Dynamic combinatorial carbohydrate libraries: probing the binding site of the concanavalin A lectin

Dynamic combinatorial chemistry (DCC) has emerged as an efficient approach to receptor/ligand identification based on the generation of combinatorial libraries by reversible interconversion of the library constituents. In this study, the implementation of such libraries on carbohydrate-lectin interactions was examined with the plant lectin Concanavalin A as a target species. Dynamic carbohydrate libraries were generated from a pool of carbohydrate aldehydes and hydrazide linker/scaffold components through reversible acylhydrazone exchange, resulting in libraries containing up to 474 constituents. Dynamic deconvolution allowed the efficient identification of the structural features required for binding to Concanavalin A and the selection of a strong binder, a tritopic mannoside, showing an IC(50)-value of 22 microM.     

Modification of microcrystalline cellulose with pyridone derivatives for removal of cationic dyes from aqueous solutions

Microcrystalline cellulose (MCC) was modified with pyridone derivatives such as pyridone diester (PDE) and pyridone diacid (PDA) by using succinic acid anhydride as a linker. The modified MCCs were characterized by the fourier transform infrared spectroscopy, scanning electron microscopy, thermal gravimetric analysis, elemental analysis and solid state ¹³C NMR. The adsorption capacities of the modified MCCs to cationic dyes were examined by using methylene blue (MB) as a model dye. It was found that the kinetic adsorption data followed the pseudo-second-order kinetic model, and the adsorption equilibriums were reached less than 10 min. The isothermal adsorption data were fitted with the Langmuir isotherm model very well, from which the maximum adsorption capacities of the MCCs modified with PDE and PDA were determined to be 101.01 and 142.86 mg/g, respectively. Further investigation showed that the modified MCCs were pH-dependent for adsorption of MB in aqueous solutions. The modified MCCs could be used for removal of MB from an aqueous solution at pH 8, and reused by regeneration in an acidic solution. It was tested that the modified MCCs had a high reusability for removal of MB from aqueous solutions, and still maintained high adsorption capacities even after multiple cycles of desorption–adsorption processes. Hence, the MCCs modified with PDE and PDA could be an effective and efficient approach to removal of cationic dyes from aqueous solutions.     

Recent advances in fabrication of monolayer colloidal crystals and their inverse replicas

Monolayer colloidal crystals(MCCs)are two-dimensional(2D)colloidal crystals consisting of a monolayer of monodisperse colloidal particles arrayed with a 2D periodic order.In recent years,MCCs have attracted intensive interest because they can act as 2D photonic crystals and be used as versatile templates for fabrication of various 2D nanostructure arrays.In this review,we provide an overview of the recent progress in the controllable fabrication of MCCs and their inverse replicas.First,some newly-developed methods for the self-assembly of MCCs based on different strategies including interfacial assembly and convective assembly are introduced.Second,some representative novel methods regarding the fabrication of various functional2D inverse replicas of MCCs,such as 2D arrays of nanobowls,nanocaps,and hollow spheres,as well as 2D monolayer inverse opals(MIOs),are described.In addition,the potential applications of MCCs and their inverse replicas are discussed.     

Glycosamino acids: building blocks for combinatorial synthesis-implications for drug discovery

The unique functions of carbohydrates, including energy storage, transport, modulation of protein function, intercellular adhesion, signal transduction, malignant transformation, and viral and bacterial cell-surface recognition, underlie a significant pharmaceutical potential. The development of combinatorial carbohydrate libraries in this important arena has been slow, in contrast to the rapid development of combinatorial synthesis in the area of small-molecule libraries and biopolymers. This is largely as a result of the inherent difficulties presented by this class of polyfunctional compounds. Nevertheless, strategies to cope with these problems have been devised over the past seven years, and combinatorial carbohydrate libraries have appeared. The incorporation of an amino acid moiety into the carbohydrate scaffold generates glycosamino acids, which are attractive building blocks for the preparation of carbohydrate-based libraries because of the well-established automated peptide synthesis. Derivatization as well as homo- and heterooligomerization of glycosamino acids can be used to create novel structures with unique properties. Glycosamino acids are hybrid structures of carbohydrates and amino acids which can be utilized to generate potential glycomimetics and peptidomimetics. The incorporation of glycosamino acids into peptides allows the engineering of carbohydrate-binding sites into synthetic polypeptides, which may also influence the pharmacokinetic and dynamic properties of the peptides. Furthermore, sugar-amino acid hybrids offer a tremendous structural and functional diversity, which is largely unexplored and requires combinatorial strategies for efficient exploitation. This article provides an overview of previous work on glycosamino acids and discusses their use in combinatorial synthesis and drug discovery. Supporting information for this article is available on the WWW under http://www.angewandte.com or from the author.     

The use of carbohydrate microarrays to study carbohydrate-cell interactions and to detect pathogens

The use of carbohydrate microarrays to investigate the carbohydrate binding specificities of bacteria, to detect pathogens, and to screen antiadhesion therapeutics is reported. This system is ideal for whole-cell applications because microarrays present carbohydrate ligands in a manner that mimics interactions at cell-cell interfaces. Other advantages include assay miniaturization, since minimal amounts (approximately picomoles) of a ligand are required to observe binding, and high throughput, since thousands of compounds can be placed on an array and analyzed in parallel. Pathogen detection experiments can be completed in complex mixtures of cells or protein using the known carbohydrate binding epitopes of the pathogens in question. The nondestructive nature of the arrays allows the pathogen to be harvested and tested for antibacterial susceptibility. These investigations allow microarray-based screening of biological samples for contaminants and combinatorial libraries for antiadhesion therapeutics.     

Sol-gel multicapillary columns for gas-solid chromatography

In this work, we report the method for the preparation of multicapillary columns (MCCs) for gas-solid chromatography. The porous layer adsorbent is formed on capillary walls by the hydrolysis of aluminum alkoxide in the presence of polypropylene glycol (PPG) and HCl. Porosity and selectivity of the adsorbent depend on reaction conditions and the concentration of PPG. Sol-gel MCCs are well suited for high-speed chromatographic analysis of light hydrocarbons by gas-solid chromatography. Nine-component mixtures of C1-C4 hydrocarbons are separated within 8-12 s. The efficiency of 25-30 cm long alumina sol-gel MCCs consisting of approximately 1400 capillaries of 40 microm diameter is up to 2500-3000 theoretical plates.     

Orthogonal sulfation strategy for synthetic heparan sulfate ligands

[reaction: see text] An orthogonal sulfation strategy involving six different protecting groups has been developed for generating sulfated carbohydrate libraries based on heparan. Chemoselective cleavage conditions (optimized for a heparan disaccharide) can be performed in the presence of sulfate esters as well as the remaining protecting groups.     

Mechanistic studies and methods to prevent aglycon transfer of thioglycosides

Thioglycosides have been employed extensively for the synthesis of complex oligosaccharides, carbohydrate libraries, and mimetics of O-glycosides. While very useful, aglycon transfer is a problematic side reaction with thioglycosides. In this paper, a series of mechanistic studies are described. The aglycon transfer process is shown to affect both armed and disarmed thioglycosides, cause anomerization of the carbon-sulfur bond of a thioglycoside, and destroy the product of a glycosylation reaction. The results indicate that the aglycon transfer process can be a major problem for a wide range of thioglycosides. This side reaction is especially important to consider when carrying out complex reactions such as solid-phase glycosylations, one-pot or orthogonal multicomponent glycosylations, and construction of carbohydrate libraries. To prevent transfer, a number of modified aglycons were examined. The 2,6-dimethylphenyl (DMP) aglycon was found to effectively block transfer in a variety of model studies and glycosylation reactions. The DMP group can be installed in one step from a commercially available thiol (2,6-dimethylthiophenol) and is useable as a glycosyl donor. On the basis of these features, the DMP group is proposed as a convenient and improved aglycon for thioglycosides.     

Complex formation of cyclomaltononaose delta-cyclodextrin (delta-CD) with macrocyclic compounds

The complex forming ability of delta-cyclodextrin delta-CD with 7 kinds of macrocyclic compounds (MCCs) with 8-15 carbon atoms in the ring as models of large guest molecules was studied in aqueous solution and compared with the complexation properties of alpha-, beta- and gamma-CD. Both alpha- and beta-CD formed relatively stable complexes with small MCCs, while gamma- and delta-CD were more efficient in binding larger MCCs. The solid MCC/delta-CD complexes were precipitated with the larger MCCs with 11-15 carbon atoms in the ring, while no such precipitates were obtained with smaller MCCs with only 8-10 carbon atoms in the ring. The formation of the solid complexes was confirmed by powder X-ray diffractometry and differential scanning calorimetry. The cell dimensions of cycloundecanone (11 carbon atoms in the ring)/delta-CD complex were determined by X-ray crystallography. The preliminary crystal data were: Monoclinic, P21, a=32.50 (2)A, b=19.02 (3)A, c=16.60 (1) A, beta3=98.37 (5)degrees, V=10148 (16) A3.     

Combinatorial chemistry in glycobiology

The application of combinatorial chemistry to glycobiology historically has proven challenging due to numerous synthetic hurdles. The advent of novel methodologies has enabled the production of natural as well as mimetic analogues for proof-of-concept experiments and SAR. This review highlights some of the recent synthetic advances in combinatorial carbohydrate synthesis. The application of carbohydrate libraries in glycobiology is also discussed.     

An Access to Glycoconjugate Libraries through Multicomponent Reactions

Four-component reactions : The Ugi reaction of four suitably functionalized carbohydrate derivatives (as a per-O-benzylated amine, an aldehyde, a carboxylic acid, and an isocyanide) allow the effective assembly of diverse compound libraries. The complex glycoconjugates formed can be deprotected (see the picture for an example), and the resulting glycomimetics are of high interest for screening purposes.     

Glycopeptide and Oligosaccharide Libraries

Despite the burgeoning interest in the various biological functions and consequent therapeutic potential of the vast number of oligosaccharides found in nature on glycoproteins and cell surfaces, the development of combinatorial carbohydrate chemistry has not progressed as rapidly as expected. The reason for this imbalance is rooted in the difficulty of oligosaccharide assembly and analysis that renders synthesis a rather cumbersome endeavor. Parallel approaches that generate series of analogous compounds rather than real libraries have therefore typically been used. Since generally low affinity is obtained for interactions between carbohydrate receptors and modified oligosaccharides designed as mimetics of natural carbohydrate ligands, glycopeptides have been explored as alternative mimics. Glycopeptides have been proven in many cases to be superior ligands with higher affinity for a receptor than the natural carbohydrate ligand. High-affinity glycopeptide ligands have been found for several types of receptors including the E-, P-, and L-selectins, toxins, glycohydrolases, bacterial adhesins, and the mannose-6-phosphate receptor. Furthermore, the assembly of glycopeptides is considerably more facile than that of oligosaccharides and the process can be adapted to combinatorial synthesis with either glycosylated amino acid building blocks or by direct glycosylation of peptide templates. The application of the split and combine approach using ladder synthesis has allowed the generation of very large numbers of compounds which could be analyzed and screened for binding of receptors on solid phase. This powerful technique can be used generally for the identification and analysis of the complex interaction between the carbohydrates and their receptors.     

Vanadium bromoperoxidase-coupled fluorescent assay for flow cytometry sorting of glucose oxidase gene libraries in double emulsions

A Vanadium bromoPeroxidase-coupled fluorescent assay (ViPer) for ultrahigh-throughput screening of glucose oxidase (GOx) gene libraries employing double emulsions and flow cytometry was developed. The assay is based on detection of the product of a GOx reaction, hydrogen peroxide, that is first converted to a hypobromide by vanadium bromoperoxidase in the presence of sodium bromide. The hypobromide is afterwards detected in a reaction with a fluorogenic probe, 3-carboxy-7-(4'-aminophenoxy)-coumarine, where fluorescent 3-carboxy-coumarine is released. The ViPer screening system is three times more sensitive than a horseradish peroxidase coupled detection system and more resistant to bleaching of fluorescence in excess of peroxide. Using the ViPer screening system a high epPCR gene library containing 100,000 different GOx variants was screened for active clones in less than 1 h by flow cytometry. A library containing 0.15% of yeast cells expressing active enzyme variants and with an average GOx activity in the liquid culture of 0.47 U/mL, after one round of sorting, had 28.12% of the yeast cells expressing the active GOx (an enrichment factor of 200) and 26.8 U/mL of the GOx activity in the liquid culture (an enrichment factor of 57). The developed screening system could be adapted and used in a directed evolution of GOx and other hydrogen peroxide-producing enzymes (oxidases) and glycosidases if coupled with a carbohydrate oxidase.     

基于二硫代氨基甲酸盐自组装的糖芯片制备与表征

糖基传感芯片是定量研究糖-蛋白相互作用的有力工具。传统糖基传感芯片的制备过程通常涉及糖基硫醇衍生物的合成,过程复杂且产率较低。本文采用脱氧氨基糖与二硫化碳温和条件下一步反应合成了一类新型糖基自组装功能分子-糖基二硫代氨基甲酸盐(DTC)化合物,进而在金衬底芯片上构筑了糖基传感功能膜。采用X射线光电子能谱(XPS)分析了该糖基传感功能膜的元素组成和元素化学环境;采用表面等离子体共振(SPR)和酶联凝集素分析(ELLA)技术定量分析了其在蛋白质水平的糖生物学活性。通过混合自组装的方法,制备了一系列表面葡萄糖密度不同的糖基传感功能膜并测定了伴刀豆球蛋白(Con A)吸附的热力学和动力学数据。通过调控表面密度,我们观察到了蛋白在葡萄糖表面吸附的多价态现象。当自组装溶液中葡萄糖-DTC摩尔分数低于1%时,Con A呈现单价态吸附,其解离平衡常数(Kd)为(39.10±0.12)μmol?L-1;当自组装溶液中葡萄糖-DTC摩尔分数高于2%时,Con A呈现多价态吸附,解离平衡常数降至(1.17±0.18)μmol?L-1。本文所发展的糖基自组装功能分子合成方法快速便捷、适用范围广,通过混合自组装可以实现蛋白结合价态的调控,是一种深入研究基于糖-蛋白相互作用的诸多生物过程的有效工具。     

What are the limits to the size of effective dynamic combinatorial libraries?

Using simple computer simulations of model dynamic combinatorial libraries, we show that the best binders can be amplified to useful concentrations in libraries containing 10-10(6) compounds. [structure: see text]     

Carbohydrate-derived amino-alcohol ligands for asymmetric alkynylation of aldehydes

[reaction: see text] Conformationally restricted amino alcohols based on carbohydrate scaffolds provide flexible and fine-tuneable libraries that greatly expand the range of ligands available in the Zn(OTf)(2)-mediated addition of alkynes to aldehydes, in some cases with very high stereoselectivities.     

Synthesis of Functionalized Thiodisaccharides by Conjugate Addition

Abstract

Oligosaccharides containing thioglycosidic linkages are resistant to enzyme-catalysed hydrolysis and therefore interesting material for studies of carbohydrate hydrolases. Some of these were shown to be competitive inhibitors for several glycanases such as α-amylase,¹ cellobiohydrolase I and II,² and for α-l-fucosidase,³ a glycosidase. Thio-oligosaccharides have also been used to prepare column material for affinity chromatography to isolate carbohydrate hydrolases. In contrast, affinity material containing normal O-glycosidic bonds was hydrolysed and led to column deterioration. By employing this approach, affinity materials containing 1,4-dithiocellobiose and 1,4,4′-trithiocellotriose could be used successfully to separate the cellobiohydrolases of Trichoderma reesei.²     

Synthesis and mass spectrometry studies of branched oxime ether libraries. Mapping the substitution motif via linker stability and fragmentation pattern.

The oxime ether chemistry has recently been used as a convenient approach to preparing potentially highly diverse combinatorial libraries. The synthetically easiest way to form the libraries is convergent, i.e., via reaction of a branched scaffold containing two or more aminooxy linker groups, with a variety of carbonyl substituents. We show here that such reactions between aldehydes and ketones of different structure with the scaffolds containing different types of aminooxy groups can lead to the formation of virtually all expected components in the model mixtures 1-3 formed from three scaffolds (7-9) and eight substituents (R(1)-R(8)). One important problem with the branched libraries is that the libraries formed from the more complex scaffolds, such as 11, contain multiple regioisomers. The results of extensive analysis of a variety of library components by mass spectrometry presented here show that the differences in the MS-MS fragmentation energies for different linkers yield regiochemical information essential for identification of individual library components.     

Ribosomal synthesis of unnatural peptides

Combinatorial libraries of non-biological polymers and drug-like peptides could in principle be synthesized from unnatural amino acids by exploiting the broad substrate specificity of the ribosome. The ribosomal synthesis of such libraries would allow rare functional molecules to be identified using technologies developed for the in vitro selection of peptides and proteins. Here, we use a reconstituted E. coli translation system to simultaneously re-assign 35 of the 61 sense codons to 12 unnatural amino acid analogues. This reprogrammed genetic code was used to direct the synthesis of a single peptide containing 10 different unnatural amino acids. This system is compatible with mRNA-display, enabling the synthesis of unnatural peptide libraries of 10(14) unique members for the in vitro selection of functional unnatural molecules. We also show that the chemical space sampled by these libraries can be expanded using mutant aminoacyl-tRNA synthetases for the incorporation of additional unnatural amino acids or by the specific posttranslational chemical derivitization of reactive groups with small molecules. This system represents a first step toward a platform for the synthesis by enzymatic tRNA aminoacylation and ribosomal translation of cyclic peptides comprised of unnatural amino acids that are similar to the nonribosomal peptides.     

A peptide-based catalyst approach to regioselective functionalization of carbohydrates

Two small peptide libraries (150 members and 36 members) have been subjected to screening experiments to evaluate their potential for regioselective (i.e. site-selective) acylation of carbohydrate monomers. Two substrates, one diol derived from N-acetyl glucosamine and one tetraol derived from glucose, have served as the test cases. In each case, the inherent regioselection of catalyzed acylation was defined as that derived from the reaction where N-methylimidazole (NMI) is used as the catalyst. With both substrates, peptides were found to perturb the inherent selectivities from those observed with NMI. From the libraries, the catalysts that provide the largest deviation from NMI were subjected to optimization studies. The work sets the groundwork for studies of expanded peptide libraries and development of structure-selectivity relationships to obtain catalysts that can selectively derivatize the unique sites in stereochemically complex polyols.