site that lacks a number of the residues that are conserved in other sialidases, implying a new, endo-sialidase-specific catalytic mechanism. Using synthetic trifluoromethylumbelliferyl oligosialoside substrates, kinetic parameters for hydrolysis at a single cleavage site were determined. Measurement of k_cat/K_m at a series of pH values revealed a dependence on a single protonated group of pK_a 5. Mutation of a putative active site acidic residue, E581A, resulted in complete loss of sialidase activity. Direct ¹H NMR analysis of the hydrolysis of trifluoromethylumbelliferyl sialotrioside revealed that endoNF is an inverting sialidase. All other wild type sialidases previously reported are retaining glycosidases, implying a new mechanism of sialidase action specific to this family of endo-sialidases.     

Stereoselective hydrogenolysis of dioxolane-type benzylidene derivatives: Synthesis of some benzyl ethers of benzyl β-d-arabinopyranoside

The following derivatives of benzyl β-d-arabinopyranoside are described: exo-3,4-O-benzylidene (2), endo-3,4-O-benzylidene (3), and the 2-benzyl ether derivatives (4 and 5) of 2 and 3. Hydrogenolysis (LiAlH₄-AlCl₃) of the exo-isomers (2 and 4) gave mainly 4-hydroxy-3-O-benzyl derivatives (6 and 11), whereas the endo-isomers (3 and 5) gave mainly 3-hydroxy-4-O-benzyl derivatives (7 and 12). Acid hydrolysis of 4 and 5 yielded the 2-O-benzyl derivative (10).     

Molecularly imprinted polymer catalysis of a Diels-Alder reaction

A series of synthetic polymers were designed and synthesized for enhancing the rate of the Diels-Alder cycloaddition reaction of 1,3-butadiene carbamic acid benzyl ester (1) and N,N-dimethyl acrylamide (2), to yield the corresponding endo- (3) and exo- (4) reaction products. Putative transition state analogues (TSAs) for the endo- (5) and exo- (6) reaction pathways were used as templates for the synthesis of molecularly imprinted methacrylic acid (MAA)–divinylbenzene (DVB) copolymers. The polymer system utilized was selected based upon a series of ¹H NMR studies of complex formation between template and a functional monomer analogue (K_d (app) ≈ 70 mM, d₈-toluene, 293 K). Batch binding studies revealed that the imprinted polymers were selective for the TSA corresponding to the template used in the polymer synthesis. Studies on the influence of the polymers on the catalysis of the reaction of 1 and 2 demonstrated a 20-fold enhancement of the rate of the reaction relative to the solution reaction. A surprising temperature dependence of the reaction of 1 and 2 in the presence of the polymers was observed, which provides support for the role of template-functional monomer complexes in the catalysis of the Diels-Alder reaction.     

Pectin polysaccharides of rowan Sorbus aucuparia L.

Water-soluble polysaccharide fractions were extracted from the fruit of rowan Sorbus aucuparia L. by water and 0.7% ammonium oxalate water solution. The total yield was 4.2%. It is demonstrated that these fractions are pectin polysaccharides, and their carbon chains are primarily composed of galactunoric acid residue (up to 68%), arabinose and galactose. Sephacryl S-500 gelfiltration of rowan fruit pectin polysaccharides proved their relative homogeneity pertaining to their molecular weights, whereas endo-polygalacturonase enzymatic hydrolysis gives evidence of the presence of extended galacturonan (rhamnogalacturonan) ranges in their carbohydrate chains. Methylation of rowan pectin polysaccharides shows that their carbohydrate pendants are formed by 1,5-linked arabinofuranose residue, 1,4-linked glucopyranose residue, 1,6-linked galactopyranose residue, 1,3,6-linked mannopyranose residue and 1,3,6-linked galactopyranose residue. Glucopyranose residue is identified at non reducible ends of these pendants. It was demonstrated that antioxidant activity of water solutions of pectin polysaccharides extracted from rowan S. aucuparia L. (0.5 mg/mL) is 37?C53% of trolox activity, which is 100%.     

Pheromones released during inter- and intra-sex response of the scolytid beetle Dendroctonus brevicomis

Pheromones of Dendroctonus brevicomis released variously during inter- and intra-sex response (including stridulation by both sexes) were the known pheromones exo-brevicomin, endo-brevicomin, frontalin and verbenone, and substances identified as pinocarvone, trans-pinocarveol, and myrtenol. These substances are present in emergent beetles and thus attack of a host tree is not essential for their initial production.     

Some Properties of Endo-polygalacturonase from Trichosporon penicillatum SNO-3

Some properties of the endo-polygalacturonase from Trichosporon penicillatum were investigated. The enzyme showed the highest activity around pH 5.0 and was stable at this pH up to 50°C. The enzyme catalyzed the hydrolysis of galacturonic acid oligomers as well as its polymer. The pentamer was degraded to a trimer and a dimer, the tetramer to a trimer and a monomer, and the trimer to a dimer and a monomer, respectively, whereas the dimer was not degraded. The kinetic constant V_max and Km values changed with the substrate chain-length; the Km values tended to decrease, whereas the V_max values tended to increase with increasing chain-length of the substrate. The amino acid residue participating in the active site of the enzyme was studied and it was found to be histidine.     

N-phenylglucosylamine hydrolysis: a mechanistic probe of β-glucosidase

The spontaneous hydrolysis of glycosylamines, where the aglycone is either a primary amine or ammonia, is over a hundred million-times faster than that of O- or S-glycosides. The reason for this (as pointed out by Capon and Connett in 1965) is that, in contrast to the mechanism for O- or S-glycoside hydrolysis, hydrolysis of these N-glycosides (e.g., glc-NHR) involves an endocyclic C-O bond cleavage resulting in formation of an imine (iminium ion) which then reacts with water. Since ring-opening is kinetically favored with glycosylamines, compounds such as phenylglucosylamine can be a useful probes of enzymes that have been suggested to possibly follow this mechanism. With β-glucosidase from sweet almonds, the enzyme is highly efficient in catalyzing the hydrolysis of phenyl glucoside (k_cat/k_non ∼ 10¹⁴) and phenyl thioglucoside (k_cat/k_non ∼ 10¹⁰) while with either the almond or the Aspergillus niger enzyme or with yeast α-glucosidase, there is no detectable catalysis of phenylglucosylamine hydrolysis (k_cat/k_non < 20). These results are consistent with the generally accepted mechanism involving exocyclic bond cleavage by these enzymes.