Rapid, iterative assembly of octyl alpha-1,6-oligomannosides and their 6-deoxy equivalents

Mycobacterium tuberculosis is the cause of the deadly human disease tuberculosis. In studies over the last 40 years it has been revealed that this organism possesses a complex cell wall including glycophospholipids such as the phosphatidylinositiol mannosides (PIMs), lipomannan (LM) and lipoarabinomannan (LAM). These glycolipids all contain a common alpha-1,6-linked mannoside core, and the higher PIMs and LAM possess alpha-1,2-linked mannosyl residues. It has been shown that simple alpha-1,6-linked oligomannosides can act as substrates for alpha-1,6-mannosyltransferases in mycobacteria. Here we report a simple iterative synthesis of a series of hydrophobic octyl alpha-1,6-linked oligomannosides from mono- through to tetrasaccharides. We have utilized a single thioglycoside donor and alcohol acceptor. Further, we have developed conditions for the conversion of each of these compounds to the 6-deoxy congeners. Deoxygenation of the 6-position of the terminal mannosyl residue should prevent these compounds acting as substrates for the abundant alpha-1,6-mannosyltransferases in mycobacteria and should permit detection of the elusive alpha-1,2-mannosyltransferase activity responsible for elaboration of LM to mature LAM and the biosynthesis of the higher PIMs.     

Rapid assay of beta-galactosidase and sialyltransferase by lectin affinity high performance liquid chromatography with fluorescence detection

Fluorescein isothiocyanate (FITC)-labelled asialotransferrin and pyridyl aminated oligosaccharides were prepared from asialotransferrin and human milk using affinity chromatography and high performance liquid chromatography (HPLC), respectively. These substances were incubated with galactosidase or sialyltransferase and then examined by lectin affinity HPLC. The elution patterns changed according to the period of incubation and amount of enzyme. This analytical method using lectin affinity HPLC with fluorescence labelled glycoprotein or oligosaccharides as the substrates has great value for detecting these enzyme under the same chromatographic conditions. In addition, differences were noted in the activity of beta-galactosidase toward oligosaccharides having the Gal beta(1----3)GlcNAc or Gal beta(1----4)GlcNAc structure at reducing termini.     

Tandem exploitation of Helix pomatia glycosyltransferases: facile syntheses of H-antigen-bearing oligosaccharides

Snails from the family Helicidae produce in their albumen glands a highly branched galactan, which consists almost exclusively of D- and L-galactose. The D-Gal residues are glycosydically beta(1-->6)- or beta(1-->3)-linked, whereas the L-Gal moieties are attached alpha(1-->2). Up until the present time, two beta(1-->6)-D-galactosyl transferases and one alpha(1-->2)-L-galactosyl transferase have been identified in a membrane preparation of these glands. These were used to synthesise various oligosaccharides by successive addition of the NDP-activated (NDP=nucleoside-5'-diphosphate) D-Gal or L-Fuc moieties, up to a heptasaccharide by starting from the disaccharide D-Gal-beta(1-->3)-D-Gal-beta(1-->OMe. Even larger oligosaccharides up to a tridecasaccharide were obtained by starting with the hexasaccharide D-Gal-[beta(1-->3)-D-Gal]4-beta(1-->4)-D-Glc as an acceptor substrate. This tandem exploitation process has high potential for the easy introduction of D-Gal and L-Fuc residues into a great variety of oligosaccharides, which can be used in ligand/acceptor studies.     

Structural analysis of underivatized neutral human milk oligosaccharides in the negative ion mode by nano-electrospray MS(n) (part 2: application to isomeric mixtures)

A complex mixture of isomeric neutral oligosaccharides from pooled human milk was analyzed by nano-electrospray ionization (ESI) in a quadrupole ion trap mass spectrometer (QIT-MS) in the negative ion mode. Since deprotonated molecules of neutral oligosaccharides follow distinct fragmentation rules, which have been elucidated by using model compounds (see [1]), spectra obtained from consecutive CID experiments allowed the differentiation of isomers out of this highly complex mixture. With this method new human milk oligosaccharides of previously unknown isomeric structures have been identified, e.g., the occurence of three isomeric fucosylated lacto-N-hexaoses could be determined precisely, which have not been described before: (1) Fuc (alpha1-->2) Gal (beta1-->3) GlcNac (beta1-->3) Gal (beta1-->4) GlcNac (beta1-->3) Gal (beta1-->4) Glc, (2) Gal (beta1-->4) GlcNAc [(alpha1-->3) Fuc] (beta1-->3) Gal (beta1-->4) GlcNac (beta1-->3) Gal (beta1-->4) Glc, (3) Gal (beta1-->4) GlcNAc (beta1-->3) Gal (beta1-->4) GlcNac [(alpha1-->3) Fuc] (beta1-->3) Gal (beta1-->4) Glc.     

Synthesis and characterisation of a ligand that forms a stable tetrahedral intermediate in the active site of the Aureobacterium species (-) gamma-lactamase

The crystal structure of a (-) gamma-lactamase from an Aureobacterium species showed a molecule bound covalently to the active site serine residue. This enzyme complex represented the first structure of a stably bound tetrahedral intermediate for an alpha/beta hydrolase fold enzyme. The structural elucidation of tetrahedral intermediates is important for the understanding of enzymatic mechanism, substrate recognition and enzyme inhibition. In this paper, we report the synthesis and subsequent characterisation of (3aR,7aS)-3a,4,7,7a-tetrahydrobenzo-[1,3]-dioxol-2-one (BD1), the molecule modelled into the Aureobacterium (-) gamma-lactamase active site. This molecule has been confirmed to be an inhibitor and to be displaced from the enzyme by the racemic gamma-lactam substrate.     

Differentiation of type 1 and type 2 chain linkages of native glycosphingolipids by positive-ion fast-atom bombardment mass spectrometry with collision-induced dissociation and linked scanning.

Two underivatized glycosphingolipids, Le(b) and Le(y), isomeric in carbohydrate structure (Fuc alpha 1-->2Gal beta 1--> 3[Fuc alpha 1-->4]GlcNAc beta 1-->3Gal beta 1-->4Glc beta 1-->1Cer and Fuc alpha 1-->2Gal beta 1-->4[Fuc alpha 1-->3]GlcNAc beta 1-->3Gal beta 1--> 4Glc beta 1-->1Cer, respectively), were analyzed by positive-ion fast-atom bombardment (FAB) mass spectrometry with high energy collision-induced dissociation (CID) and linked scanning. The two isomers were distinguishable by the abundance of product ions derived from the non-reducing terminal tetrasaccharide fragment via sequential beta-eliminations of vicinally linked saccharide residues. Following earlier studies from other laboratories, which have dealt primarily with positive-ion FAB-CID mass spectrometry of simple model oligosaccharides, these results exemplify the practical application of two-sector methodology to underivatized complex glycoconjugates commonly encountered in the biomedical field.     

Structural and Kinetic Dissection of the endo‐α‐1,2‐Mannanase Activity of Bacterial GH99 Glycoside Hydrolases from Bacteroides spp.

Glycoside hydrolase family 99 (GH99) was created to categorize sequence‐related glycosidases possessing endo‐α‐mannosidase activity: the cleavage of mannosidic linkages within eukaryotic N‐glycan precursors (Glc_1–3Man₉GlcNAc₂), releasing mono‐, di‐ and triglucosylated‐mannose (Glc_1–3‐1,3‐Man). GH99 family members have recently been implicated in the ability of Bacteroides spp., present within the gut microbiota, to metabolize fungal cell wall α‐mannans, releasing α‐1,3‐mannobiose by hydrolysing αMan‐1,3‐αMan→1,2‐αMan‐1,2‐αMan sequences within branches off the main α‐1,6‐mannan backbone. We report the development of a series of substrates and inhibitors, which we use to kinetically and structurally characterise this novel endo‐α‐1,2‐mannanase activity of bacterial GH99 enzymes from Bacteroides thetaiotaomicron and xylanisolvens. These data reveal an approximate 5 kJ mol^?1 preference for mannose‐configured substrates in the ?2 subsite (relative to glucose), which inspired the development of a new inhibitor, α‐mannopyranosyl‐1,3‐isofagomine (ManIFG), the most potent (bacterial) GH99 inhibitor reported to date. X‐ray structures of ManIFG or a substrate in complex with wild‐type or inactive mutants, respectively, of B. xylanisolvens GH99 reveal the structural basis for binding to D ‐mannose‐ rather than D ‐glucose‐configured substrates.     

Rhodium-catalyzed reductive cyclization of 1,6-diynes and 1,6-enynes mediated by hydrogen: catalytic C-C bond formation via capture of hydrogenation intermediates

Catalytic hydrogenation of carbon-, nitrogen- and oxygen-tethered 1,6-diynes 1a-9a and 1,6-enynes 10a-18a using cationic Rh(I) precatalysts at ambient temperature and pressure enables reductive carbocyclization to afford 1,2-dialkylidene cyclopentanes 1b-9b and monoalkylidene cyclopentanes 10b-18b, respectively, in good to excellent yields and as single alkene stereoisomers. Notably, the 1,3-diene and alkene containing cyclization products 1b-9b and 10b-18b are not subject to over-reduction under the conditions of catalytic hydrogenation in which they are formed. Reductive cyclization 1,6-diyne 1a and 1,6-enyne 10a performed under an atmosphere of D(2) provides the carbocyclization products deuterio-1b and deuterio-10b, respectively, which incorporate two deuterium atoms. The collective data are consistent with a catalytic mechanism involving heterolytic activation of elemental hydrogen (H(2) + Rh(+)X(-) --> Rh-H + HX) followed by Rh(I)-mediated oxidative cyclization of the 1,6-diyne or 1,6-enyne substrates to afford (hydrido)Rh(III)-based metallocyclopentadiene and metallocyclopentene intermediates, respectively. These transformations represent the first examples of metal-catalyzed reductive carbocyclization mediated by hydrogen.     

Fast carbon-carbon bond formation by a promiscuous lipase

Lipase B from Candida antarctica was redesigned to catalyze the promiscuous reaction of carbon-carbon bond formation. Mutation of the catalytic serine to alanine afforded a mutant that catalyzed Michael additions of 1,3-dicarbonyls to alpha,beta-unsaturated carbonyl compounds at high specific rates, such as 4000 s-1. The enzyme-catalyzed Michael addition reaction followed saturation kinetics and showed substrate inhibition. The designed enzyme showed high rate enhancements with a catalytic proficiency higher than 108, which is on the same level as that observed for enzymes with native substrates.     

Synthesis of Chitin Oligosaccharides Using Dried <Emphasis Type="Italic">Stenotrophomonas maltophilia</Emphasis> Cells Containing a Transglycosylation Reaction-Catalyzing β<Emphasis Type="Italic">-N-</Emphasis>Acetylhexosaminidase as a Whole-Cell Catalyst

Bacterial strain NYT501, which we previously isolated from soil, was identified as Stenotrophomonas maltophilia, and it was confirmed that this strain produces an intracellular β-N-acetylhexosaminidase exhibiting transglycosylation activity. Several properties of this enzyme were characterized using a partially purified enzyme preparation. Using N,N′-diacetylchitobiose (GlcNAc)₂ and N,N′,N″-triacetylchitotriose (GlcNAc)₃ as substrates and dried cells of this bacterium as a whole-cell catalyst, chitin oligosaccharides of higher degrees of polymerization were synthesized. (GlcNAc)₃ was generated from (GlcNAc)₂ as the major transglycosylation product, and a certain amount of purified sample of the trisaccharide was obtained. By contrast, in the case of the reaction using (GlcNAc)₃ as a substrate, the yield of higher-degree polymerization oligosaccharides was comparatively low.     

大粒车前子多糖组分PLP-1的结构表征

研究了由大粒车前子多糖分离纯化所得组分PLP-1的一级精细结构特征. 通过单糖组成分析、部分酸水解及甲基化分析,并结合NMR,GC和GC-MS等技术测定了PLP-1的一级结构. 结果表明,PLP-1由Ara（33.98%）,Xyl（58.23%）,Rha（2.36%）,Glc（2.23%）,Gal（2.36%）和Man（0.83%）组成,糖醛酸以GlcA形式存在. PLP-1中主要糖残基有α-T-linked Araf（9.58%）,β-T-linked Xylp（8.71%）,α-1,3-linked Araf（18.22%）,β-1,3-linked Xylp（8.05%）,β-1,4-linked Xylp（5.85%）,β-1,2,4-linked Xylp（16.98%）和β-1,3,4-linked Xylp（27.52%）,GlcA以α-T-linked GlcAp形式存在;此外还有1,2-linked Rhap,T-linked Glcp,1,6-linked Glcp,T-linked Galp,1,3-linked Galp和1,3,6-linked Galp等少量其它残基. 根据所得结果推断出PLP-1可能的一级结构.     

Opposed steric constraints in human DNA polymerase beta and E. coli DNA polymerase I

DNA polymerase selectivity is crucial for the survival of any living species, yet varies significantly among different DNA polymerases. Errors within DNA polymerase-catalyzed DNA synthesis result from the insertion of noncanonical nucleotides and extension of misaligned DNA substrates. The substrate binding characteristics among DNA polymerases are believed to vary in properties such as shape and tightness of the binding pocket, which might account for the observed differences in fidelity. Here, we employed 4'-alkylated nucleotides and primer strands bearing 4'-alkylated nucleotides at the 3'-terminal position as steric probes to investigate differential active site properties of human DNA polymerase beta (Pol beta) and the 3'-->5'-exonuclease-deficient Klenow fragment of E. coli DNA polymerase I (KF(exo-)). Transient kinetic measurements indicate that both enzymes vary significantly in active site tightness at both positions. While small 4'-methyl and -ethyl modifications of the nucleoside triphosphate perturb Pol beta catalysis, extension of modified primer strands is only marginally affected. Just the opposite was observed for KF(exo-). Here, incorporation of the modified nucleotides is only slightly reduced, whereas size augmentation of the 3'-terminal nucleotide in the primer reduces the catalytic efficiency by more than 7000- and 260,000-fold, respectively. NMR studies support the notion that the observed effects derive from enzyme substrate interactions rather than inherent properties of the modified substrates. These findings are consistent with the observed differential capability of the investigated DNA polymerases in fidelity such as processing misaligned DNA substrates. The results presented provide direct evidence for the involvement of varied steric effects among different DNA polymerases on their fidelity.     

Glycosylidene Carbenes. Part 10. Regioselective Glycosidation of 4,6-O-Benzylidene-D-altropyranosides

Glycosidation by the diazirine 1 , the trichloroacetimidate 4 , and the bromide 5 of the altro-diol 2 , possessing an intramolecular H-bond (HO? C(3) to O? C(1)) in solution, but not in the solid state, proceeds with high and complementary regioselectivity. From 2 and 1 , one obtains mostly the 1,2-linked disaccharides 10 and 11 (β-D > α-D ), together with the 1,3-linked isomers 12 and 13 (α-D > β-D ; 1,2-/1,3-linked products ca. 9:1), the demethylated 1,3-linked disaccharides 24–27 , the trisaccharides 19–22 , the lactone azines 23 , and the hydroxyglucal 18 , while 2 reacted with 4 or 5 to yield mostly the 1,3-linked disaccharides (1,2-/1,3-linked products ca. 1:9). The disaccharides were additionally characterized as acetates (→ 14–17, 28–31 ). Yields and stereoselectivity depended upon the donor, stoichiometry, solvent, temperature, and concentration. Glycosidation of the 1,3-linked disaccharides with 1 yielded the trisaccharides 19–22 . Reaction of the β-D -altro-diol 3 with 1 gave the 1,2- and 1,3-linked disaccharides 32/33 and 34/35 in a 1:1 ratio, characterized as the acetates 36–39 , while glycosidation with 5 according to Lemieux proceeded regioselectively (1,2-/1,3-linked products 91:9). The monotosylates 6 and 7 reacted with 1 to yield the anomeric pairs 40/41 , and 42/43 of the tosylated disaccharides; the oxiranes 44 and 45 were not observed.     

Modification of Cyclodextrins for Use as Artificial Enzymes

The magical powers of enzymes have been attributed to their ability to bind specific substrates and catalyze reactions of the bound substrate. Artificial enzymes synthetically mimic the binding and the catalytic site to produce molecules that are not only smaller in size but also potentially have similar activity to the real enzymes. The main objective of our research is to create artificial redox enzymes by using cyclodextrins as binding sites and attaching flavin derivatives as the catalytic site. We have developed a strategy to attach a catalytic site to cyclodextrin exclusively at the 2-, 3- or the 6-position. The evaluation of the artificial enzyme in which flavin is attached to the 2-position gives a 647-fold acceleration factor. Although this is modest compared to those of real enzymes (which can have acceleration factors of a trillion), the artificial enzymes allow us to understand the elements that contribute to the incredible catalytic power of enzymes.     

Anion radicals and dianions as electron transfer reagents

The catalytic regeneration of depolarizers by certain substrates has been demonstrated by means of cyclic voltammetry. As depolarizers we have employed anion radicals of aromatic hydrocarbons, heteroaromatic compounds, ketones, esters, nitriles, and olefins, and dianions of aromatic hydrocarbons, heteroaromatic compounds, ketones, and esters. As substrates we have investigated simple aromatic and aliphatic halides, 1,2- and 1,3-dihalides, carbon dioxide, and activated olefins. A requirement for the observation of a catalytic wave is that the reduced substrate undergoes a practically irreversible reaction after the reaction with the reduced depolarizer; for simple halides it is a cleavage reaction, for 1,2- and 1,3-dihalides an elimination, for carbon dioxide an addition, and for activated olefins a coupling. Electrochemical investigations of these kinds of reactions may be of interest in connection with the mechanism of several types of reactions in organic chemistry.     

The C-terminal domain of pancreatic lipase: functional and structural analogies with c2 domains

The 3D structure of pancreatic lipase (PL) consists of two functional domains. The N-terminal domain belongs to the alpha/beta hydrolase fold and contains the active site, which involves a catalytic triad analogous to that present in serine proteases. The beta-sandwich C-terminal domain of PL plays an important part in the binding process between the lipase and colipase, the specific PL cofactor. Recent structure-function studies have suggested that the PL C-terminal domain may have an extra role apart from that of binding colipase. This domain contains an exposed hydrophobic loop (beta5') which was found to be located on the same side as the hydrophobic loops surrounding the active site, and it may be involved in the lipid binding process. Indirect evidence for this new function of the PL C-terminal domain has been provided by studies with monoclonal antibodies directed against the beta5' loop. The catalytic activity of the PL-antibody complexes on water insoluble substrates decreased drastically, whereas their esterase activity on a soluble substrate remained unchanged. During the last few years, a number of protein structures (15-lipoxygenase, alpha-toxin from Clostridium perfringens) have been determined that contain domains with close structural homologies with the beta-sandwich C-terminal domain of PL. Generally speaking, these domains show structural homologies with the C2 domains occurring in a wide range of proteins involved in signal transduction (e.g. phosphoinositide-specific phospholipase C, protein kinase C, cytosolic phospholipase A2), membrane traffic (e.g. synaptotagmin I, rabphilin) and membrane disruption (e.g. perforin). Here it is proposed to review the structure and function of the C2 domains, based on the recent 3D structures and improved sequence alignments.     

Structural Basis of Chitin Oligosaccharide Deacetylation

Cell signaling and other biological activities of chitooligosaccharides (COSs) seem to be dependent not only on the degree of polymerization, but markedly on the specific de‐N‐acetylation pattern. Chitin de‐N‐acetylases (CDAs) catalyze the hydrolysis of the acetamido group in GlcNAc residues of chitin, chitosan, and COS. A major challenge is to understand how CDAs specifically define the distribution of GlcNAc and GlcNH₂ moieties in the oligomeric chain. We report the crystal structure of the Vibrio cholerae CDA in four relevant states of its catalytic cycle. The two enzyme complexes with chitobiose and chitotriose represent the first 3D structures of a CDA with its natural substrates in a productive mode for catalysis, thereby unraveling an induced‐fit mechanism with a significant conformational change of a loop closing the active site. We propose that the deacetylation pattern exhibited by different CDAs is governed by critical loops that shape and differentially block accessible subsites in the binding cleft of CE4 enzymes.     

Linear total synthetic routes to beta-D-C-(1,6)-linked oligoglucoses and oligogalactoses up to pentaoses by iterative Wittig olefination assembly

Two complementary routes, A and B, have been followed for the stepwise iterative assembly of beta-D-(1,6)-glucopyranose and galactopyranose residues through methylene bridges. In route A the building block was constituted by 2,3,4-tri-O-benzyl-6-O-tert-butyldiphenylsilyl (O-TBDPS) beta-linked galactosylmethylenephosphorane, while in route B the building block was a beta-linked formyl C-glycopyranoside with a similar orthogonal protection of hydroxy groups. In route A each cycle consisted of the reaction of the phosphorane building block with a sugar residue bearing a formyl group at the C-5 carbon atom (coupling) and transformation of the O-TBDPS-protected primary alcohol into the formyl group (arming). Accordingly, route A is defined as the aldehyde route. On the other hand, each cycle in route B involved the coupling of the sugar aldehyde building block with a substrate bearing a phosphorus ylide at C-6 and introduction of the phosphonium group in the arming step as a precursor of the ylide functionality. Accordingly, route B is defined as the ylide route. The efficiency of route A proved to be seriously hampered by the 1,2-elimination of BnOH under the basic reaction conditions of the Wittig olefination, giving rise to the formation of substantial amounts of enopyranose. On the other hand, the ylide route B proved to be more efficient since very good yields (70-93%) of the isolated Wittig products were obtained throughout four consecutive cycles. Individual olefins and polyolefins obtained by routes A and B using gluco and galacto substrates were reduced and debenzylated in one pot by H(2)/Pd(OH)(2) to give the corresponding beta-D-C-(1,6)-linked oligosaccharides up to the pentaose stage. The latter compounds were fully characterized by high-field NMR spectroscopy (500 MHz).     

Ionic-liquid-based MS probes for the chemo-enzymatic synthesis of oligosaccharides

A new N-benzenesulfonyl-based ionic-liquid mass spectroscopy label (I-Tag2) for covalent attachment to substrates has been prepared. I-Tag2 was used to monitor oligosaccharide elongation and serve as a purification handle. Starting from chemically synthesized I-Tag2-labelled N-acetyl glucosamine (GlcNAc) 1, I-Tag2-LacNAc (Galβ(1-4)GlcNAc) 2 and I-Tag2-Lewis(X) (Galβ(1-4)[Fucα(1-3)]GlcNAc) 3, which are oligosaccharides of biological relevance, were enzymatically prepared. The apparent kinetic parameters for the enzyme catalysed transformations with β-1,4-galactosyltransferase (β-1,4-GalT) and fucosyltransferase VI (FucT VI) were measured by LC-MS demonstrating the applicability and versatility of the new I-Tags in enzymatic transformations with glycosyltransferases.     

桑叶多糖SJB的结构分析和蛋白酪氨酸磷酸酯酶PTP1B抑制活性

通过DEAE-纤维素和凝胶过滤柱色谱对桑叶碱提粗多糖进行分级分离, 获得均一多糖SJB, 进行结构鉴定. 采用蛋白酪氨酸磷酸酯酶PTP1B体外模型对SJB进行降血糖活性测定. 结果表明: SJB的相对分子质量为5.4×104, 由鼠李糖、阿拉伯糖、葡萄糖、半乳糖、半乳糖醛酸组成的酸性杂多糖; 主链由1,2-、1,2,4-连接的鼠李糖和1,4-、1,3,4-连接的半乳糖醛酸组成; 侧链包括末端、1,5-、1,3,5-连接的阿拉伯糖; 末端、1,4-连接的葡萄糖以及末端、1,3-、1,4-、1,6-连接的半乳糖, 主要通过鼠李糖的O4位和半乳糖醛酸的O3位与主链相连. 该多糖为首次从桑叶中获得的酸性杂多糖. 20 μg/mL SJB对PTP1B的抑制率为31.7%.