Glycosidic bond

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A glycosidic bond or glycosidic linkage is a type of ether bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate.

Contents

Formation of ethyl glucoside: Glucose and ethanol combine to form ethyl glucoside and water. The reaction often favors formation of the a-glycosidic bond as shown due to the anomeric effect. Ethyl-glucoside.png
Formation of ethyl glucoside: Glucose and ethanol combine to form ethyl glucoside and water. The reaction often favors formation of the α-glycosidic bond as shown due to the anomeric effect.

A glycosidic bond is formed between the hemiacetal or hemiketal group of a saccharide (or a molecule derived from a saccharide) and the hydroxyl group of some compound such as an alcohol. A substance containing a glycosidic bond is a glycoside.

The term 'glycoside' is now extended to also cover compounds with bonds formed between hemiacetal (or hemiketal) groups of sugars and several chemical groups other than hydroxyls, such as -SR (thioglycosides), -SeR (selenoglycosides), -NR1R2 (N-glycosides), or even -CR1R2R3 (C-glycosides).

Particularly in naturally occurring glycosides, the compound ROH from which the carbohydrate residue has been removed is often termed the aglycone, and the carbohydrate residue itself is sometimes referred to as the 'glycone'.

S-, N-, C-, and O-glycosidic bonds

Adenosine, a component of RNA, results from the sugar ribose and adenine via the formation of an N-glycosidic bond (shown as the vertical line between the N and the sugar cycle) Adenosin.svg
Adenosine, a component of RNA, results from the sugar ribose and adenine via the formation of an N-glycosidic bond (shown as the vertical line between the N and the sugar cycle)

Glycosidic bonds of the form discussed above are known as O-glycosidic bonds, in reference to the glycosidic oxygen that links the glycoside to the aglycone or reducing end sugar. In analogy, one also considers S-glycosidic bonds (which form thioglycosides), where the oxygen of the glycosidic bond is replaced with a sulfur atom. In the same way, N-glycosidic bonds, have the glycosidic bond oxygen replaced with nitrogen. Substances containing N-glycosidic bonds are also known as glycosylamines. C-glycosyl bonds have the glycosidic oxygen replaced by a carbon; the term "C-glycoside" is considered a misnomer by IUPAC and is discouraged. [1] All of these modified glycosidic bonds have different susceptibility to hydrolysis, and in the case of C-glycosyl structures, they are typically more resistant to hydrolysis.

Numbering, and α/β distinction of glycosidic bonds

A b-1,6 glucan molecule showing how carbons are numbered. The terminal saccharide is linked via a b-1,6 glycosidic bond. The remaining linkages are all b-1,3. Beta-1,6-linkage.svg
A β-1,6 glucan molecule showing how carbons are numbered. The terminal saccharide is linked via a β-1,6 glycosidic bond. The remaining linkages are all β-1,3.

When an anomeric center is involved in a glycosidic bond (as is common in nature) then one can distinguish between α- and β-glycosidic bonds by the relative stereochemistry of the anomeric position and the stereocenter furthest from C1 in the saccharide. [2]

Pharmacologists often join substances to glucuronic acid via glycosidic bonds in order to increase their water solubility; this is known as glucuronidation. Many other glycosides have important physiological functions.

Chemical approaches

Nüchter et al. (2001) have shown a new approach to Fischer glycosidation. [3] [4] [5] Employing a microwave oven equipped with refluxing apparatus in a rotor reactor with pressure bombs, Nüchter et al. (2001) were able to achieve 100% yield of α- and β-D-glucosides. This method can be performed on a multi-kilogram scale.

Vishal Y Joshi's method

Joshi et al. (2006) [6] propose the Koenigs-Knorr reaction in the stereoselective synthesis of alkyl D-glucopyranosides via glycosylation, with the exception of using lithium carbonate which is less expensive and toxic than the conventional method of using silver or mercury salts. D-glucose is first protected by forming the peracetate by addition of acetic anhydride in acetic acid, and then addition of hydrogen bromide which brominates at the 5-position. On addition of the alcohol ROH and lithium carbonate, the OR replaces the bromine and on deprotecting the acetylated hydroxyls the product is synthesized in relatively high purity. It was suggested by Joshi et al. (2001) that lithium acts as the nucleophile that attacks the carbon at the 5-position and through a transition state the alcohol is substituted for the bromine group. Advantages of this method as well as its stereoselectivity and low cost of the lithium salt include that it can be done at room temperature and its yield compares relatively well with the conventional Koenigs-Knorr method. [7]

Vishal Joshi.png

Glycoside hydrolases

Glycoside hydrolases (or glycosidases), are enzymes that break glycosidic bonds. Glycoside hydrolases typically can act either on α- or on β-glycosidic bonds, but not on both. This specificity allows researchers to obtain glycosides in high epimeric excess, one example being Wen-Ya Lu's conversion of D-Glucose to Ethyl β-D-glucopyranoside using naturally-derived glucosidase. It is worth noting that Wen-Ya Lu utilized glucosidase in a reverse manner opposite to the enzyme's biological functionality: [8]

Lu, Wen-Ya et al. Practical methods for Biocatalysis and Biotransformations. 2010, 236-239. Glucosidase-catalyzed glycosidation of D-Glucose to Ethyl b-D-glucopyranoside.png
Lu, Wen-Ya et al. Practical methods for Biocatalysis and Biotransformations. 2010, 236–239.

Glycosyltransferases

Before monosaccharide units are incorporated into glycoproteins, polysaccharides, or lipids in living organisms, they are typically first "activated" by being joined via a glycosidic bond to the phosphate group of a nucleotide such as uridine diphosphate (UDP), guanosine diphosphate (GDP), thymidine diphosphate (TDP), or cytidine monophosphate (CMP). These activated biochemical intermediates are known as sugar nucleotides or sugar donors. Many biosynthetic pathways use mono- or oligosaccharides activated by a diphosphate linkage to lipids, such as dolichol. These activated donors are then substrates for enzymes known as glycosyltransferases, which transfer the sugar unit from the activated donor to an accepting nucleophile (the acceptor substrate).

Fluorine.Directed.Glycosylation.tif

Disaccharide phosphorylases

Different biocatalytic approaches have been developed toward the synthesis of glycosides in the past decades, which using "glycosyltransferases" and "glycoside hydrolases" are among the most common catalysis. The former often needs expensive materials and the later often shows low yields, De Winter et al. [10] investigated use of cellobiose phosphorylase (CP) toward synthesis of alpha-glycosides in ionic liquids. The best condition for use of CP was found to be in the presence of IL AMMOENG 101 and ethyl acetate.

Directed glycosylations

Multiple chemical approaches exist to encourage selectivity of α- and β-glycosidic bonds. The highly substrate specific nature of the selectivity and the overall activity of the pyranoside can provide major synthetic difficulties. The overall specificity of the glycosylation can be improved by utilizing approaches which take into account the relative transition states that the anomeric carbon can undergo during a typical glycosylation. Most notably, recognition and incorporation of Felkin-Ahn-Eisenstein models into rationale chemical design can generally provide reliable results provided the transformation can undergo this type of conformational control in the transition state.

Fluorine directed glycosylations represent an encouraging handle for both B selectivity and introduction of a non-natural biomimetic C2 functionality on the carbohydrate. One innovative example provided by Bucher et al. provides a way to utilize a fluoro oxonium ion and the trichloroacetimidate to encourage B stereoselectivity through the gauche effect. [11] This reasonable stereoselectivity is clear through visualization of the Felkin-Ahn models of the possible chair forms.

This method represents an encouraging way to selectivity incorporate B-ethyl, isopropyl and other glycosides with typical trichloroacetimidate chemistry.

Control of Oxonium ion - Felkin-Ahn stereoselectivity Control of Oxonium ion - Felkin-Ahn stereoselectivity .png
Control of Oxonium ion – Felkin-Ahn stereoselectivity

O-linked glycopeptides; pharmaceutical uses of O-glycosylated peptides

Control of oxonium ion - Felkin-Ahn stereoselectivity chair forms Control of Oxonium ion - Felkin-Ahn stereoselectivity2.png
Control of oxonium ion – Felkin-Ahn stereoselectivity chair forms

O-linked glycopeptides recently have been shown to exhibit excellent CNS permeability and efficacy in multiple animal models with disease states. In addition one of the most intriguing aspects thereof is the capability of O-glycosylation to extend half life, decrease clearance, and improve PK/PD thereof the active peptide beyond increasing CNS penetration. The innate utilization of sugars as solubilizing moieties in Phase II and III metabolism (glucuronic acids) has remarkably allowed an evolutionary advantage in that mammalian enzymes are not directly evolved to degrade O glycosylated products on larger moieties.

The peculiar nature of O-linked glycopeptides is that there are numerous examples which are CNS penetrant. The fundamental basis of this effect is thought to involve "membrane hopping" or "hop diffusion". The non-brownian motion driven "hop diffusion" process is thought to occur due to discontinuity of the plasma membrane. "Hop diffusion" notably combines free diffusion and intercomparmental transitions. Recent examples notably include high permeability of met-enkephalin analogs amongst other peptides. The full mOR agonist pentapeptide DAMGO is also CNS penetrant upon introduction of glycosylation. [12] [13] [14]

N-Glycosidic bonds in DNA

DNA molecules contain 5-membered carbon rings called riboses that are directly attached to two phosphate groups and a nucleobase that contains amino groups. The nitrogen atoms from the amino group in the nucleotides are covalently linked to the anomeric carbon of the ribose sugar structure through an N-glycosidic bond. Occasionally, the nucleobases attached to the ribose undergo deamination, alkylation, or oxidation which results in cytotoxic lesions along the DNA backbone. These modifications severely threaten the cohesiveness of the DNA molecule, leading to the development of diseases such as cancer. DNA glycosylases are enzymes that catalyze the hydrolysis the N-glycosidic bond to free the damaged or modified nucleobase from the DNA, by cleaving the carbon-nitrogen glycosidic bond at the 2' carbon, subsequently initiating the base excision repair (BER) pathway.

Monofunctional glycosylases catalyze the hydrolysis of the N-glycosidic bond via either a stepwise, SN1 like mechanism, or a concerted, SN2 like mechanism. The stepwise function, the nucleobase acts as a leaving group before the anomeric carbon gets attacked by the water molecule, producing a short-lived unstable oxacarbenium ion intermediate. This intermediate rapidly reacts with the nearby water molecule to substitute the N-glycosidic bond of the ribose and the nucleobase with an O-glycosidic bond with a hydroxy group. The concerted mechanism, the water acts as a nucleophile and attacks at the anomeric carbon before the nucelobase gets to act like a leaving group. The intermediate produced is a similar oxacarbenium ion where both the hydroxy groups and the nucleobase are still attached to the anomeric carbon. Both mechanisms theoretically yield the same product. Most ribonucleotides are hydrolyzed via the concerted SN2 like mechanism, while most deoxyribonucleotides proceed through the stepwise like mechanism.

These reactions are practically irreversible. Due to the fact that the cleavage of the N-glycosidic bond from the DNA backbone can lead to detrimental mutagenic and cytotoxic responses in an organism, have the ability to also catalyze the synthesis of N-glycosidic bonds by way of an abasic DNA site and a specific nucleobase. [15]

Related Research Articles

<span class="mw-page-title-main">Carbohydrate</span> Organic compound that consists only of carbon, hydrogen, and oxygen

A carbohydrate is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms, usually with a hydrogen–oxygen atom ratio of 2:1 and thus with the empirical formula Cm(H2O)n, which does not mean the H has covalent bonds with O. However, not all carbohydrates conform to this precise stoichiometric definition, nor are all chemicals that do conform to this definition automatically classified as carbohydrates.

<span class="mw-page-title-main">Disaccharide</span> Complex sugar

A disaccharide is the sugar formed when two monosaccharides are joined by glycosidic linkage. Like monosaccharides, disaccharides are simple sugars soluble in water. Three common examples are sucrose, lactose, and maltose.

Hydrolysis is any chemical reaction in which a molecule of water breaks one or more chemical bonds. The term is used broadly for substitution, elimination, and solvation reactions in which water is the nucleophile.

<span class="mw-page-title-main">Nucleotide</span> Biological molecules constituting nucleic acids

Nucleotides are organic molecules composed of a nitrogenous base, a pentose sugar and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth. Nucleotides are obtained in the diet and are also synthesized from common nutrients by the liver.

<span class="mw-page-title-main">Nucleoside</span> Any of several glycosylamines comprising a nucleobase and a sugar molecule

Nucleosides are glycosylamines that can be thought of as nucleotides without a phosphate group. A nucleoside consists simply of a nucleobase and a five-carbon sugar whereas a nucleotide is composed of a nucleobase, a five-carbon sugar, and one or more phosphate groups. In a nucleoside, the anomeric carbon is linked through a glycosidic bond to the N9 of a purine or the N1 of a pyrimidine. Nucleotides are the molecular building blocks of DNA and RNA.

<span class="mw-page-title-main">Maltose</span> Chemical compound

Maltose, also known as maltobiose or malt sugar, is a disaccharide formed from two units of glucose joined with an α(1→4) bond. In the isomer isomaltose, the two glucose molecules are joined with an α(1→6) bond. Maltose is the two-unit member of the amylose homologous series, the key structural motif of starch. When beta-amylase breaks down starch, it removes two glucose units at a time, producing maltose. An example of this reaction is found in germinating seeds, which is why it was named after malt. Unlike sucrose, it is a reducing sugar.

<span class="mw-page-title-main">Ribonucleotide</span> Nucleotide containing ribose as its pentose component

In biochemistry, a ribonucleotide is a nucleotide containing ribose as its pentose component. It is considered a molecular precursor of nucleic acids. Nucleotides are the basic building blocks of DNA and RNA. Ribonucleotides themselves are basic monomeric building blocks for RNA. Deoxyribonucleotides, formed by reducing ribonucleotides with the enzyme ribonucleotide reductase (RNR), are essential building blocks for DNA. There are several differences between DNA deoxyribonucleotides and RNA ribonucleotides. Successive nucleotides are linked together via phosphodiester bonds.

<span class="mw-page-title-main">Glycoside</span> Molecule in which a sugar is bound to another functional group

In chemistry, a glycoside is a molecule in which a sugar is bound to another functional group via a glycosidic bond. Glycosides play numerous important roles in living organisms. Many plants store chemicals in the form of inactive glycosides. These can be activated by enzyme hydrolysis, which causes the sugar part to be broken off, making the chemical available for use. Many such plant glycosides are used as medications. Several species of Heliconius butterfly are capable of incorporating these plant compounds as a form of chemical defense against predators. In animals and humans, poisons are often bound to sugar molecules as part of their elimination from the body.

<span class="mw-page-title-main">Amino sugar</span>

In organic chemistry, an amino sugar is a sugar molecule in which a hydroxyl group has been replaced with an amine group. More than 60 amino sugars are known, with one of the most abundant being N-Acetyl-D-glucosamine, which is the main component of chitin.

An Endoglycosidase is an enzyme that releases oligosaccharides from glycoproteins or glycolipids. It may also cleave polysaccharide chains between residues that are not the terminal residue, although releasing oligosaccharides from conjugated protein and lipid molecules is more common.

<span class="mw-page-title-main">Glycosyltransferase</span> Class of enzymes

Glycosyltransferases are enzymes that establish natural glycosidic linkages. They catalyze the transfer of saccharide moieties from an activated nucleotide sugar to a nucleophilic glycosyl acceptor molecule, the nucleophile of which can be oxygen- carbon-, nitrogen-, or sulfur-based.

<span class="mw-page-title-main">Glycoside hydrolase</span> Class of enzymes which break glycosidic bonds via hydrolysis

In biochemistry, glycoside hydrolases are a class of enzymes which catalyze the hydrolysis of glycosidic bonds in complex sugars. They are extremely common enzymes, with roles in nature including degradation of biomass such as cellulose (cellulase), hemicellulose, and starch (amylase), in anti-bacterial defense strategies, in pathogenesis mechanisms and in normal cellular function. Together with glycosyltransferases, glycosidases form the major catalytic machinery for the synthesis and breakage of glycosidic bonds.

<span class="mw-page-title-main">Tunicamycin</span> Chemical compound

Tunicamycin is a mixture of homologous nucleoside antibiotics that inhibits the UDP-HexNAc: polyprenol-P HexNAc-1-P family of enzymes. In eukaryotes, this includes the enzyme GlcNAc phosphotransferase (GPT), which catalyzes the transfer of N-acetylglucosamine-1-phosphate from UDP-N-acetylglucosamine to dolichol phosphate in the first step of glycoprotein synthesis. Tunicamycin blocks N-linked glycosylation (N-glycans) and treatment of cultured human cells with tunicamycin causes cell cycle arrest in G1 phase. It is used as an experimental tool in biology, e.g. to induce unfolded protein response. Tunicamycin is produced by several bacteria, including Streptomyces clavuligerus and Streptomyces lysosuperificus.

A chemical glycosylation reaction involves the coupling of a glycosyl donor, to a glycosyl acceptor forming a glycoside. If both the donor and acceptor are sugars, then the product is an oligosaccharide. The reaction requires activation with a suitable activating reagent. The reactions often result in a mixture of products due to the creation of a new stereogenic centre at the anomeric position of the glycosyl donor. The formation of a glycosidic linkage allows for the synthesis of complex polysaccharides which may play important roles in biological processes and pathogenesis and therefore having synthetic analogs of these molecules allows for further studies with respect to their biological importance.

Intramolecular aglycon delivery is a synthetic strategy for the construction of glycans. This approach is generally used for the formation of difficult glycosidic linkages.

The Crich β-mannosylation in organic chemistry is a synthetic strategy which is used in carbohydrate synthesis to generate a 1,2-cis-glycosidic bond. This type of linkate is generally very difficult to make, and specific methods like the Crich β-mannosylation are used to overcome these issues. The technique takes its name from its developer, Professor David Crich.

<span class="mw-page-title-main">Oxocarbenium</span>

An oxocarbeniumion is a chemical species characterized by a central sp2-hybridized carbon, an oxygen substituent, and an overall positive charge that is delocalized between the central carbon and oxygen atoms. An oxocarbenium ion is represented by two limiting resonance structures, one in the form of a carbenium ion with the positive charge on carbon and the other in the form of an oxonium species with the formal charge on oxygen. As a resonance hybrid, the true structure falls between the two. Compared to neutral carbonyl compounds like ketones or esters, the carbenium ion form is a larger contributor to the structure. They are common reactive intermediates in the hydrolysis of glycosidic bonds, and are a commonly used strategy for chemical glycosylation. These ions have since been proposed as reactive intermediates in a wide range of chemical transformations, and have been utilized in the total synthesis of several natural products. In addition, they commonly appear in mechanisms of enzyme-catalyzed biosynthesis and hydrolysis of carbohydrates in nature. Anthocyanins are natural flavylium dyes, which are stabilized oxocarbenium compounds. Anthocyanins are responsible for the colors of a wide variety of common flowers such as pansies and edible plants such as eggplant and blueberry.

Carbohydrate synthesis is a sub-field of organic chemistry concerned specifically with the generation of natural and unnatural carbohydrate structures. This can include the synthesis of monosaccharide residues or structures containing more than one monosaccharide, known as oligosaccharides.

<i>N</i>-linked glycosylation Attachment of an oligosaccharide to a nitrogen atom

N-linked glycosylation, is the attachment of an oligosaccharide, a carbohydrate consisting of several sugar molecules, sometimes also referred to as glycan, to a nitrogen atom, in a process called N-glycosylation, studied in biochemistry. The resulting protein is called an N-linked glycan, or simply an N-glycan.

<span class="mw-page-title-main">Ribose</span> Group of simple sugar and carbohydrate compounds

Ribose is a simple sugar and carbohydrate with molecular formula C5H10O5 and the linear-form composition H−(C=O)−(CHOH)4−H. The naturally-occurring form, d-ribose, is a component of the ribonucleotides from which RNA is built, and so this compound is necessary for coding, decoding, regulation and expression of genes. It has a structural analog, deoxyribose, which is a similarly essential component of DNA. l-ribose is an unnatural sugar that was first prepared by Emil Fischer and Oscar Piloty in 1891. It was not until 1909 that Phoebus Levene and Walter Jacobs recognised that d-ribose was a natural product, the enantiomer of Fischer and Piloty's product, and an essential component of nucleic acids. Fischer chose the name "ribose" as it is a partial rearrangement of the name of another sugar, arabinose, of which ribose is an epimer at the 2' carbon; both names also relate to gum arabic, from which arabinose was first isolated and from which they prepared l-ribose.

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