Modeling and biochemical analysis of the activity of antibiofilm agent Dispersin B.

Bacteria in a biofilm are enmeshed in a self-synthesized extracellular polysaccharide matrix (PGA), which is a linear polymer of beta(1,6)-linked N-acetylglucosamine (GlcNAc) residues. Dispersin B (DspB), a soluble glycoside hydrolase produced by the periodontal pathogen Actinobacillus actinomycetemcomitans degrades PGA. The enzyme DspB is an alpha/beta TIM-barrel protein and belongs to family 20 glycosyl hydrolases members. The enzyme activity of DspB with regard to its substrate specificity towards beta(1,6)-linked GlcNAc polymers and its endo/exo character was investigated through ligand docking and the hydrolysis of synthetic oligosaccharides. Ligand docking analysis suggested that beta(1,6)-linked GlcNAc oligosaccharide bound to the active site better that beta(1,4)-linked GlcNAc oligosaccharide. Our combined results indicate that DspB is an exo-acting enzyme that hydrolyzes beta(1,6)-linked N-acetylglucosamine oligomers.

Effect of temperature on subsite map of Bacillus licheniformis alpha-amylase.

To elucidate how temperature effects subsite mapping of a thermostable alpha-amylase from Bacillus licheniformis (BLA), a comparative study was performed by using 2-chloro-4-nitrophenyl (CNP) beta-maltooligosides with degree of polymerisation (DP) 4-10 as model substrates. Action patterns, cleavage frequencies and subsite binding energies were determined at 50 degrees C, 80 degrees C and 100 degrees C. Subsite map at 80 degrees C indicates more favourable bindings compared to the hydrolysis at 50 degrees C. Hydrolysis at 100 degrees C resulted in a clear shift in the product pattern and suggests significant differences in the active site architecture. Two preferred cleavage modes were seen for all substrates in which subsite (+2) and (+3) were dominant, but CNP-G1 was never formed. In the preferred binding mode of shorter oligomers, CNP-G2 serves as the leaving group (79%, 50%, 59% and 62% from CNP-G4, CNP-G5, CNP-G6 and CNP-G7, respectively), while CNP-G3 is the dominant hydrolysis product from CNP-G8, CNP-G9, and CNP-Gl0 (62%, 68% and 64%, respectively). The high binding energy value (-17.5 kJ/mol) found at subsite (+2) is consistent with the significant formation of CNP-G2. Subsite mapping at 80 degrees C and 100 degrees C confirms that there are no further binding sites despite the presence of longer products.

Synthesis of the alpha-L-Araf-(1-->2)-beta-D-Galp-(1-->6)-beta-D-Galp-(1-->6)-[alpha-L-Araf-(1-->2)]-beta-D-Galp-(1-->6)-D-Gal hexasaccharide as a possible repeating unit of the cell-cultured exudates of Echinacea purpurea arabinogalactan.

For the characterization of the supposed epitope of an arabinogalactan, isolated from the extract of the cell-cultured Echinacea purpurea, the title hexasaccharide was synthesized. The whole synthetic route was based on the 6-O-(methoxydimethyl)methyl ether (MIP) protecting group strategy. 2-O-Benzyl-3,4-O-isopropylidene-6-O-(methoxydimethyl)methyl-beta-D-galactopyranosyl-(1-->6)-1,2:3,4-di-O-isopropylidene-alpha-D-galactopyranose was used to prepare the desired glycosyl donor and glycosyl acceptor both carrying a persistent O-benzyl group at position 2'. Reaction of the digalactose donor and the digalactose acceptor resulted in a beta-(1-->6)-linked galactose-containing tetrasaccharide in which OH-2' and OH-2"' were substituted with benzyl groups. Hydrogenolytic removal of the benzyl groups of the tetragalactose compound gave the diol aglycon which was diarabinosylated in one step to furnish the protected target compound, whose deprotection led to the title hexasaccharide. All of the synthesized compounds were characterized by 1H and 13C NMR spectra, as well as by MALDI-TOF mass-spectrometry measurements.

A new mixed acetal-type substitution pattern for alpha-cyclodextrin. Preparation of hexakis (3-O-benzyl)- alpha-cyclodextrin.

alpha-CD was converted into hexakis[2,6-di-O-(methoxydimethyl)methyl]-alpha-CD by a proton-catalyzed reaction with 2-methoxypropene. Subsequent benzylation under Brimacombe conditions resulted in the fully protected compound, from which the acid-sensitive acetal groups were removed to obtain hexakis(3-O-benzyl)-alpha-cyclodextrin. The structure of all of the compounds synthesized was confirmed by 13C J-ECHO, COSY, HETCOR and HMBC NMR measurements.

Synthesis of the alpha-D-GlcpA-(1-->3)-alpha-L-Rhap-(1-->2)-L-Rha trisaccharide isolated from the cell wall hydrolyzate of the green alga, Chlorella vulgaris.

The title trisaccharide was synthesized from 6-O-acetyl-2,3,4-tri-O-benzyl-alpha-D-glucopyranosyl chloride (10), ethyl 2,4-di-O-benzyl-1-thio- (5) and benzyl 3,4-di-O-benzyl-alpha-L-rhamnopyranoside (9). The disaccharide 11 obtained from compounds 5 and 10 was used as the glycosyl donor to glycosylate the rhamnopyranoside derivative 9 having free OH-2 using the NIS-AgOTf-mediated glycosylation methodology. Zemplén deacetylation of the trisaccharide 12 resulted in the 6"-OH derivative (13), which was selectively oxidized with CrO3 to the uronic acid derivative 14. The benzyl groups were removed by catalytic hydrogenolysis to furnish the target trisaccharide (1).

Identification and structural analysis of synthetic oligosaccharides of Shigella sonnei using MALDI-TOF MS.

MALDI-TOF mass spectroscopy was used for the molecular weight determination of protected synthetic oligosaccharides related to a cell surface bacterial polysaccharide. By-products containing chlorinated protecting groups caused isotopic patterns characteristic of the natural isotopic distribution of chlorine, were identified on the basis of isotopic distribution. 2,4,6-Trihydroxyacetophenone (THAP) as a matrix was better than 2,5-dihydroxybenzoic acid (DHB) for compounds containing chlorine, since monoisotopic resolution and no fragmentation were observed. In the post source decay (PSD) mode the identification of the oligosaccharide sequence through cleavage of the interglycosidic linkages was also possible, thus providing a sensitive and accurate tool for the structural verification of synthetic oligosaccharide intermediates.

Chemoenzymatic synthesis of 2-chloro-4-nitrophenyl beta-maltoheptaoside acceptor-products using glycogen phosphorylase b.

In the present work, we aimed at developing a chemoenzymatic procedure for the synthesis of beta-maltooligosaccharide glycosides. The primer in the enzymatic reaction was 2-chloro-4-nitrophenyl beta-maltoheptaoside (G(7)-CNP), synthesised from beta-cyclodextrin using a convenient chemical method. CNP-maltooligosaccharides of longer chain length, in the range of DP 8-11, were obtained by a transglycosylation reaction using alpha-D-glucopyranosyl-phosphate (G-1-P) as a donor. Detailed enzymological studies revealed that the conversion of G(7)-CNP catalysed by rabbit skeletal muscle glycogen phosphorylase b (EC 2.4.1.1) could be controlled by acarbose and was highly dependent on the conditions of transglycosylation. More than 90% conversion of G(7)-CNP was achieved through a 10:1 donor-acceptor ratio. Tranglycosylation at 37 degrees C for 30 min with 10 U enzyme resulted in G(8-->12)-CNP oligomers in the ratio of 22.8, 26.6, 23.2, 16.5, and 6.8%, respectively. The reaction pattern was investigated using an HPLC system. The preparative scale isolation of G(8-->11)-CNP glycosides was achieved on a semipreparative HPLC column. The productivity of the synthesis was improved by yields up to 70-75%. The structures of the oligomers were confirmed by their chromatographic behaviours and MALDI-TOF MS data.

Synthesis of the repeating unit of the O-specific polysaccharide of Shigella sonnei and quantitation of its serologic activity.

The chemical synthesis of the zwitterionic disaccharide 2 is described that corresponds to the repeating unit of the O-specific polysaccharide (1) of the gram-negative human pathogen Shigella sonnei. Passive hemolysis inhibition tests using a hyperimmune rabbit serum raised against S. sonnei showed that the serologic activity of the disaccharide 2 is nearly 2- to 3-fold higher than those of its component monosaccharides. NMR data of 2 are in support of the proposed structure of the O-specific polysaccharide.

Synthesis of L-glucose from D-gulono-1,4-lactone.

An efficient method for the synthesis of L-glucose from D-gulono-1,4-lactone via 1,2,3,4,5-penta-O-benzyl/acetyl/benzoyl-D-gulitol is described in 34-53% overall yield.

Scope and limitation of the application of the (methoxydimethyl)methyl group in the synthesis of 2'-O-, 6'-O- and 2',6'-di-O-(alpha-L-arabinofuranosyl)-beta-D-galactopyranosyl- (1-->6)-D-galactoses.

For the characterisation of the anticipated epitope of an arabinogalactan, isolated from the extract of Echinacea purpurea, the trisaccharide alpha-L-Araf-(1-->2)-beta-D-Galp- (1-->6)-D-Gal was synthesized. The easily available 3,4-O-isopropylidene-6-O-(methoxydimethyl)methyl-beta-D-galactopyr anosyl- (1-->6)-1,2:3,4-di-O-isopropylidene-alpha-D-galactopyranose having the OH-2' free served as aglycone upon direct arabinosylation at the 2' position under Helferich conditions. The formed HgBr2 cleaved the acid sensitive protecting group at position 6', but under basic conditions the desired, fully protected trisaccharide, or its symmetrical dimerization derivative linked 6'- to 6'-position via an isopropylidene bridge, could be obtained. An alternative route involved arabinosylation of a hepta-O-acetylated digalactose with free OH-2'. Two other oligosaccharides, namely, alpha-L-Araf-(1-->6)-beta-D-Galp-(1-->6)-D-Gal and (alpha-L-Araf)2-(1-->2,6)-beta-D-Galp-(1-->6)-D-Gal were also synthesized and characterised.

Synthesis of p-trifluoroacetamidophenyl (4,6-dideoxy-4-formamido-3-C-methyl-2-O-methyl-alpha-L-mannopyranosyl)- (1-->3)-(2-O-methyl-alpha-D-rhamnopyranosyl)-(1-->3)- (2-O-methyl-alpha-L-fucopyranosyl)-(1-->3)-(alpha-L-rhamnopyranosyl)- (1-->2)-6-deoxy-alpha-L-talopyranoside: a spacer-armed pentasaccharide glycopeptidolipid antigen of Mycobacterium avium serovar 14.

Syntheses of p-trifluoroacetamidophenyl glycosides of the haptenic pentasaccharide and the non-reducing disaccharide unit of the title pentasaccharide are reported. The synthesis of the terminal N-formylkansosamine unit started from methyl 6-deoxy-2,3-O-isopropylidene-alpha-L-lyxo- hexopyran-4-uloside which, after C-3 methylation, was transformed into a glycosyl donor [3-O-benzyl-4-N-benzylformamido-4,6-dideoxy-3-C-methyl-2-O-methyl- alpha,beta-L-mannopyranosyl trichloroacetimidate (20), and used for the synthesis of p-trifluoroacetamidophenyl (4-formamido-4,6-dideoxy-3-C-methyl-2-O-methyl-alpha-L-mannopyranosyl)- (1-->3)-6-deoxy-2-O-methyl-alpha-D-mannopyranoside (29). Ethyl (3-O-benzyl-4-N-benzylformamido-4,6-dideoxy-3-C-methyl-2-O-methyl- alpha-L-mannopyranosyl)-(1-->3)-4-O-benzyl-6-deoxy-2-O-methyl-1-thio- alpha-D-mannopyranoside (31), prepared by glycosylation of ethyl 4-O-benzyl-6-deoxy-2-O-methyl-1-thio-alpha-D-mannopyranoside with 20, served as glycosyl donor in a 2 + 3 block synthesis of the title pentasaccharide.

Synthesis of chromogenic substrates of alpha-amylases on a cyclodextrin basis.

One-pot acetylation and subsequent partial acetolysis of alpha-, beta- and gamma-cyclodextrins resulted in crystalline peracetylated malto-hexaose, -heptaose, and -octaose, respectively. Prolonged acetolysis of beta-cyclodextrin gave a mixture of acetylated maltooligosaccharides, from which peracetylated malto-triose, -tetraose, and -pentaose were isolated. The acetylated oligosaccharides were converted into alpha-acetobromo derivatives, and then transformed into 4-nitrophenyl and 2-chloro-4-nitrophenyl beta-glycosides. From the 4-nitrophenyl glycosides 4,6-O-benzylidene derivatives were prepared, which were used together with the free glycosides as substrates of porcine pancreatic alpha-amylase.

Galactosylation with beta-galactosidase from bovine testes employing modified acceptor substrates.

In this study beta1-3 linked analogues of the T-antigen determinant were synthesized in preparative scale by transgalactosylation using beta-galactosidase from bovine testes to give synthetic antigens. Acceptors with modifications of the sugar residue such as alpha-glycosylated spacers, as well as GlcNAc-alphaOR- and 2dGal-alphaOR-substrates opened further possibilities for galactosylation.

Action pattern of porcine pancreatic alpha-amylase on three different series of beta-maltooligosaccharide glycosides.

A technique for the investigation of the action pattern of porcine pancreatic amylase (PPA) has been developed by utilising as model substrates 2-chloro-4-nitrophenyl (CNP) and 4-nitrophenyl (NP) beta-glycosides of maltooligosaccharides of dp 4-8 and some NP derivatives modified at the nonreducing end with a 4,6-O-benzylidene (Bnl) group. The action pattern was investigated by the method of product analysis, using an HPLC method. The product pattern and cleavage frequency was very similar in the CNP- and NP-oligomers and showed that the glucopyranose residue could be replaced by the aglycon group. Modification of the nonreducing end of NP glycosides to give a 4,6-O-benzylidene-D-glucopyranosyl group indicated a favourable interaction between the Bnl group and the subsites (-3) and (-5) but an unfavourable one with subsite (-4), which resulted in a clear shift in the product pattern. The results obtained with the digestion of the benzylidene-protected substrates confirm a multiple attack mechanism for PPA.

Conformational stabilization of the altruronic acid residue in the O-specific polysaccharide of Shigella sonnei/Plesiomonas shigelloides.

Complete assignments for the 1H- and the 13C-NMR spectra of the O-specific polysaccharide of S. sonnei/Plesiomonas shigelloides are reported. Evidence is presented that in this polysaccharide both pyranose residues exist preferentially in the 4C1 chair conformation and that the polysaccharide exists in the zwitterion form.

A convenient new pathway for stereospecific epimerization of monosaccharide moieties in disaccharides.

The disaccharides benzyl 4,6-O-benzylidene-2-O-alpha-D-mannopyranosyl-beta- D-glucopyranoside (2), 6-O-beta-D-galactopyranosyl-1,2:3,4-di-O-isopropylidene-alpha-D- galactopyranose (4), and phenyl 4-O-beta-D-galactopyranosyl-1-thio-beta-D-glucopyranoside (7) were selectively acetalated with chloral-dicyclohexylcarbodiimide in a nonclassical pathway. During acetalation, the D-mannopyranosyl moiety of the disaccharide 2 and the unprotected beta-D-galactopyranosyl moieties of 4 and 7 were epimerized at their 3-positions, generating D-altro- and D-gulo-pyranosyl moieties, respectively.

Synthesis of a fucosylated and a non-fucosylated core structure of xylose-containing carbohydrate chains from N-glycoproteins.

The synthesis is reported of methyl 2-acetamido-4-O-[2-acetamido-2-deoxy-O-(3,6-di-O-alpha-D- mannopyranosyl-2-O-beta-D-xylopyranosyl-beta-D-mannopyranosyl)-beta-D- glucopyranosyl]-2-deoxy-beta-D-glucopyranoside (4) and methyl 2-acetamido-4-O-[2-acetamido-2-deoxy-4-O- (3,6-di-O-alpha-D- mannopyranosyl-2-O-beta-D-xylopyranosyl-beta-D-mannopyranosyl)-beta-D- glucopyranosyl]-2-deoxy-6- O-alpha-L-fucopyranosyl-beta-D-glucopyranoside (5), which represent the invariant hexasaccharide core structure of the xylose-containing glycans of N-glycoproteins and its 6-O- fucosylated derivative. Ethyl 4-O-[3-O-allyl-4-O-benzoyl-6-O-tert-butyldimethylsilyl-2-O- (2,3,4-tri-O-acetyl-beta-D-xylopyranosyl)- beta-D-mannopyranosyl]-3,6-di-O-benzyl-2-deoxy-2-phthalimido-1- thio-beta-D-glucopyranoside (9) was coupled with methyl 3,6-di-O-benzyl-2-deoxy-2-phthalimido-beta-D- glucopyranoside (11). Desilylation of the resulting tetrasaccharide derivative, followed by condensation with 2,3,4,6- tetra-O-acetyl-alpha-D-mannopyranosyl trichloroacetimidate (7), gave methyl 4-O-(4-O-[3-O-allyl-4- O-benzoyl-6-O-(2,3,4,6-tetra-O-acetyl-alpha-D-mannopyranosyl)-2-O-(2,3,4 -tri-O- acetyl-beta-D-xylopyranosyl)- beta-D-mannopyranosyl]-3,6-di-O-benzyl-2-deoxy-2-phthalimido-beta-D- glucopyranosyl)- 3,6-di-O-benzyl-2-deoxy-2-phthalimido-beta-D-glucopyranoside (14). Deallylation of 14, followed by condensation with 7 and deprotection, gave hexasaccharide 4. Ethyl 3,6-di-O- benzyl-2-deoxy-4-O- [4,6-di-O-acetyl-3-O-allyl-2-O-(2,3,4-tri-O-acetyl-beta-D-xylopyranosyl) - beta-D-mannopyranosyl]-2- phthalimido-1-thio-beta-D-glucopyranoside (17) was coupled with methyl 3-O- benzyl-2-deoxy-6-O- (4-methoxybenzyl)-2-phthalimido-beta-D-glucopyranoside. Demethoxybenzylation of the tetrasaccharide derivative thus obtained, followed by fucosylation using ethyl 2,3,4-tri-O- benzyl-1-thio- beta-L-fucopyranoside, gave methyl 3-O-benzyl-2-deoxy-4-O-[3,6-di-O-benzyl-2- deoxy-4-O-[4,6- di-O-acetyl-3-O-allyl-2-O-(2,3,4-tri-O-acetyl-beta-D-xylopyranosyl)-beta -D- mannopyranosyl]-2-phthalimido- beta-D-glucopyranosyl)-2-phthalimido-6-O-(2,3,4-tri-O-benzyl-alpha-L- fucopyranosyl)-beta-D-glucopyranoside (23). O-Deacetylation followed by tert-butyldimethylsilylation, benzoylation, and desilylation gave methyl 4-O-(4-O-[3-O-allyl-4-O-benzoyl-2-O-(2,3,4-tri-O-benzoyl-beta-D- xylopyranosyl)- beta-D-mannopyranosyl]-3,6-di-O-benzyl-2-deoxy-2-phthalimido-beta- D-glucopyranosyl)-3- O-benzyl-2-deoxy-2-phthalimido-6-O-(2,3,4-tri-O-benzyl-alpha-L-fucopy ran osyl)- beta-D-glucopyranoside (24). Mannosylation of 24 using 7, followed by deallylation, further mannosylation with 7, and deprotection, gave the heptasaccharide 5.

Chemical synthesis of the pyruvic acetal-containing trisaccharide unit of the species-specific glycopeptidolipid from Mycobacterium avium serovariant 8.

The functionalized, pyruvic acetal-containing haptenic trisaccharide, p-trifluoroacetamidophenyl 6-deoxy-2-O-(3-O-[4,6-O-(S)-(1-methoxycarbonylethylidene)-3-O-meth yl- beta-D-glucopyranosyl]-alpha-L-rhamnopyranosyl)-alpha-L-talopyranosid e (19), a component of the glycolipid from Mycobacterium avium serovar 8 was synthesized. For the preparation of the terminal pyruvic acetal-containing unit, benzyl 2-O-benzyl-3-O-methyl-beta-D-glucopyranoside (6) was condensed with methyl 2,2-di(ethylthio)propionate (1) in the presence of SO2Cl2-CF3SO3H catalyst to yield benzyl 2-O-benzyl-4,6-O-(S)-(1-methoxycarbonylethylidene)-3-O-methyl-beta -D- glucopyranoside (7S), which was then converted into the suitably substituted glycosyl donor 2-O-acetyl-4,6-O-(S)-(1-methoxycarbonylethylidene)-3-O-methyl-alph a-D- glucopyranosyl trichloroacetimidate (11). The disaccharide glycosyl acceptor p-nitrophenyl endo-3,4-O-benzylidene-6-deoxy-2-O-(2,4-di-O-benzyl-alpha-L-rhamnopyrano syl)- alpha-L-talopyranoside (15) was glycosylated with 11 in the presence of trimethyl trifluoromethanesulfonate to furnish the protected trisaccharide p-nitrophenyl 2-O-(3-O-[2-O-acetyl-4,6-O-(S)-(1-methoxycarbonylethylidene)-3-O-m ethyl-beta- D-glucopyranosyl]-2,4-di-O-benzyl-alpha-L-rhamnopyranosyl)-endo-3,4- O-benzylidene-6-deoxy-alpha-L-talopyranoside (16). After deprotection, this gave the spacer-armed unprotected haptenic trisaccharide 19.