Toward automated oligosaccharide synthesis

Carbohydrates have been shown to play important roles in biological processes. The pace of development in carbohydrate research is, however, relatively slow due to the problems associated with the complexity of carbohydrate structures and the lack of general synthetic methods and tools available for the study of this class of biomolecules. Recent advances in synthesis have demonstrated that many of these problems can be circumvented. In this Review, we describe the methods developed to tackle the problems of carbohydrate-mediated biological processes, with particular focus on the issue related to the development of the automated synthesis of oligosaccharides. Further applications of carbohydrate microarrays and vaccines to human diseases are also highlighted.     

Carbohydrate chemistry in drug discovery

The multitude of roles that carbohydrates and their glyco-conjugates play in biological processes has stimulated great interest in determining the nature of their interactions in both normal and diseased states. Manipulating such interactions will provide leads for drug discovery. Of the major classes of biomolecule, carbohydrates are the most structurally diverse. This hetereogeneity makes isolation of pure samples, and in sufficient amounts, from biological sources extremely difficult. Chemical synthesis offers the advantage of producing pure and structurally defined oligosaccharides for biological investigations. Although the complex nature of carbohydrates means that this is challenging, recent advances in the field have facilitated access to these molecules. The synthesis and isolation of oligosaccharides combined with progress in glycoarray technology have aided the identification of new carbohydrate-binding drug targets. This review aims to provide an overview of the latest advancements in carbohydrate chemistry and the role of these complex molecules in drug discovery, focusing particularly on synthetic methodologies, glycosaminoglycans, glycoprotein synthesis and vaccine development over the last few years.     

Lessons from nature: biomimetic organocatalytic carbon-carbon bond formations

Nature utilizes simple C2 and C3 building blocks, such as dihydroxyacetone phosphate (DHAP), phosphoenolpyruvate (PEP), and the "active aldehyde" in various enzyme-catalyzed carbon-carbon bond formations to efficiently build up complex organic molecules. In this Perspective, we describe the transition from using enantiopure chemical synthetic equivalents of these building blocks, employing our SAMP/RAMP hydrazone methodology and metalated chiral alpha-amino nitriles, to the asymmetric organocatalytic versions developed in our laboratory. Following this biomimetic strategy, the DHAP equivalent 2,2-dimethyl-1,3-dioxan-5-one (dioxanone) has been used in the proline-catalyzed synthesis of carbohydrates, aminosugars, carbasugars, polyoxamic acid, and various sphingosines. Proline-catalyzed aldol reactions involving a PEP-like equivalent have also allowed for the asymmetric synthesis of ulosonic acid precursors. By mimicking the "active aldehyde" nucleophilic acylations in Nature catalyzed by the thiamine-dependent enzyme, transketolase, enantioselective N-heterocyclic carbene-catalyzed benzoin and Stetter reactions have been developed. Finally, based on Nature's use of domino reactions to convert simple building blocks into complex and highly functionalized molecules, we report on our development of biomimetic asymmetric multicomponent domino reactions which couple enamine and iminium catalysis.     

Solution syntheses of protected type II Lewis blood group oligosaccharides: study for automated synthesis

Glycosyl phosphate and trichloroacetimidate monosaccharide building blocks were used in a stepwise solution-phase synthesis of three Lewis blood group oligosaccharides. The syntheses were conducted to establish general routes for the automated assembly of the oligosaccharide portion of biologically important glycolipids. The H-type II pentasaccharide, Le(x) pentasaccharide, and Le(y) hexasaccharide were prepared in high yield. These syntheses served to evaluate the utility and limitations of the 2-(azidomethyl)benzoate ester (AZMB) for the construction of complex carbohydrates. Development of a glucosamine building block containing a N-trichloroacetamide group to mask the C2 amine improved coupling yields and was key for completion of the Le(x) and Le(y) structures.     

Metal-biomolecule frameworks (MBioFs)

Biomolecules are the building blocks of life. Nature has evolved countless biomolecules that show promise for bridging metal ions. These molecules have emerged as an excellent source of biocompatible building blocks that can be used to design Metal-Biomolecule Frameworks (MBioFs). This feature article highlights the advances in the synthesis of this class of MOFs. Special emphasis is provided on the crystal structures of these materials, their miniaturization to the submicron length scale, and their new potential storage, catalytic, and biomedical applications.     

Carbohydrates as the next frontier in pharmaceutical research

Synthetic carbohydrates and glycoconjugates are used to study their roles in biological important processes such as inflammation, cell-cell recognition, immunological response, metastasis, and fertilization. The development of an automated oligosaccharide synthesizer greatly accelerates the assembly of complex, naturally occurring carbohydrates as well as chemically modified oligosaccharide structures and promises to have major impact on the field of glycobiology. Tools such as microarrays, surface plasmon resonance spectroscopy, and fluorescent carbohydrate conjugates to map interactions of carbohydrates in biological systems are presented. Case studies of the successful application of carbohydrates as active agents are discussed, for example, fully synthetic oligosaccharide vaccines to combat tropical diseases (e.g., malaria), bacterial infections (e.g., tuberculosis), viral infections such as HIV, and cancer. Aminoglycosides serve as examples of drugs acting through carbohydrate-nucleic-acid interactions, while heparin works by carbohydrate-protein interactions. A general, modular strategy for the complete stereoselective synthesis of defined heparin oligosaccharides is presented. A carbohydrate-functionalized fluorescent polymer has been shown to detect miniscule amounts of bacteria faster than commonly used methods.     

Utilization of glycosyltransferases to change oligosaccharide structures

Carbohydrates on cell surfaces are important biomolecules in various biological recognition processes. Elucidation of the biological roles of complex oligosaccharides necessitates an efficient methodology to synthesize these compounds and their analogs. Enzymatic synthesis renders itself to be useful in the construction of an oligosaccharide structure owing to its mild reaction condition, high regio- and stereoselectivity. This review article focuses on the recent progress in oligosaccharide syntheses catalyzed by glycosyltransferases, namely sialyltransferase, galactosyltransferase, fucosyltransferase, andN-acetylglucosaminyltransferase. A survey of the latest patent and literature related to this field is also included.     

作为信息分子的糖类

糖生物学是生物化学中最后一个重大的研究前沿。糖类研究的复杂性在于其结构的复杂多变, 但是近年来对糖类结构, 特别是糖复合物中的糖部分的测定取得了很大进展。糖结构的复杂性, 也使糖类成为携带着最大信息量的生物分子。作为信息分子的糖类在生物体内发挥多方面的生物作用: 决定了分子的抗原性和细胞的表型; 在很多生理和病理过程中起了关键的识别作用; 也可作为动态和时空调节的信号。     

Structural dependence of electron transfer to non-covalent polar complexes

Electron attachment to polar molecules and their non-covalent complexes can lead to different kinds of anions which differ from their excess electron localization. Spectroscopic methods for studying anion structures are reviewed. In many cases, the neutral and anion structures are identical and can be deduced from the electron attachment properties. Examples are given for complexes containing polar solvents or building blocks of biomolecules (nucleobases, amino acid residues...).     

Energy, charge, and spin transport in molecules and self-assembled nanostructures inspired by photosynthesis

Electron transfer in biological molecules provides both insight and inspiration for developing chemical systems having similar functionality. Photosynthesis is an example of an integrated system in which light harvesting, photoinduced charge separation, and catalysis combine to carry out two thermodynamically demanding processes, the oxidation of water and the reduction of carbon dioxide. The development of artificial photosynthetic systems for solar energy conversion requires a fundamental understanding of electron-transfer reactions between organic molecules. Since these reactions most often involve single-electron transfers, the spin dynamics of photogenerated radical ion pairs provide important information on how the rates and efficiencies of these reactions depend on molecular structure. Given this knowledge, the design and synthesis of large integrated structures to carry out artificial photosynthesis is moving forward. An important approach to achieving this goal is the development of small, functional building blocks, having a minimum number of covalent bonds, which also have the appropriate molecular recognition sites to facilitate self-assembly into a complete, functional artificial photosynthetic system.     

Sugar amino acid based scaffolds--novel peptidomimetics and their potential in combinatorial synthesis

To meet the growing demands for the development of new molecular entities for discovering new drugs and materials, organic chemists have started looking for new concepts to supplement traditional approaches. In one such approach, the expertise gained over the years in the area of organic synthesis and the rational drug-design concepts are combined together to create "nature-like" and yet unnatural organic molecules that are expected to provide leads in discovering new molecules. Emulating the basic principles followed by nature to build its vast repertoire of biomolecules, organic chemists are developing many novel multifunctional building blocks. Sugar amino acids constitute an important class of such polyfunctional scaffolds where the carboxyl, amino and hydroxyl groups provide an excellent opportunity for organic chemists to create structural diversities akin to nature's molecular arsenal. Recent advances in the area of combinatorial chemistry give unprecedented technological support for rapid compilations of sugar amino acid-based libraries exploiting the diversities of carbohydrate molecules and well-developed solid-phase peptide synthesis methods. This review chronicles the development of sugar amino acids as a novel class of peptidomimetic building blocks and their applications in generating desired secondary structures in peptides as well as in creating mimics of natural biopolymers.     

寡糖合成中的“预活化”策略

寡糖及其缀合物因其重要的生物学功能而日益受到人们的关注,由于糖链结构的复杂性与多样性,寡糖的化学合成具有很大的挑战性。为了减少合成及分离步骤,提高寡糖合成的效率,糖基化策略十分重要。"一釜合成法"由于进行多个连续的糖基化反应但不需分离中间体而具有很大优势,但传统"一釜法"在设计单糖模块时需要进行精细复杂的保护基操作和离去基调整而影响其合成效率。"预活化"寡糖合成策略不依赖于糖基供体与糖基受体的活性差异,无需复杂的保护基操作,所有偶联反应在同一条件下一釜完成,实现了寡糖的高效、快速合成。本文在简要介绍传统"一釜合成法"的基础上,对"预活化"策略的研究进展进行综述,重点介绍"预活化"策略的基本原理,发展过程及其在生物活性寡糖合成上的应用。     

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.     

Library design practices for success in lead generation with small molecule libraries

The generation of novel structures amenable to rapid and efficient lead optimization comprises an emerging strategy for success in modern drug discovery. Small molecule libraries of sufficient size and diversity to increase the chances of discovery of novel structures make the high throughput synthesis approach the method of choice for lead generation. Despite an industry trend for smaller, more focused libraries, the need to generate novel lead structures makes larger libraries a necessary strategy. For libraries of a several thousand or more members, solid phase synthesis approaches are the most suitable. While the technology and chemistry necessary for small molecule library synthesis continue to advance, success in lead generation requires rigorous consideration in the library design process to ensure the synthesis of molecules possessing the proper characteristics for subsequent lead optimization. Without proper selection of library templates and building blocks, solid phase synthesis methods often generate molecules which are too heavy, too lipophilic and too complex to be useful for lead optimization. The appropriate filtering of virtual library designs with multiple computational tools allows the generation of information-rich libraries within a drug-like molecular property space. An understanding of the hit-to-lead process provides a practical guide to molecular design characteristics. Examples of leads generated from library approaches also provide a benchmarking of successes as well as aspects for continued development of library design practices.     

ZEOBUILDER: A GUI toolkit for the construction of complex molecular structures on the nanoscale with building blocks

In this paper, a new graphical toolkit, ZEOBUILDER, is presented for the construction of the most complex zeolite structures based on building blocks. Molecular simulations starting from these model structures give novel insights in the synthesis mechanisms of micro- and mesoporous materials. ZEOBUILDER is presented as an open-source code with easy plug-in facilities. This architecture offers an ideal platform for further development of new features. Another specific aspect in the architecture of ZEOBUILDER is the data structure with multiple reference frames in which molecules and molecular building blocks are placed and which are hierarchically ordered. The main properties of ZEOBUILDER are the feasibility for constructing complex structures, extensibility, and transferability. The application field of ZEOBUILDER is not limited to zeolite science but easily extended to the construction of other complex (bio)molecular systems. ZEOBUILDER is a unique user-friendly GUI toolkit with advanced plug-ins allowing the construction of the most complex molecular structures, which can be used as input for all ab initio and molecular mechanics program packages.     

Automated Synthesis of Arabinoxylan‐Oligosaccharides Enables Characterization of Antibodies that Recognize Plant Cell Wall Glycans

Monoclonal antibodies that recognize plant cell wall glycans are used for high‐resolution imaging, providing important information about the structure and function of cell wall polysaccharides. To characterize the binding epitopes of these powerful molecular probes a library of eleven plant arabinoxylan oligosaccharides was produced by automated solid‐phase synthesis. Modular assembly of oligoarabinoxylans from few building blocks was enabled by adding (2‐naphthyl)methyl (Nap) to the toolbox of orthogonal protecting groups for solid‐phase synthesis. Conjugation‐ready oligosaccharides were obtained and the binding specificities of xylan‐directed antibodies were determined on microarrays.     

Automated solid-phase synthesis of protected oligosaccharides containing beta-mannosidic linkages

For automated oligosaccharide synthesis to impact glycobiology, synthetic access to most carbohydrates has to become efficient and routine. Methods to install "difficult" glycosidic linkages have to be established and incorporated into the overall synthetic concept. Described here is the first automated solid-phase synthesis of oligosaccharides containing the challenging beta-mannosidic linkage. Carboxybenzyl mannoside building blocks proved effective beta-mannosylation agents and resulted in excellent conversion and good to moderate selectivities. [(Triisopropylsilyl)oxy]-methyl ether (Tom), served as an orthogonal, minimally intrusive, and readily cleavable protecting group for the elongation of the C3 position of mannose. The desired oligosaccharide products were readily separated from by-products containing unwanted stereoisomers using reverse-phase HPLC. The methods described here expand the scope of carbohydrates currently accessible by automation as many oligosaccharides of biological interest contain beta-mannosidic linkages.     

Recent Progress in Enzymatic Synthesis of Sugar Nucleotides

Glycosylation is one of the most important reactions in nature as it results in the formation of glycoconjugates with diverse biological functions. Sugar nucleotides serve as the natural donor molecules for the biosynthesis of such glycoconjugates and other carbohydrates. Furthermore, these donor molecules are also indispensable building blocks for the enzymatic synthesis of carbohydrates in vitro using Leloir-type glycosyltransferases. Given such importance, the biosynthetic pathways of sugar nucleotides have been exploited, enabling the development of both chemical and enzymatic approaches to produce these molecules. A survey of recent progress in enzymatic synthesis of common mammalian sugar nucleotides as well as their derivatives is thus presented. As a popular strategy, conjugation of sugar nucleotide synthesis with glycosyltransfer reactions and in vivo production of sugar nucleotides are also included.     

Merging organic and polymer chemistries to create glycomaterials for glycomics applications

[Image: see text] Oligosaccharides at cell surfaces are known to play a critical role in many biological processes such as biorecognition, interactions between cells and with artificial surfaces, immune response, infection and inflammation. In order to facilitate studies of the role of sugars, an increasing number of novel tools are becoming available. New synthetic strategies now provide much more efficient access to complex carbohydrates or glycoconjugates. Branched carbohydrates and hybrids of carbohydrates conjugated to polymers have been prepared using solution and/or solid-phase synthesis and advanced methods of polymerization. These materials are essential for the development of methodologies to study and map the molecular structure-function relationship at interfaces. This article highlights recent advances in the synthesis of carbohydrates and polymer hybrids mimicking the properties and functionalities of the natural oligosaccharides, as well as selected applications in biology, biotechnology and diagnostics.     

Recent advances in the preparation of glycopolymer bioconjugates

The significant progress made in understanding the role of carbohydrates and carbohydrates based therapeutics at molecular level has highlighted the importance of carbohydrate bioconjugates in the field of biology, chemistry and therapeutics. The glycosylation of biomolecules is a nature-inspired approach, to impart structural and functional properties to the biomolecules. The availability of facile techniques to synthesize well-defined glycopolymers of varying molecular weights, compositions and shape and their facile conjugation with biomolecules of interest have helped researchers in understanding many aspects of their biological functions at the molecular level. This review focuses on the development of glycopolymer-bioconjugates and provides a comprehensive overview of the present bioconjugation tools for their synthesis. The glycosylation of biomolecules is achieved by either pre or post-polymerization modification approaches. The review highlights the potential of living radical polymerization for the facile synthesis of glycopolymer bioconjugates using both pre and post-polymerization bioconjugation approaches, and without disrupting the native structure and functions of the biological molecules. Non-covalent carbohydrate–carbohydrate and carbohydrate–protein interactions play a significant role in many biological and pathological events. The non-covalent interactions of synthetic glycopolymers with biomolecules are also discussed in this review.