What is a glycosidic bond and what does it connect?

A glycosidic bond, also known as a glycosidic linkage, is a type of ether bond that connects a carbohydrate (sugar) molecule to another group. This other group can either be another carbohydrate or a non-carbohydrate molecule.

What chemical groups are involved in the formation of a glycosidic bond?

A glycosidic bond is typically formed between the hemiacetal or hemiketal group of a saccharide (or a derivative of a saccharide) and the hydroxyl group of another compound, such as an alcohol.

A glycoside is a substance that contains a glycosidic bond. In the context of naturally occurring glycosides, the carbohydrate portion is often referred to as the 'glycone', and the non-carbohydrate portion is called the 'aglycone'.

How has the definition of 'glycoside' been extended beyond traditional glycosidic bonds?

The term 'glycoside' has been extended to include compounds where the hemiacetal or hemiketal groups of sugars form bonds with chemical groups other than hydroxyls. These include sulfur (thioglycosides), selenium (selenoglycosides), nitrogen (N-glycosides), and carbon (C-glycosides).

What are the four main types of glycosidic bonds based on the atom linking the sugar?

The four main types of glycosidic bonds are O-glycosidic bonds (linking through oxygen), S-glycosidic bonds (linking through sulfur), N-glycosidic bonds (linking through nitrogen), and C-glycosidic bonds (linking through carbon).

What are thioglycosides and glycosylamines?

Thioglycosides are compounds that contain an S-glycosidic bond, where a sulfur atom replaces the oxygen atom in a typical glycosidic bond. Glycosylamines are substances that contain an N-glycosidic bond, where a nitrogen atom replaces the glycosidic oxygen.

What is IUPAC's position on the term 'C-glycoside'?

The term 'C-glycoside' is considered a misnomer by IUPAC and is generally discouraged. C-glycosyl bonds involve a direct carbon-to-carbon linkage between the sugar and the aglycone.

How do the different types of modified glycosidic bonds (S, N, C) compare in terms of hydrolysis resistance?

Modified glycosidic bonds exhibit varying susceptibility to hydrolysis. Specifically, C-glycosyl structures are typically more resistant to hydrolysis compared to O-, S-, or N-glycosidic bonds.

How are alpha (α) and beta (β) glycosidic bonds distinguished?

Alpha (α) and beta (β) glycosidic bonds are distinguished by the relative stereochemistry at the anomeric position of the saccharide. This distinction is particularly relevant when the anomeric center is involved in the glycosidic bond, as is common in naturally occurring compounds.

What is glucuronidation and why is it used pharmacologically?

Glucuronidation is a process where substances are joined to glucuronic acid via glycosidic bonds. Pharmacologists use this process to increase the water solubility of various substances, aiding in their administration or excretion.

What chemical approach did Nüchter et al. develop for Fischer glycosidation?

Nüchter et al. developed a new approach to Fischer glycosidation using a microwave oven equipped with a refluxing apparatus and pressure bombs. This method allowed for the synthesis of alkyl glycosides.

What were the results and scalability of Nüchter et al.'s microwave-assisted Fischer glycosidation?

Nüchter et al. achieved a 100% yield of α- and β-D-glucosides using their microwave-assisted method. Importantly, this technique can be performed on a multi-kilogram scale, indicating its potential for larger-scale synthesis.

What are the advantages of Joshi et al.'s modified Koenigs-Knorr method?

The advantages of Joshi et al.'s method include the use of less expensive and less toxic lithium carbonate, the ability to perform the reaction at room temperature, good stereoselectivity, and yields that compare favorably to the conventional Koenigs-Knorr method.

What are glycoside hydrolases and what is their function?

Glycoside hydrolases, also known as glycosidases, are enzymes that catalyze the breakdown (hydrolysis) of glycosidic bonds. They play a crucial role in the metabolism of carbohydrates.

How specific are glycoside hydrolases regarding glycosidic bonds?

Glycoside hydrolases typically exhibit specificity, meaning they can act on either α-glycosidic bonds or β-glycosidic bonds, but generally not both. This specificity is valuable for researchers aiming to produce specific glycosides.

What role do sugar nucleotides play in biosynthesis?

Before monosaccharides are incorporated into larger molecules like glycoproteins or polysaccharides, they are often 'activated' by being joined via a glycosidic bond to the phosphate group of a nucleotide. These activated intermediates are called sugar nucleotides or sugar donors.

What are glycosyltransferases and what is their function?

Glycosyltransferases are enzymes that transfer a sugar unit from an activated sugar donor (like a sugar nucleotide) to an acceptor substrate, which is typically a nucleophile. This process is fundamental in the biosynthesis of complex carbohydrates.

What biocatalytic approaches are commonly used for glycoside synthesis?

The most common biocatalytic approaches for synthesizing glycosides involve using either glycosyltransferases or glycoside hydrolases. However, glycosyltransferases often require expensive materials, and glycoside hydrolases can sometimes yield low amounts of product.

What did De Winter et al. investigate regarding cellobiose phosphorylase (CP)?

De Winter et al. investigated the use of cellobiose phosphorylase (CP) for the synthesis of alpha-glycosides in ionic liquids. They found that the best conditions for using CP involved the ionic liquid AMMOENG 101 and ethyl acetate.

What challenges exist in achieving selectivity in glycosylation reactions?

Achieving selectivity, particularly for α- and β-glycosidic bonds, can be challenging due to the highly substrate-specific nature of the reactions and the overall activity of the pyranoside. Synthetic strategies often need to consider the transition states involved.

How do fluorine-directed glycosylations aid in selectivity?

Fluorine-directed glycosylations provide a useful method for achieving β-selectivity and introducing non-natural functionalities. The presence of fluorine can influence the stereochemical outcome of the reaction, often through effects like the gauche effect, promoting β-stereoselectivity.

What pharmaceutical potential have O-linked glycopeptides shown?

O-linked glycopeptides have demonstrated excellent central nervous system (CNS) permeability and efficacy in animal models of disease. Additionally, O-glycosylation can extend the half-life, decrease clearance, and improve the pharmacokinetic/pharmacodynamic properties of peptides.

What is the proposed mechanism for the CNS penetration of O-linked glycopeptides?

The CNS penetration of O-linked glycopeptides is thought to involve a process called 'membrane hopping' or 'hop diffusion'. This mechanism, which is not driven by Brownian motion, is believed to occur due to discontinuities in the plasma membrane and combines free diffusion with inter-compartmental transitions.

How are N-glycosidic bonds formed in DNA molecules?

In DNA, N-glycosidic bonds are formed when nitrogen atoms from the amino groups of nucleobases become covalently linked to the anomeric carbon of the deoxyribose sugar structure.

What are the consequences of nucleobase modifications in DNA related to N-glycosidic bonds?

Modifications such as deamination, alkylation, or oxidation of nucleobases attached to the deoxyribose sugar can lead to cytotoxic lesions along the DNA backbone. These lesions threaten the DNA's cohesiveness and can contribute to diseases like cancer.

What is the role of DNA glycosylases in repairing damaged DNA?

DNA glycosylases are enzymes that catalyze the hydrolysis of the N-glycosidic bond in damaged or modified nucleobases. By cleaving this bond, they free the damaged base from the DNA, initiating the base excision repair (BER) pathway.

What are the two proposed mechanisms by which monofunctional glycosylases cleave N-glycosidic bonds?

Monofunctional glycosylases can cleave N-glycosidic bonds via either a stepwise, S N 1-like mechanism, where the nucleobase leaves before water attacks, or a concerted, S N 2-like mechanism, where water attacks the anomeric carbon as the nucleobase leaves.

How do the mechanisms of N-glycosidic bond cleavage differ between ribonucleotides and deoxyribonucleotides?

Most deoxyribonucleotides are hydrolyzed via the stepwise S N 1-like mechanism, which involves an oxacarbenium ion intermediate. In contrast, most ribonucleotides are hydrolyzed through the concerted S N 2-like mechanism.

Are the reactions catalyzed by DNA glycosylases reversible?

No, the reactions catalyzed by DNA glycosylases to cleave the N-glycosidic bond are practically irreversible. This is significant because the cleavage can lead to detrimental mutagenic and cytotoxic effects if not properly repaired.

What is the significance of the anomeric effect in glycosidic bond formation?

The anomeric effect can influence the stereochemistry of glycosidic bond formation, often favoring the formation of the alpha (α) glycosidic bond, as seen in the example of ethyl glucoside formation.

What is the 'glycone' and the 'aglycone' in the context of glycosides?

In naturally occurring glycosides, the 'glycone' refers to the carbohydrate residue itself, while the 'aglycone' is the non-carbohydrate compound (often an alcohol or other organic molecule) from which the carbohydrate residue has been removed.

What is the primary function of glycosyltransferases in biological systems?

Glycosyltransferases are crucial enzymes that build complex carbohydrates by transferring sugar units from activated donors (like nucleotide sugars) to acceptor molecules, forming glycosidic bonds in the process.

What is the 'hop diffusion' process related to O-linked glycopeptides?

Hop diffusion is a proposed mechanism for how O-linked glycopeptides cross the blood-brain barrier. It involves a combination of free diffusion and movement between cellular compartments, facilitated by discontinuities in the cell membrane, rather than continuous Brownian motion.

What is the difference between a glycosidic bond and a C-glycosidic bond?

A standard glycosidic bond typically involves an oxygen, sulfur, or nitrogen atom linking a carbohydrate to another group. A C-glycosidic bond, however, involves a direct carbon-to-carbon linkage between the carbohydrate and the other group, making it more resistant to hydrolysis.

What is the role of the anomeric carbon in forming a glycosidic bond?

The anomeric carbon, which is the carbon atom in a sugar molecule that was part of the carbonyl group (aldehyde or ketone) in the open-chain form, is typically involved in the formation of the glycosidic bond.

What are some examples of sugar nucleotides used as activated donors in glycosylation?

Examples of sugar nucleotides that serve as activated donors in glycosylation include uridine diphosphate (UDP), guanosine diphosphate (GDP), thymidine diphosphate (TDP), and cytidine monophosphate (CMP).

How does the Felkin-Ahn model relate to directed glycosylations?

The Felkin-Ahn-Eisenstein models are incorporated into the rational chemical design of directed glycosylations. Recognizing and applying these models can help predict and control the stereochemical outcomes of glycosylation reactions, particularly by considering conformational control in the transition state.

What is the significance of O-glycosylation in mammalian metabolism?

O-glycosylation is significant in mammalian metabolism because mammalian enzymes are not typically evolved to degrade O-glycosylated products on larger molecules. This contributes to the evolutionary advantage of sugars as solubilizing moieties, as seen in Phase II metabolism.

What is the base excision repair (BER) pathway, and how is it initiated in relation to N-glycosidic bonds in DNA?

The base excision repair (BER) pathway is a cellular mechanism for repairing damaged DNA. It is initiated when enzymes called DNA glycosylases cleave the N-glycosidic bond of a damaged or modified nucleobase, freeing it from the DNA backbone.

What is the difference between an O-glycosidic bond and an S-glycosidic bond?

An O-glycosidic bond involves an oxygen atom linking the carbohydrate to another group, which is the most common type. An S-glycosidic bond, found in thioglycosides, replaces this oxygen atom with a sulfur atom.

What is the purpose of protecting the hydroxyl groups of D-glucose in Joshi et al.'s method?

In Joshi et al.'s method, the hydroxyl groups of D-glucose are protected by forming a peracetate. This protection step is part of the process to prepare the sugar for subsequent reactions, preventing unwanted side reactions at these hydroxyl groups before the glycosidic bond is formed.

What is the 'anomeric effect' and how does it relate to the formation of ethyl glucoside?

The anomeric effect is a stereoelectronic effect that can influence the stability of different anomers. In the formation of ethyl glucoside from glucose and ethanol, the anomeric effect often favors the formation of the alpha (α) glycosidic bond, as depicted in the provided diagram.

What are some examples of N-glycosidic bonds found in biological molecules?

N-glycosidic bonds are crucial in biological molecules, notably forming the link between the nitrogen atom of a nucleobase (like adenine) and the anomeric carbon of the ribose sugar in RNA and DNA. Adenosine, a component of RNA, is an example of a molecule formed via an N-glycosidic bond.

What is the significance of the gauche effect in fluorine-directed glycosylations?

The gauche effect, influenced by the presence of fluorine, can promote β-stereoselectivity in certain glycosylation reactions. This effect helps control the orientation of the incoming nucleophile relative to the anomeric center, leading to a preference for the β-glycosidic bond.

What are the potential health implications if N-glycosidic bonds in DNA are not repaired?

If the N-glycosidic bonds in DNA are cleaved and the resulting damage is not repaired, it can lead to detrimental mutagenic and cytotoxic responses within an organism. This can compromise the integrity of the DNA molecule and potentially lead to diseases like cancer.

What is the difference between a glycoside and a glycosylamine?

A glycoside typically refers to a compound with an O-glycosidic bond, linking a sugar to another group via oxygen. A glycosylamine is a specific type of glycoside where the linkage is an N-glycosidic bond, involving a nitrogen atom instead of oxygen.

How can glycosylation be used to improve the properties of peptides for pharmaceutical applications?

Glycosylation of peptides, particularly through O-linked glycopeptides, can enhance their properties for pharmaceutical use. It can improve their ability to cross the blood-brain barrier, extend their half-life in the body, reduce their clearance rate, and generally improve their pharmacokinetic and pharmacodynamic profiles.

Glycosidic Bond Wiki: The Molecular Nexus: Understanding Glycosidic Bonds

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What is a Glycosidic Bond?

A Fundamental Linkage

A glycosidic bond, also known as a glycosidic linkage, is a type of ether bond that covalently joins a carbohydrate molecule (a sugar) to another group. This other group may or may not be another carbohydrate.

Formation Mechanism

This bond is formed between the hemiacetal or hemiketal group of a saccharide (or a derivative) and the hydroxyl group of another compound, such as an alcohol. The resulting compound containing a glycosidic bond is termed a glycoside.

Expanding the Definition

The term 'glycoside' has evolved to include compounds where bonds are formed between the hemiacetal or hemiketal groups of sugars and various chemical groups beyond hydroxyls. This includes linkages involving sulfur (-SR, thioglycosides), selenium (-SeR, selenoglycosides), and nitrogen (-NR¹R², N-glycosides). While C-glycosyl bonds, where oxygen is replaced by carbon, exist, the term 'C-glycoside' is considered a misnomer by IUPAC and is generally discouraged.

Types of Glycosidic Bonds

O-Glycosidic Bonds

These are the most common type of glycosidic bonds, characterized by the presence of a glycosidic oxygen atom linking the saccharide to the aglycone or another sugar residue. They are fundamental in forming disaccharides, polysaccharides, and many natural products.

S-Glycosidic Bonds

In thioglycosides, the oxygen atom of the glycosidic bond is replaced by a sulfur atom. These bonds exhibit different susceptibility to hydrolysis compared to their O-glycosidic counterparts.

N-Glycosidic Bonds

Here, the glycosidic bond involves a nitrogen atom, forming glycosylamines. These are critically important in biological systems, notably forming the linkage between the sugar (ribose or deoxyribose) and the nitrogenous base in nucleic acids like DNA and RNA.

C-Glycosidic Bonds

In C-glycosyl structures, the glycosidic oxygen is replaced by a carbon atom. These bonds are generally more resistant to hydrolysis than O- or N-glycosidic bonds, making them stable structural motifs.

Bond Formation & Structure

Aglycone and Glycone

In naturally occurring glycosides, the compound from which the carbohydrate residue is removed is often referred to as the aglycone. The carbohydrate portion itself is sometimes called the 'glycone'. This terminology helps in describing the structure and origin of complex glycosidic compounds.

Alpha (α) and Beta (β) Distinction

When a glycosidic bond involves an anomeric center (common in natural glycosides), it can be classified as either α- or β-glycosidic. This distinction is based on the relative stereochemistry between the anomeric position (C1) and the stereocenter furthest from C1 in the saccharide ring. This stereochemistry is crucial for the biological function and recognition of the molecule.

The α- and β- designation refers to the orientation of the bond at the anomeric carbon (C1) relative to the CH₂OH group at the highest numbered chiral center. In a pyranose ring, if the C1 substituent is on the opposite side of the ring from the CH₂OH group, it's α; if it's on the same side, it's β.

For example, in a β-1,6 linkage shown in diagrams, the bond connecting the two sugar units is oriented upwards (beta configuration), and the linkage occurs between carbon 1 of one sugar and carbon 6 of the other.

Chemical Approaches

Fischer Glycosidation & Microwave Synthesis

An updated approach to Fischer glycosidation, utilizing microwave irradiation with refluxing apparatus in sealed reactors, has demonstrated the ability to achieve 100% yield of α- and β-D-glucosides. This method is scalable to multi-kilogram quantities, offering an efficient route for synthesizing alkyl glycosides.

Koenigs-Knorr Reaction Variants

The classic Koenigs-Knorr reaction, traditionally using expensive and toxic silver or mercury salts, has seen modifications. One notable method employs lithium carbonate, a more cost-effective and less toxic alternative, for the stereoselective synthesis of alkyl D-glucopyranosides. This approach involves protecting the glucose molecule, brominating it, and then reacting with an alcohol in the presence of lithium carbonate, followed by deprotection. This method can be performed at room temperature and yields high purity products.

Fluorine-Directed Glycosylation

Utilizing fluorine atoms can provide a handle for achieving specific β-selectivity and introducing non-natural functionalities. Methods employing fluorine-directed glycosylation, such as those involving fluoro oxonium ions and trichloroacetimidates, leverage the gauche effect to promote β-stereoselectivity. This approach offers reliable stereochemical control, particularly useful for synthesizing various β-glycosides.

Biological Significance

Pharmaceutical Applications

Glycosidic bonds play a vital role in drug development and delivery. For instance, attaching sugars via glycosidic bonds, a process known as glucuronidation, is a common strategy to increase the water solubility of drugs. This enhances their bioavailability and facilitates their metabolism and excretion. Many other glycosides possess significant physiological functions.

CNS Penetration and Half-Life Extension

O-linked glycopeptides have shown remarkable potential for crossing the blood-brain barrier (CNS penetration) and exhibiting efficacy in various disease models. Furthermore, glycosylation can significantly extend the half-life of peptides, reduce their clearance rates, and improve their pharmacokinetic and pharmacodynamic profiles. This is partly due to mammalian enzymes not being specifically evolved to degrade larger glycosylated molecules.

Synthesis Strategies

Chemical Synthesis

Various chemical methods exist to control the stereoselectivity of glycosidic bond formation, favoring either α or β configurations. These approaches often involve careful manipulation of protecting groups, activation strategies, and reaction conditions to achieve desired outcomes. The Felkin-Ahn-Eisenstein models are sometimes used to rationalize and predict stereochemical outcomes based on transition state conformations.

Enzymatic Synthesis

Biocatalytic approaches offer alternative routes for glycoside synthesis. Enzymes like glycosyltransferases and glycoside hydrolases (glycosidases) are employed. While glycosyltransferases typically require activated sugar donors (sugar nucleotides), glycoside hydrolases can be used in reverse reactions to form glycosidic bonds, though yields can sometimes be low. Cellobiose phosphorylase (CP) has also been investigated for the synthesis of α-glycosides in ionic liquids.

Enzymatic Roles

Glycoside Hydrolases (Glycosidases)

These enzymes are responsible for breaking glycosidic bonds. They typically exhibit high specificity, acting on either α- or β-glycosidic bonds, but not both. This specificity is valuable in research and synthesis for obtaining specific glycosides.

Glycosyltransferases

In living organisms, monosaccharide units are activated by joining them to nucleotide diphosphates (e.g., UDP, GDP) to form sugar nucleotides. These activated donors serve as substrates for glycosyltransferases, enzymes that transfer the sugar unit to an acceptor molecule, forming new glycosidic bonds. This is a fundamental process in the biosynthesis of complex carbohydrates like glycoproteins and polysaccharides.

Glycosidic Bonds in DNA

The N-Glycosidic Linkage

DNA molecules feature N-glycosidic bonds that link the nitrogenous bases to the anomeric carbon of the deoxyribose sugar ring. These bonds are essential for the structural integrity of DNA.

Repair Mechanisms

Damage to DNA, such as deamination, alkylation, or oxidation of nucleobases, can lead to cytotoxic lesions. Enzymes called DNA glycosylases play a critical role in DNA repair by catalyzing the hydrolysis of the N-glycosidic bond, releasing the damaged base and initiating the base excision repair (BER) pathway. This process is vital for maintaining genomic stability.

Reaction Mechanisms

The cleavage of the N-glycosidic bond by monofunctional glycosylases can occur via two primary mechanisms: a stepwise S_N1-like pathway or a concerted S_N2-like pathway. Both mechanisms involve the formation of an oxocarbenium ion intermediate and ultimately lead to the substitution of the N-glycosidic bond with an O-glycosidic bond or the release of the base. These reactions are generally irreversible and crucial for cellular health.

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The Molecular Nexus

💡 Dive in with Flashcard Learning! 💡

What is a Glycosidic Bond? 🔗

covalent A Fundamental Linkage

🧬 Formation Mechanism

🧪 Expanding the Definition

Types of Glycosidic Bonds 🗂️

💧 O-Glycosidic Bonds

⚡ S-Glycosidic Bonds

नाइट्रोजन N-Glycosidic Bonds

💎 C-Glycosidic Bonds

Bond Formation & Structure 📐

🔄 Aglycone and Glycone

📐 Alpha (α) and Beta (β) Distinction

Chemical Approaches 🔬

⚡ Fischer Glycosidation & Microwave Synthesis

💎 Koenigs-Knorr Reaction Variants

💡 Fluorine-Directed Glycosylation

Biological Significance 🌿

💊 Pharmaceutical Applications

🧠 CNS Penetration and Half-Life Extension

Synthesis Strategies 🛠️

🔬 Chemical Synthesis

🦠 Enzymatic Synthesis

Enzymatic Roles ⚙️

✂️ Glycoside Hydrolases (Glycosidases)

🏗️ Glycosyltransferases

Glycosidic Bonds in DNA 📜

🧬 The N-Glycosidic Linkage

🩹 Repair Mechanisms

➡️ Reaction Mechanisms

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📜 Important Notice

Dive in with Flashcard Learning!

What is a Glycosidic Bond?

A Fundamental Linkage

Formation Mechanism

Expanding the Definition

Types of Glycosidic Bonds

O-Glycosidic Bonds

S-Glycosidic Bonds

N-Glycosidic Bonds

C-Glycosidic Bonds

Bond Formation & Structure

Aglycone and Glycone

Alpha (α) and Beta (β) Distinction

Chemical Approaches

Fischer Glycosidation & Microwave Synthesis

Koenigs-Knorr Reaction Variants

Fluorine-Directed Glycosylation

Biological Significance

Pharmaceutical Applications

CNS Penetration and Half-Life Extension

Synthesis Strategies

Chemical Synthesis

Enzymatic Synthesis

Enzymatic Roles

Glycoside Hydrolases (Glycosidases)

Glycosyltransferases

Glycosidic Bonds in DNA

The N-Glycosidic Linkage

Repair Mechanisms

Reaction Mechanisms

Teacher's Corner

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Discover other topics to study!

References

Feedback & Support

Disclaimer

Important Notice