Location and identity of the acyl substituents on the extracellular polysaccharides of Rhizobium trifolii and Rhizobium leguminosarum

The basic structures of the extracellular polysaccharides of Rhizobium leguminosarum and Rhizobium trifolii were found to be identical, but their acylation patterns differ. Liquid hydrogen fluoride at −40° degrades the two polysaccharides to a series of oligosaccharides representing the repeating units of the polysaccharides and their higher homologs. At −23°, it degrades the polymers to a mixture of oligosaccharides from which a tetrasaccharide constituting a unit of the backbone of the polysaccharide, and a trisaccharide representing all but the non-reducing terminus of the side chain, could be readily purified. The location and identity of the acyl substituents were determined by ¹H-n.m.r. spectroscopy, methylation analysis, and f.a.b. mass spectrometry. The unusual substituent d-3-hydroxybutanoate was found esterified to O-3 of a terminal 4,6-O-pyruvic acetalated d-galactose in both strains of R. leguminosarum, and in one of the three strains of R. trifolii tested. All of the strains tested contained a 3-O-acetyl substituent on the (1→4)-β-d-glucopyranosyl residues in the backbone of the polysaccharide. Only the R. leguminosarum polysaccharides contained a combination of 2- and 3-O-acetyl groups on the branching sugar of the backbone of the polymer.     

Structural studies of the capsular polysaccharide of Klebsiella type 59.

The structure of the capsular polysaccharide from Klebsiella type 59 has been investigated by methylation analysis, a modified Smith-degradation procedure, and uronic acid degradation followed by oxidation and elimination of the substituents of the oxidized residue. The oligomeric fragments produced by these degradative procedures were isolated and characterized. O-Acetyl groups were identified and their position determined. The polysaccharide consists of the following pentasaccharide repeating-unit (dotted lines indicate that only some of the residues carry the O-acetyl substituent). See article.     

Structural determination and biosynthetic studies of the O-antigenic polysaccharide from the enterohemorrhagic Escherichia coli O91 using 13C-enrichment and NMR spectroscopy.

The structure of the O-antigenic polysaccharide from the enterohemorrhagic Escherichia coli O91 has been determined using primarily NMR spectroscopy on the (13)C-enriched polysaccharide. The O-antigen is composed of pentasaccharide repeating units with the following structure: -->4)-beta-D-Galp-(1-->4)-beta-D-GlcpNAc-(1-->4)-beta-D-GlcpA-6-N- Gly -(1-->3)-beta-D-GlcpNAc-(1-->4)-alpha-D-Quip-3-N-[(R)-3-hydroxy butyra mido]-(1-->. The bacterium was grown with D-[UL-(13)C]glucose in the medium which resulted in an overall degree of labeling of approximately 65% in the sugar residues and approximately 50% in the N-acyl substituents, indicating some metabolic dilution in the latter. The (13)C-enrichment of the polysaccharide proved valuable since NMR assignments could be made on the basis of (13)C, (13)C-connectivity in uniformly labeled residues. The biosynthesis of the (R)-3-hydroxybutyramido substituent via C(2) fragments was identified by NMR spectroscopy. The (R)-configuration at C3 is in accord with fatty acid biosynthesis. Additional cultures with specifically labeled D-[1-(13)C]glucose or D-[6-(13)C]glucose corroborated the direct incorporation of glucose as the building block for the hexose skeletons in the polysaccharide and the biosynthesis of acyl substituents occurring via the triose pool followed by decarboxylation to give acetyl building blocks labeled with (13)C at the methyl group.     

Structural study of the extracellular polysaccharide gum from Rhizobium strain CB744

The structure of the extracellular polysaccharide gum from nitrogen-fixing Rhizobium sp. strain CB744 (a member of the slow-growing Cowpea group) has been investigated. Gas-chromatographic analysis of the alditol acetates of the acid hydrolysate showed the gum to be composed of galactose, 4-O-methylgalactose, mannose, and glucose in the molar ratio of 1:2.5:3.5:7.0. The polysaccharide is unusual in that it contains no carbonyl substituent, although such substituents are common amongst polysaccharides produced by the slow-growing group. The native and de-branched polysaccharides were examined by methylation analysis. The anomeric configurations were determined by ¹³C-n.m.r. and oxidation by chromium trioxide. It is concluded that there are two β-(1→4)-linked glycopyranosyl residues for each α-(1→4)-linked mannopyranosyl residue, and that each mannose is substituted at O-6 by a β-galactopyranosyl residue, with 71% of the galactose groups being present as 4-O-methylgalactose.     

Acetylated methylmannose polysaccharide of Streptomyces griseus. Locations of the acetyl groups.

The positions of esterification of the 4 to 5 acetyl residues in the acetylated methylmannose-containing polysaccharide from Streptomyces griseus have been established by the methyl replacement technique, wherein ester substituents are specifically replaced with methyl ether substituents. The newly incorporated methyl groups were distinguished from 3-O-methyl groups by the use of polysaccharide containing radioactively labeled endogenous methyl groups. The positions of methyl group localization were established by a proton magnetic resonance study of the intact methyl-replaced polysaccharide combined with an analysis of the constituent monosaccharides by gas-liquid chromatography-electron impact mass spectrometry of their alditol acetate derivatives. These studies demonstrate that the acetyl groups are located at position 6 of approximately half of the 10 contiguous alpha(1 leads to 4)-linked 3-O-methyl-D-mannose residues. Purification of the polysaccharide was accomplished by an added step involving affinity chromatography on a column containing immobilized palmitoyl residues. The affinity of the polysaccharide for this long chain lipid suggests that its plays a role similar to the methylmannose-containing polysaccharide of Mycobacterium smegmatis in its regulation of the bacterium's fatty acid synthetase.     

Acylated oligosaccharides from Klebsiella K63 capsular polysaccharide: Depolymerization by partial hydrolysis and by bacteriophage-borne enzymes

The extracellular polysaccharide from Klebsiella K63 is unique in having acetic and formic ester groups attached to the d-galactopyranosyluronic residues in the trisaccharide repeating-sequence. These O-acyl substituents are shown to be some what resistant to mild hydrolysis by both acid and alkali. Bacteriophage-induced depolymerization of the polysaccharide generated a series of acylated oligosaccharides comprising one, or more, repeating unit(s). By mild hydrolysis with acid, the same series of oligomers was released from the polysaccharide, together with the corresponding non-acylated compounds and the expected acylated and non-acylated aldobiouronic acids. A study of these oligosaccharides, as well as of a number of their related compounds, is described, with particular emphasis on the methods used to locate the formic and acetic ester groups. The location of the O-acyl substituents on the galactosyluronic residues was further supported by the results obtained from the high-resolution, 400-MHz, p.m.r. spectra and ¹³C-n.m.r. spectra of a number of the oligosaccharides.     

Preliminary studies on the composition and rheological properties of the extracellular polysaccharide synthesized by Pseudomonas PBI (NCIB 11264).

A microorganism isolated from a carbohydrate-rich industrial effluent synthesized an exocellular slime polysaccharide composed of glucose and galactose in a molar ratio of 7.45 +/- 0.68 : 1, and two non-carbohydrate substituents acetate (3--4%) and pyruvate (5--9%). Contamination by rhamnose and mannose was detectable in crude polysaccharide samples. Solutions of the polysaccharide were pseudoplastic, but not thixotropic, and formed gels in the presence of certain trivalent cations.     

Full NMR assignment and revised structure for the capsular polysaccharide from Streptococcus pneumoniae type 15B

The capsular polysaccharide from Streptococcus pneumoniae Type 15B is a component of the 23-valent polysaccharide vaccine against pneumococcal disease. We report full NMR assignments for the native and de-O-acetylated polysaccharide, and confirm that the phosphorylated substituent is glycerol-2-phosphate rather than phosphocholine, located on O-3 of the side chain beta-Galp residue. The polysaccharide is O-acetylated on the terminal alpha-Gal residue, distributed between O-2, O-3, O-4 and O-6 in a ratio of 6:12:12:55, with approximately 15% of the repeat units not O-acetylated.     

Preliminary studies on the composition and rheological properties of the extracellular polysaccharide synthesized by pseudomonas PB1 (NCIB 11264)

A microorganism isolated from a carbohydrate-rich industrial effluent synthesized an exocellular slime polysaccharide composed of glucose and galactose in a molar ratio of 7.45 ± 0.68: 1, and two non-carbohydrate substituents acetate (3–4%) and pyruvate (5–9%). Contamination by rhamnose and mannose was detectable in crude polysaccharide samples. Solutions of the polysaccharide were pseudoplastic, but not thixotropic, and formed gels in the presence of certain trivalent cations.     

The structure of the nonreducing terminal groups in the O-specific polysaccharides from two strains of Bordetella bronchiseptica.

The structures of the polysaccharide chains of the LPS from Bordetella bronchiseptica strains 110H and Bp512 were analysed by NMR spectroscopy and mass spectrometry. The polysaccharides consist of alpha-(1-4)-linked 2,3-diacetamido-2,3-dideoxy-L-galacturonic acid repeating units. Polysaccharides from both strains have 2,3, 4-triamino-2,3,4-trideoxy-alpha-galacturonamide derivatives at their nonreducing ends, a monosaccharide identified for the first time in nature. The polymers from the two strains differ in the nature of the acylation of the amino groups of this monosaccharide. In the strain 110H, the residue is formylated at positions 3 and 4, and has N-formyl-L-alanyl or L-alanyl substituents at N-2. In the strain Bp512, the amino group at position 2 is acetylated, at position 3 it is formylated, and the amino group at position 4 bears a 2-methoxypropionyl substituent. The distribution of the acyl groups was determined from long range 1H-13C correlation (HMBC) NMR spectra. Measurement of the spectra under different pH conditions showed that carboxyl groups of the inner uronic acid residues of the polymeric chain are free, and that carboxyl groups of the terminal residues are amidated. These conclusions were confirmed by the results of mass spectrometric analysis.     

3-(3-hydroxy-2,3-dimethyl-5-oxoprolyl)amino-3,6-dideoxy-D-glucose: a new amino sugar of the antigenic polysaccharide from Pseudomonas fluorescens

O-specific polysaccharide chain of the Pseudomonas fluorescens lipopolysaccharide is composed of 6-deoxy-L-talose, N-acetyl-D-fucosamine and N-acyl-3,6-dideoxy-D-glucose. Analysis of the latter sugar, obtained from the polysaccharide hydrolysate, by 1H NMR (including NOE), 13C NMR, and FAB mass spectrometry proved the unusual N-acyl substituent to be a 3-hydroxy-2,3-dimethyl-5-oxoproline residue.     

Chemical structure and biodegradability of halogenated aromatic compounds. Substituent effects on 1,2-dioxygenation of catechol.

1. The influence of halogen substituents on the 1,2-dioxygenation of catechols was investigated. The results obtained with the two isoenzymes pyrocatechase I and pyrocatechase II from the haloarene-utilizing Pseudomonas sp. B 13 and the pyrocatechase from benzoate-induced cells of Alcaligenes eutrophus B.9 were compared. 2. Substituents on catechol were found to interfere with O2 binding by the two isoenzymes from Pseudomonas sp. B 13, whereas the Km value for catechol kept constant at different O2 concentrations. 3. Electron-attracting substituents decreased the Km values for catechols. 4. Results from binding studies with substituted catechols demonstrated narrow stereospecificities of pyrocatechase I from pseudomonas sp. B 13 and the pyrocatechase from alcaligenes eutrophus B.9. In contrast, a low steric hindrance by substituents in the binding of catechols with pyrocatechase II was observed. 5. Low pK'1 values of substituted catechols resulted in low Michaelis constants. 6. Electron-attracting substituents such as halogen decreased the reaction rates of catechol 1,2-dioxygenation. The correlation of the Vmax. values observed with pyrocatechase II from Pseudomonas sp. B 13 with the substituent constant sigma+ (Okamoto--Brown equation) was distinctly greater than with Hammett's sigma values. The corresponding logVmax. against sigma+ correlation for pyrocatechase I was considerably disturbed by steric influences of the substituents.     

Molecular distinctions between heparan sulphate and heparin. Analysis of sulphation patterns indicates that heparan sulphate and heparin are separate families of N-sulphated polysaccharides.

Heparan sulphate and heparin are chemically related alpha beta-linked glycosaminoglycans composed of alternating sequences of glucosamine and uronic acid. The amino sugars may be N-acetylated or N-sulphated, and the latter substituent is unique to these two polysaccharides. Although there is general agreement that heparan sulphate is usually less sulphated than heparin, reproducible differences in their molecular structure have been difficult to identify. We suggest that this is because most of the analytical data have been obtained with degraded materials that are not necessarily representative of complete polysaccharide chains. In the present study intact heparan sulphates, labelled biosynthetically with [3H]glucosamine and Na2(35)SO4, were isolated from the surface membranes of several types of cells in culture. The polysaccharide structure was analysed by complete HNO2 hydrolysis followed by fractionation of the products by gel filtration and high-voltage electrophoresis. Results showed that in all heparan sulphates there were approximately equal numbers of N-sulpho and N-acetyl substituents, arranged in a similar, predominantly segregated, manner along the polysaccharide chain. O-Sulphate groups were in close proximity to the N-sulphate groups but, unlike the latter, the number of O-sulphate groups could vary considerably in heparan sulphates of different cellular origins ranging from 20 to 75 O-sulphate groups per 100 disaccharide units. Inspection of the published data on heparin showed that the N-sulphate frequency was very high (greater than 80% of the glucosamine residues are N-sulphated) and the concentration of O-sulphate groups exceeded that of the N-sulphate groups. We conclude from these and other observations that heparan sulphate and heparin are separate families of N-sulphated glycosaminoglycans.     

Isolation and antioxidant property of the extracellular polysaccharide from <Emphasis Type="Italic">Rhodella reticulata</Emphasis>

The extracellular polysaccharide from Rhodella reticulata was separated from the culture medium followed by concentration and ethanol precipitation, and purified by anion exchange chromatography on DEAE-Sepharose Fast Flow. This study compared the free radical-scavenging property and antioxidant activity with various treatments of crude extracellular polysaccharides of R. reticulata. The results showed that both the crude extracellular polysaccharide and deproteinized crude extracellular polysaccharide gave evidence of the free radical scavenging and antioxidant activity in a dose-dependent manner. The crude extracellular polysaccharide exhibited higher free radical scavenging capacity and better antioxidant activity than the various treatments of crude extracellular polysaccharide samples. The superoxide anion radical scavenging ability of various samples was significantly higher compared to standard antioxidant (α-tocopherol). These results indicate that the extracellular polysaccharide of R. reticulata is a potent natural antioxidant.     

Aromatic phosphonates inhibit the lysophospholipase D activity of autotaxin

Autotaxin (ATX) is an attractive target for the anticancer therapeutics that inhibits angiogenesis, invasion and migration. ATX is an extracellular lysophospholipase D that hydrolyzes lysophosphatidylcholine to form the bioactive lipid lysophosphatidic acid. The aromatic phosphonate S32826 was the first described nanomolar inhibitor of ATX. However, the tridecylamide substituent on aromatic ring contributed to its poor solubility and bioavailability, severely limiting its utility in vivo. c Log P calculations revealed that the lipophilicity of S32826 could be lowered by shortening its hydrophobic chain and by introducing substituents alpha to the phosphonate. Herein, we describe the synthesis of a small set of α-substituted phosphonate analogs of S32826, and we show that shortening the chain and adding α-halo or α-hydroxy substituents increased solubility; however, ATX inhibition was reduced by most substitutions. An optimal compound was identified for examination of biological effects of ATX inhibition in vivo.     

Quantitative structure-activity relationship study on affinity profile of a series of 1,8-naphthyridine antagonists toward bovine adenosine receptors

The affinity profiles for the bovine adenosine receptors, A(1) and A(2A), of a series of 1,8-naphthyridine derivatives were quantitatively analyzed using physicochemical and structural parameters of the substituents, present at varying positions of the molecules. The derived significant correlation, for bovine A(1) receptor, suggested that a R(1) substituent having a higher van der Waals volume, a R(2) substituent being a hydrogen-bond donor and a R(3) substituent able to transmit a higher field effect are helpful in augmenting the pK(i) of a compound. Similarly the study, pertaining to bovine A(2A) receptor, revealed that a less bulky substituent at R(2) and a strong electron-withdrawing substituent at R(3) are desirable in improving the binding affinity of a compound while substituents at R(1) remain insignificant to any interaction.     

Maleylacetate reductase of Pseudomonas sp. strain B13: specificity of substrate conversion and halide elimination.

Maleylacetate reductase (EC 1.3.1.32) plays a major role in the degradation of chloroaromatic compounds by channelling maleylacetate and some chlorinated derivatives into the 3-oxoadipate pathway. Several substituted maleylacetates were prepared in situ by alkaline or enzymatic hydrolysis of dienelactones as the precursor. The conversion of these methyl-, chloro-, fluoro-, and bromo-substituted maleylacetates by malelacetate reductase from 3-chlorobenzoate-grown cells of Pseudomonas sp. strain B13 was studied. Two moles of NADH per mole of substrate was consumed for the conversion of maleylacetates which contain a halogen substituent in the 2 position. In contrast, only 1 mol of NADH was necessary to convert 1 mol of substrates without a halogen substituent in the 2 position. The conversion of 2-fluoro-, 2-chloro-, 2,3-dichloro-, 2,5-dichloro-, 2,3,5-trichloro-, 2-bromo-, 2,3-dibromo-, 2,5-dibromo-, 2-bromo-5-chloro-, 2-chloro-3-methyl-, and 2-chloro-5-methylmaleylacetate was accompanied by the elimination of halide from the 2 position and the temporary occurrence of the corresponding dehalogenated maleylacetate as an intermediate consuming the second mole equivalent of NADH. The properties of the halogen substituents influenced the affinity to the enzyme in the following manner. Km values increased with increasing van der Waals radii and with decreasing electronegativity of the halogen substituents (i.e., low steric hindrance and high electronegativity positively influenced the binding).The Km values obtained with 2-methyl-,3-methyl-, and 5-methylmaleylacetate showed that a methyl substituent negatively affected the affinity in the following order: 2 position >/ = 3 position >> 5 position. A reaction mechanism explaining the exclusive elimination of halogen substituents from the 2 position is proposed.     

ADMET rules of thumb II: A comparison of the effects of common substituents on a range of ADMET parameters

A systematic analysis of data generated in key in vitro assays within GSK has been undertaken to identify what impact a range of common substituents have on a range of ADMET parameters. These include; P450 1A2, 2C9, 2C19, 2D6 and 3A4 inhibition, hERG inhibition, phosphate buffer solubility and artificial membrane permeability. We do this by identifying all matched molecular pairs, differing by the replacement of a hydrogen atom with a list of predefined substituents.For each substituent we calculate the mean difference in the ADMET parameter for all the matched molecular pairs identified, making a statistical assessment of the difference, as well as assessing the diversity for each example to ensure that the results can be generalized. We also relate the change in activity observed for each substituent to differences in their molecular properties in an effort to identify any structural alerts.     

Effects of backbone substitutions on the conformational behavior of Shigella flexneri O-antigens: implications for vaccine strategy

The O-antigen (O-Ag), the polysaccharide part of the lipopolysaccharide, is the major target of the serotype-specific protective humoral response elicited upon host infection by Shigella flexneri, the main causal agent of the endemic form of bacillary dysentery. The O-Ag repeat units (RUs) of 12 S. flexneri serotypes share the tetrasaccharide backbone →2)-α-l-Rhap-(1?→?2)-α-l-Rhap-(1?→?3)-α-l-Rhap-(1?→?3)-β-d-GlcpNAc-(1→, with site-selective glucosylation(s) and/or O-acetylation defining the serotypes. To investigate the conformational basis of serotype specificity, we sampled conformational behaviors during 60?ns of molecular dynamic simulations for oligosaccharides representing three RUs of each one of the O-Ags corresponding to serotypes 1a, 1b, 2a, 2b, 3a, 3b, 4a, 4b, 5a, 5b, X and Y, respectively. The calculated trajectories were checked by nuclear magnetic resonance (NMR) for 1a, 2a, 3a and 5a O-Ags. The simulations predict that in all O-Ags, but 1a and 1b, serotype-specific substitutions of the backbone do not induce any new backbone conformations compared with the linear type O-Ag Y, although they restrain locally the accessible conformational space. Moreover, the influence of any given substituent on the backbone is independent of the eventual presence of other substituents. Finally, only slight differences in conformational behavior between terminal and inner RUs were observed. These results suggest that the reported serotype-specificity of the protective immune response is not due to recognition of distinct backbone conformations, but to binding of the serotype-defining substituents in the O-Ag context. The gained knowledge is discussed in terms of impact on the development of a broad-serotype coverage vaccine.