The Synthesis of a New Class of Potential Inhibitors for Glycoside Hydrolases†

Some attempts toward the synthesis of novel inhibitors of glycosyl transferases are described. More successfully, the synthesis of an activated cyclopropacyclohexene and an amide and an amine of a cyclopropa‐fused pyranose are described. None of these three novel compounds proved to be a significant inhibitor of a retaining α‐glucosidase from barley.     

Substrate‐Guided Front‐Face Reaction Revealed by Combined Structural Snapshots and Metadynamics for the Polypeptide N‐Acetylgalactosaminyltransferase 2

The retaining glycosyltransferase GalNAc‐T2 is a member of a large family of human polypeptide GalNAc‐transferases that is responsible for the post‐translational modification of many cell‐surface proteins. By the use of combined structural and computational approaches, we provide the first set of structural snapshots of the enzyme during the catalytic cycle and combine these with quantum‐mechanics/molecular‐mechanics (QM/MM) metadynamics to unravel the catalytic mechanism of this retaining enzyme at the atomic‐electronic level of detail. Our study provides a detailed structural rationale for an ordered bi–bi kinetic mechanism and reveals critical aspects of substrate recognition, which dictate the specificity for acceptor Thr versus Ser residues and enforce a front‐face S_Ni‐type reaction in which the substrate N‐acetyl sugar substituent coordinates efficient glycosyl transfer.     

Directed evolution of new glycosynthases from Agrobacterium beta-glucosidase: a general screen to detect enzymes for oligosaccharide synthesis

BACKGROUND: Oligosaccharide synthesis is becoming increasingly important to industry as diverse therapeutic roles for these molecules are discovered. The chemical synthesis of oligosaccharides on an industrial scale is often prohibitively complex and costly. An alternative, that of enzymatic synthesis, is limited by the difficulty of obtaining an appropriate enzyme. A general screen for enzymes that catalyze the synthesis of the glycosidic bond would enable the identification and engineering of new or improved enzymes. RESULTS: Glycosynthases are nucleophile mutants of retaining glycosidases that efficiently catalyze the synthesis of the glycosidic linkage by condensing an activated glycosyl fluoride donor with a suitable acceptor sugar. A novel agar plate-based coupled-enzyme screen was developed (using a two-plasmid system) and used to select an improved glycosynthase from a library of mutants. CONCLUSIONS: Plate-based coupled-enzyme screens of this type are extremely valuable for identification of functional synthetic enzymes and can be applied to the evolution of a range of glycosyl transferases.     

The Biosynthesis of Cellulose

Abstract

Cellulose is one of the major commercial products of Sweden and constitutes the most abundant of the natural polymer systems. Thus, it is of interest to review the molecular design and architecture of cellulose with particular reference to the controls of its biosynthesis. The bioassembly process is highly ordered and structured, reflecting the intricate series of events which must occur to generate a thermodynamically metastable crystalline submicroscopic, ribbonlike structure. The plant cell wall is an extremely complex composite of many different polymers. Cellulose is the “reinforcing rod” component of the wall. True architectural design demands a polymer which can withstand great flexing and torsional strain. Using comparative Hydrophobic Cluster Analysis of a bacterial cellulose synthase and other glycosyl transferases, the multidomain architecture of glycosyl transferases has been analyzed. All polymerization reactions which are processive require at least three catalytic sites located on two different domains. In contrast, retaining reactions with glycosyl transferases require only a single domain and two sites. Cellulose synthase appears to have evolved a mechanism to simultaneously bind at least three UDP-glucoses and to polymerize, by double addition, two UDP-glucoses in such a manner that the 2-fold screw axis of the β-1,4-glucan chain is maintained. Thus, no primer is required as the glucose monomers are added two-by-two to the growing chain. At the next higher level of assembly, the catalytic sites simultaneously polymerize parallel glucan chain polymers in close proximity so that they will favorably associate to crystallize into the metastable cellulose I allomorph. Recent energy analysis suggests that the first stage of this association is the formation of a minisheet through van der Waals forces, followed by layering of these minisheets to form the crystalline microfibril. In native cellulose biogenesis, the microfibril shape and size appear to be determined by a multimeric enzyme complex (TC) which resides in the plasma membrane. This complex, known as a terminal complex, was discovered through electron microscopy of freeze fracture replicas. The entire complex moves in the plane of the fluid plasma membrane as the result of polymerization/crystallization reactions. The assembly stages for native cellulose I are coordinated on a spatial/temporal scale, and they are under the genetic control of the organism. This might lead one to conclude that cellulose I could only be assembled with Nature's indigenous machinery; however, this is not the case. Recently, in collaboration with Professor Kobayashi and his colleagues in Sendai and Tokyo, we have synthesized cellulose I abiotically under conditions very different from those in the living cell or from isolated cell components. Purification of an endoglucanase from Trichoderma which serves as the catalyst and the addition of β-cellobiosyl fluoride as the substrate in acetonitrile/acetate buffer has led to the assembly of synthetic cellulose I. Although natural and synthetic assembly pathways are very different, there are similar, underlying fundamental mechanisms common to both. These mechanisms will be discussed in relation to the more thermodynamically stable allomorph of cellulose (cellulose II) first demonstrated by Professor Rånby in 1952. The evolution of cellulose biosynthesis will be summarized in terms of the demands for maintaining optimal cellular environments to generate the complex macromolecular assemblies for cell wall biogenesis. Nature provides an exceptional model for cellulose biosynthesis that will lead us toward the biotechnological production of improved natural cellulose as well as synthetic cellulose and its derivatives.     

Structural Snapshots of α‐1,3‐Galactosyltransferase with Native Substrates: Insight into the Catalytic Mechanism of Retaining Glycosyltransferases

Glycosyltransferases (GTs) are a key family of enzymes that catalyze the synthesis of glycosidic bonds in all living organisms. The reaction involves the transfer of a glycosyl moiety and can proceed with retention or inversion of the anomeric configuration. To date, the catalytic mechanism of retaining GTs is a topic of great controversy, particularly for those enzymes containing a putative nucleophilic residue in the active site, for which the occurrence of a double‐displacement mechanism has been suggested. We report native ternary complexes of the retaining glycosyltransferase α‐1,3‐galactosyltransferase (α3GalT) from Bos taurus , which contains such a nucleophile in the active site, in a productive mode for catalysis in the presence of its sugar donor UDP‐Gal, the acceptor substrate lactose, and the divalent cation cofactor. This new experimental evidence supports the occurrence of a front‐side substrate‐assisted S_Ni‐type reaction for α3GalT, and suggests a conserved common catalytic mechanism among retaining GTs.     

Formation of Orthoesters of Oleanolic Acid During Königs-Knorr Glycosidations

Summary.  The formation of orthoesters during K?nigs-Knorr reactions is described. Diphenylmethyl oleanolate reacts with 1 → 4 linked disaccharide donors to orthoesters instead of the expected glycosides. The reaction with acetobromoglucose gave a mixture of orthoester and glycoside. The influence of the structure of the glycosyl donors and of the reaction conditions on the formation of orthoesters is discussed. Received February 12, 2001. Accepted February 22, 2001     

Reconstitution and characterization of a new desosaminyl transferase, EryCIII, from the erythromycin biosynthetic pathway

EryCIII converts alpha-mycarosyl erythronolide B into erythromycin D using TDP-d-desosamine as the glycosyl donor. We report the heterologous expression, purification, in vitro reconstitution, and preliminary characterization of EryCIII. Coexpression of EryCIII with the GroEL/ES chaperone complex was found to enhance greatly the expression of soluble EryCIII protein. The enzyme was found to be highly active with a kcat greater than 100 min-1. EryCIII was quite selective for the natural nucleotide sugar donor and macrolide acceptor substrates, unlike several other antibiotic glycosyl transferases with broad specificity such as desVII, oleG2, and UrdGT2. Within detectable limits, neither 6-deoxyerythronolide B nor 10-deoxymethynolide were found to be glycosylated by EryCIII. Furthermore, TDP-d-mycaminose, which only differs from TDP-d-desosamine at the C4 position, could not be transferred to alphaMEB. These studies lay the groundwork for detailed structural and mechanistic analysis of an important member of the desosaminyl transferase family of enzymes.     

Thioglycosynthases: double mutant glycosidases that serve as scaffolds for thioglycoside synthesis

A double mutant, retaining glycosidase that lacks both the catalytic nucleophile and the catalytic acid/base residues efficiently catalyzes thioglycoside formation from a glycosyl fluoride donor and thiosugar acceptors.     

保留型与反转型β-木糖苷酶活性位点的分子动力学模拟

木聚糖是潜在的重要可再生能源, 如何提高其降解效率已成为近年来的研究热点. β-木糖苷酶是木聚糖降解过程中的关键酶之一, 按其水解机制可分为保留型与反转型酶. 目前虽然对于这两种催化机制的研究不断深入, 但很少有工作从溶液环境的角度出发探究它们的差异. 本文采用分子动力学模拟方法, 对4 个典型的β-木糖苷酶进行了显式溶剂模拟研究, 详细分析了酶的催化氨基酸间的距离和质子供体氨基酸pK_a值的动态变化. 结果显示, 反转型酶催化氨基酸间的距离约为0.8-1.0 nm, 大于保留型的0.5-0.6 nm, 与先前对糖苷酶晶体结构的统计分析结果一致. 令人意外的是, 保留型酶的质子供体通过与其附近组氨酸的相互作用, 其pK_a在两个不同的高、低值之间交替变换, 使保留型酶的双取代反应得以发生; 而反转型酶的质子供体则由附近的天冬氨酸调节, 其pK_a稳定在某个较高值, 这可能有利于其在反应pH值下获得水溶液中的氢离子, 进行反转型酶特有的单取代反应. 因此, 本工作加深了人们对β-木糖苷酶保留型与反转型水解机制的认识, 并为后续酶的理性改造与高效利用提供具有指导价值的结构与机理信息.     

Synthese D'Azotures et de Benzoates de Glycosyle a Partir de Sulfites Cycliques Enc C-1, C-2

The reaction of sugars bearing a cyclic sulfite group on C-1, C-2 with azide or benzoate ions, is strereoselective and gives trans- 1,2 glycosyl azides or glycosyl benzoates with a free hydroxyle at C-2. The reaction is performed under mild conditions and gives excellent yields of glycosyl derivatives.     

Fluorous tag method for the simultaneous synthesis of different kinds of glycolipids

A mixture of saccharide primers with partially fluorinated tails, 2-(perfluorooctyl)ethyl 4′-O-(β-d-galactopyranosyl)-β-d-glucopyranoside (Lac H2F8) and 6-(perfluorohexyl)hexyl 2′-acetamido-2′-deoxy-β-d-glucopyranoside (GN H6H6), were introduced to animal cells. The oligosaccharide of Lac H2F8 was elongated by cellular enzymes and gave a GM3-type oligosaccharide. On the other hand, GN H6F6 was galactosylated to afford a lactosamine derivative that was further sialylated. This research confirmed that simultaneous glycosylation processes took place for Lac H2F8 and GN H6F6 primers and that the presence of one did not prevent the glycosylation of the other from proceeding. Each primer was recognized independently and elongated sequentially by cellular enzymes. Significantly, the synthesis of glycolipids from a mixture of these artificial scaffolds did not prevent the synthesis of glycolipids from the natural precursor. The glycosyl transferases recognized both precursors resulting to simultaneous synthesis of glycolipids.     

Retaining60Co2+ ions from residual water on zeolites

The ion exchange between⁶⁰Co²⁺ ions contained in residual radioactive water and zeolites of the NaA, NaX and CaA types was studied. The more advanced retaining of⁶⁰Co²⁺ ions occurs for the NaA zeolite with the higher exchange capacity, as compared to NaX. With the CaA zeolite, a very weak ion exchange with⁶⁰Co²⁺ ions was observed.     

Engineered biosynthesis of hybrid macrolide polyketides containing D-angolosamine and D-mycaminose moieties

The glycosylation of natural product scaffolds with highly modified deoxysugars is often essential for their biological activity, being responsible for specific contacts to molecular targets and significantly affecting their pharmacokinetic properties. In order to provide tools for the targeted alteration of natural product glycosylation patterns, significant strides have been made to understand the biosynthesis of activated deoxysugars and their transfer. We report here efforts towards the production of plasmid-borne biosynthetic gene cassettes capable of producing TDP-activated forms of D-mycaminose, D-angolosamine and D-desosamine. We additionally describe the transfer of these deoxysugars to macrolide aglycones using the glycosyl transferases EryCIII, TylMII and AngMII, which display usefully broad substrate tolerance.     

Divergent Chemoenzymatic Synthesis of Asymmetrical‐Core‐Fucosylated and Core‐Unmodified N‐Glycans

A divergent chemoenzymaytic approach for the preparation of core‐fucosylated and core‐unmodified asymmetrical N‐glycans from a common advances precursor is described. An undecasaccharide was synthesized by sequential chemical glycosylations of an orthogonally protected core fucosylated hexasaccharide that is common to all mammalian core fucosylated N‐glycans. Antennae‐selective enzymatic extension of the undecasaccharide using a panel of glycosyl transferases afforded core fucosylated asymmetrical triantennary N‐glycan isomers, which are potential biomarkers for breast cancer. A unique aspect of our approach is that a fucosidase (FucA1) has been identified that selectively can cleave a core‐fucoside without affecting the fucoside of a sialyl Lewis^X epitope to give easy access to core‐unmodified compounds.     

Design and Synthesis of Exocyclic Cyclitol Aziridines as Potential Mechanism-Based Glycosidase Inactivators

Cyclophellitol aziridines have found wide application as mechanism-based, covalent, and irreversible inhibitors of retaining glycosidases. These compounds, like their parent compound, cyclophellitol (a natural product retaining β-glucosidase inactivator), make use of the mechanism of action of retaining glycosidases, which process their substrate through the formation of a transient covalent intermediate. In contrast, inverting glycosidases, the other main family of glycosyl hydrolases, do not employ such a covalent intermediate, and, as a consequence, useful scaffolds for mechanism-based inhibitor design have yet to be discovered. In this work, we explore chemistries that allow for the construction of cyclitol aziridines with the aziridine electrophile attached in an exocyclic fashion, more distal from the anomeric carbon – thus putatively closer to an inverting glycosidase active site nucleophile. The developed chemistries have allowed for the synthesis of a focused library of differently N-substituted, α-and β-glucopyranose configured cyclitol aziridines for future evaluation as inhibitors or inactivators of α-and β-glucosidases alike.     

Alternative donor substrates for inverting and retaining glycosyltransferases

By the use of glycosyl donors containing aromatic leaving groups linked with opposite anomeric configurations compared to those of the natural donor substrates, an inverting (Cst II) and a retaining (LgtC) glycosyltransferase were found to catalyse glycosylation reactions of natural acceptor substrates in the presence of the corresponding nucleotide.     

Toward the total synthesis of vineomycin B2: application of an efficient glycosylation methodology using 2,3-unsaturated sugars

The application of an efficient glycosylation methodology using 2,3-unsaturated sugars to synthesize critical precursors required for the total synthesis of an antibiotic, vineomycin B₂ (1), was demonstrated. The required disaccharide, the acurosyl rhodinose derivative of 1, was prepared by chemoselective glycosylation using a 2,3-saturated glycosyl acetate corresponding to the rhodinose moiety and a 2,3-unsaturated glycosyl acetate corresponding to the acurose portion. Further, the right-hand side chain of 1, consisting of β-oxo-tert-alcohol and rhodinose, was constructed by a powerful glycosylation approach using a 2,3-unsaturated glycosyl acetate in an ionic liquid under reduced pressure.     

A Rapid Synthesis of Pyranoid Glycals Promoted by β‐Cyclodextrin and Ultrasound

A convenient and environmentally benign procedure for the synthesis of glycals from glycosyl bromides with very low zinc dust loading (1.5 equiv.) is described. The process is activated by β‐cyclodextrin and ultrasound. Based on 19 samples, this method has been demonstrated to be highly effective for a broad range of glycosyl bromides, including acid‐ or base‐sensitive and disaccharide glycosyl bromides. A yield of 85%–96% of glycals was obtained.     

Anatomy of glycosynthesis: structure and kinetics of the Humicola insolens Cel7B E197A and E197S glycosynthase mutants

The formation of glycoconjugates and oligosaccharides remains one of the most challenging chemical syntheses. Chemo-enzymatic routes using retaining glycosidases have been successfully harnessed but require tight kinetic or thermodynamic control. "Glycosynthases," specifically engineered glycosidases that catalyze the formation of glycosidic bonds from glycosyl donor and acceptor alcohol, are an emerging range of synthetic tools in which catalytic nucleophile mutants are harnessed together with glycosyl fluoride donors to generate powerful and versatile catalysts. Here we present the structural and kinetic dissection of the Humicola insolens Cel7B glycosynthases in which the nucleophile of the wild-type enzyme is mutated to alanine and serine (E197A and E197S). 3-D structures reveal the acceptor and donor subsites and the basis for substrate inhibition. Kinetic analysis shows that the E197S mutant is considerably more active than the corresponding alanine mutant due to a 40-fold increase in k(cat).     

Synthesis and use of mechanism-based protein-profiling probes for retaining beta-D-glucosaminidases facilitate identification of Pseudomonas aeruginosa NagZ

The NagZ class of retaining exo-glucosaminidases play a critical role in peptidoglycan recycling in Gram-negative bacteria and the induction of resistance to beta-lactams. Here we describe the concise synthesis of 2-azidoacetyl-2-deoxy-5-fluoro-beta-d-glucopyranosyl fluoride as an activity-based proteomics probe for profiling these exo-glycosidases. This active-site directed reagent covalently inactivates this class of retaining N-acetylglucosaminidases with exquisite selectivity by stabilizing the glycosyl-enzyme intermediate. Inactivated Vibrio cholerae NagZ can be elaborated with biotin or a FLAG-peptide epitope using the Staudinger ligation or the Sharpless-Meldal click reaction and detected at nanogram levels. This ABPP enabled the profiling of the Pseudomonas aeruginosa proteome and identification at endogenous levels of a tagged protein with properties consistent with those of PA3005. Cloning of the gene encoding this hypothetical protein and biochemical characterization enabled unambiguous assignment of this hypothetical protein as a NagZ. The identification and cloning of this NagZ may facilitate the development of strategies to circumvent resistance to beta-lactams in this human pathogen. As well, this general strategy, involving such 5-fluoro inactivators, may prove to be of general use for profiling proteomes and identifying glycoside hydrolases of medical importance or having desirable properties for biotechnology.