Department of Glycochemistry, Inst. Chem., Slovak Acad. Sci.

The Department of Glycochemistry, comprised of the

• Laboratory of Sugars and Glycomimics• Laboratory of Ionized Saccharides• Laboratory of Biocatalysis and Organic Synthesis

is devoted, from several points of view of its individual laboratories, to the research of carbohydrates that are a dominant part of renewable biomass.

Renewable biomass (200 billion ton/year)

carbohydrates (95%)

non-carbohydrates(5%; fats, proteins,terpenoids, etc.)

Carbohydrates (synonym saccharides) are a group of the most abundant natural organic compounds with at least three aliphatically linked carbon atoms. They are polyhydroxycarbonyl compounds, their simple derivatives and their oligomers and polymers, in which their monosaccharide units are bound with a glycosidic bond. They are divided between monosaccharides, oligosaccharides, polysaccharides and glycoconjugates (glycoproteins, glycolipids, etc.). Monosaccharides and oligosaccharides altogether are called sugars.

Carbohydrates are formed in the process of photosynthesis (yearly about 2 1011 ton). They are building material of plants (50 to 80% of dry matter) and basic compounds of the metabolism of animals. Some saccharides are being obtained from natural resources, the others are then prepared from them synthetically.

Utilization of carbohydrates is very broad. They are used as foods and their components, raw materials for production of textile fibres and other materials, substrates for distinct fermentation technologies, and are used for production of pharmaceuticals, vitamins and special chemicals.

Carbohydrates, in addition to their long-known roles in living matter, which are the structure building and energy storage functions, play in living organisms many other vital roles that the science starts to recognize only in last decades. Thanks to their structural diversity that several times exceeds the diversity of nucleic acids and proteins, the carbohydrates are responsible, inter alia, for recognition phenomena inside cells as well as on their surface, but also for cell specialization and with that associated tissue differentiation and development of individual organs of living organisms.

Genomics is studying all the nucleotide sequences and genes (hereditary codes) of individual organisms in their genomes. At the present time culminating sequencing of the genomes, i.e., gathering the information about the arrangement of the genes in the genomes, has revealed only a basis of the knowledge about living processes. The following, much more challenging stage of learning the normal, but also abnormal living processes causing diseases, in individual organisms is Proteomics, that is the identification, characterization and quantification of all proteins involved in a particular pathway, organelle, cell, tissue, organ or organism that can be studied in concert to provide accurate and comprehensive data about that organisms and their individual subsystems.

Since the formation and transformations of carbohydrates are the results of the action of enzymes, i.e., proteins with those specific catalytic properties, the knowledge about the structure and roles of carbohydrates in all the organic subsystems of individual organisms is a significant part of Proteomics that, at the present time, starts to be considered an autonomous science, and that is called Glycomics. Thus, the knowledge about the structure and roles of carbohydrates represents an inevitable diagnostics of normal, but also abnormal development of organisms and their subsystems and, at the same time, offers new approaches for design of drugs of new generation for treatment of various, often until now even incurable diseases.

Roles of cell-surface oligosaccharides in recognition processes. (a) Mutual interaction of cells by multiple bonding of their glycoprotein oligosaccharides with protein receptors of the other cell. Oligosaccharides of glycolipids (b) and glycoproteins (c) are recognized by antibodies. Adhesion and colonization by bacterial pathogens (d) on cells starts by recognizing surface oligosaccharides. (e) Similarly, pathogenic viruses before invasion into cells are docking on the surface oligosaccharides specific to each virus. (From K. J. Yarema, C. R. Bertozzi: Chemical approaches to glycobiology and emerging carbohydrate-based therapeutic agents. Current Opinion in Chemical Biology, 2 (1998) 4961.

Schematic representation of a cell wall of animal cells. From:

http://cellbio.utmb.edu/cellbio/membrane_intro.htm and Wolfe S.L.,

Molecular and Cellular Biology, Wadsworth Publishing Company, 1993., respectively.

Schematic illustration of carbohydrate-protein-based recognition interactions between cells and between a cell and an external agent. From: BioCarb AB katalóg.

Laboratory of Sugars and Glycomimics

Synthesis of rare sugars (monosaccharides and oligosaccharides) and glycomimics (close imitations of sugars) are the primary activities of the Laboratory. Objectives of the synthesis of rare sugars are to gather knowledge about their properties including their biological properties, in order to find their possible use in induction, diagnostic and therapeutic applications for some insufficiencies of the enzymes processing carbohydrates. On the other side, the purpose of the synthesis of glycomimics is their possible use as inhibitors of the enzymes processing unwanted transformations of carbohydrates, as inhibitors of unwanted recognition processes based on carbohydrates, and as immunity stimulating agents enhancing the resistance of organisms against pathogens by a preventive generation of antibodies yet before a clash of the organism with the pathogen.

For the purposes, these new chemical transformations and new methods of synthesis of these sugars and glycomimics have been recently accomplished in the Laboratory:

Laboratory of Sugars and Glycomimics (2)

• Synthesis of oligosaccharides, particularly of the linear and branch-chain xylanes, 4-O-methylglucuronoxylanes and arabinoxylanes as structural motifs of non-cellulosic polysaccharides, one of the dominant research topics at the Institute of Chemistry during the last 25 years. A unique collection of these model compounds prepared has contributed also a significant progress in modern spectral methods (NMR and IR spectroscopy and mass spectrometry), conformational studies, biochemical studies of the hemicelluloses degrading enzymes as well as in synthesis of precursors of glycoconjugates. The experience acquired from the oligosaccharide syntheses is now being exploited and further developed in synthesis of lipid A mimics and glycosyl transferases inhibitors.

• Synthesis of derivatives of alkyl(aryl) 2-thio-3-acetamido-β-D-sorbo-furanoside as potential inhibitors of glycosyl transferases (2004-2005).

• Synthesis and structural analysis of precursors of sacharide-amino acid conjugates of the mannojirimycin and nojirimycin type as potential antiviral and anticancer agents (1997-2005).

Laboratory of Sugars and Glycomimics (3)

• Extension of the sortiment of available chemical transformations of glycosylnitromethanes for synthesis of glycomimics synthesis of inhibitors of the carbohydrate-processing enzymes

OCH2OH

HO

OH

OH

CH2NO2

OCH2OH

HO

OH

OH

CH=O OCH2OH

HO

OH

OH

CH=NOH OCH2OH

HO

OH

OH

CH2NH2 OCH2OH

HO

OH

OH

CH(OMe)2 OCH2OH

HO

OH

OH

CH(SEt)2

ozonolysis(1992)

radicalreduction

(1999)

electron-transferreduction

(2003)

acid-catalysed alcoholysis

(2004)

acid-catalysed mercaptolysis

(2005)

new chemical reactions

Laboratory of Sugars and Glycomimics (4)

• Regiospecific synthesis of five-member rings of sugars development of new antituberculotics (cell walls of pathogenic mycobacteria are built of five-member-ring galactose and arabinose-containing polysaccharides). (2003)

• Synthesis of mimics of lipid A (lipodisaccharidic endotoxin) development of immunostimulating agents for a preventive enhancement of immunity zvýšenie imunity against a septic shock. Yet the first immunologic assays of the mimics are very promising. (2004-2005)

• Extension of the Bílik reaction to the synthesis of branch-chain sugars, i.e., hammamelose (2-C-hydroxymethyl-ribose) from fructose enlargement of the sortiment of available sugars. (1999)

• Preparation of a new and stable matrix for one step affinity-chromatographic isolation of the Pinus nigra lectin biological protection of Pinus nigra seedlings against pathogenic fungus Fusarium. (2001)

• Design of new methods of synthesis of aldoses and aminodeoxyaldoses by ozonolysis of pertinent nitroalditols enlargement of the sortiment of available sugars. (1992)

Laboratory of Ionized Saccharides

Research topics are the introduction of ion-exchanging groups into carbohydrates and investigation of the properties of such derivatives. Polysaccharides, cyclodextrines and sucrose are the substrates and the objectives are to study the influence of supramolecular structure, solvents and other factors on the reactivity of the carbohydrates. In order to evaluate their influence on reactivity, also saccharides containing ion-exchange groups are being used.

New derivatives of starch, hyaluronic and polygalacturonic acid, - and -cyclodextrin as well as sucrose were prepared. Integral part of the research program of the Laboratory is also the chemical modification of plant materials with the goal to prepare materials with ion-exchange properties. Part of the research program is also to learn about the effect of ions on thermal stability of these materials.

http://www.chem.sk/people/simkovicivan/

Laboratory of Biocatalysis and Organic Synthesis

Research in the Laboratory is built up on a profound experience of its members in heterocyclic chemistry, carbohydrate chemistry and utilization of enzymes in organic synthesis.

The Laboratory methodologies are:

• development of biocatalytic methods in organic synthesis • design of strategies to minimize the number of protection and

deprotection steps in carbohydrate chemistry• preparation of new analytical substrates assigned for search for new

types of enzymes in biomass• synthesis of modified saccharides for mechanistic studies of the

enzyme action• preparation of new, carbohydrate-based and biologically significant

compounds and materials applicable in food industry and medicine

Laboratory of Biocatalysis and Organic Synthesis (2)

At the present time, the research in the Laboratory is focused mainly on the derivatization studies of carbohydrates with natural phenolic compounds using enzymatic, chemoenzymatic or standard chemical approaches. Derivatized monosaccharides are polymerized via a radical oxidative reaction catalyzed by peroxidases or laccases, with the aim to obtain a new type of biodegradable polymers, so called linear semilignins. Chemoselectivity and stereoselectivity of the enzymatic oxidative reaction is being studied by analysis of dimeric products of the lignan and neolignan types using model, monofunctional saccharides. Methods of preparation of convenient substrates for detection and study of the substrate specificity and action mechanism of the feruloyl esterase have been developed recently and are being further evolved in the laboratory. Distinct regioselective chemical and chemoenzymatic methods of acylation of carbohydrates were also elaborated and are further developed. Research of glycosidases for stereoselective preparation of aromatic glycosides is being performed in the Laboratory as well.