High-throughput chemistry toward complex carbohydrates and carbohydrate-like compounds

In the area of peptide and nucleic acid chemistry and biology, high-throughput synthesis has played an important role in providing useful small-molecule-based chemical probes in understanding the structure and function relationships. The past several years, there has been a constant rise in interest toward understanding the biological roles and functions of another important class of biomolecules, i.e., carbohydrates and carbohydrate conjugates. Although at early stages, in recent years, several groups have developed high-throughput synthetic methods to obtain complex carbohydrates or carbohydrate-like small-molecules. The present review article summarizes some of these developments.     

Application of surface plasmon resonance for the detection of carbohydrates,glycoconjugates, and measurement of the carbohydrate-specific interactions: A comparison with conventional analytical techniques. A critical review

Carbohydrates (glycans) and their conjugates with proteins and lipids contribute significantly to many biological processes. That makes these compounds important targets to be detected, monitored and identified. The identification of the carbohydrate content in their conjugates with proteins and lipids (glycoforms) is often a challenging task. Most of the conventional instrumental analytical techniques are time-consuming and require tedious sample pretreatment and utilising various labeling agents. Surface plasmon resonance (SPR) has been intensively developed during last two decades and has received the increasing attention for different applications, from the real-time monitoring of affinity bindings to biosensors. SPR does not require any labels and is capable of direct measurement of biospecific interaction occurring on the sensing surface. This review provides a critical comparison of modern analytical instrumental techniques with SPR in terms of their analytical capabilities to detect carbohydrates, their conjugates with proteins and lipids and to study the carbohydrate-specific bindings. A few selected examples of the SPR approaches developed during 2004–2011 for the biosensing of glycoforms and for glycan–protein affinity studies are comprehensively discussed.     

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.     

New Modalities for Challenging Targets in Drug Discovery

Our ever‐increasing understanding of biological systems is providing a range of exciting novel biological targets, whose modulation may enable novel therapeutic options for many diseases. These targets include protein–protein and protein–nucleic acid interactions, which are, however, often refractory to classical small‐molecule approaches. Other types of molecules, or modalities, are therefore required to address these targets, which has led several academic research groups and pharmaceutical companies to increasingly use the concept of so‐called “new modalities”. This Review defines for the first time the scope of this term, which includes novel peptidic scaffolds, oligonucleotides, hybrids, molecular conjugates, as well as new uses of classical small molecules. We provide the most representative examples of these modalities to target large binding surface areas such as those found in protein–protein interactions and for biological processes at the center of cell regulation.     

Two‐Step Functionalization of Oligosaccharides Using Glycosyl Iodide and Trimethylene Oxide and Its Applications to Multivalent Glycoconjugates

Oligosaccharide conjugates, such as glycoproteins and glycolipids, are potential chemotherapeutics and also serve as useful tools for understanding the biological roles of carbohydrates. With many modern isolation and synthetic technologies providing access to a wide variety of free sugars, there is increasing need for general methodologies for carbohydrate functionalization. Herein, we report a two‐step methodology for the conjugation of per‐O‐acetylated oligosaccharides to functionalized linkers that can be used for various displays. Oligosaccharides obtained from both synthetic and commercial sources were converted to glycosyl iodides and activated with I₂ to form reactive donors that were subsequently trapped with trimethylene oxide to form iodopropyl conjugates in a single step. The terminal iodide served as a chemical handle for further modification. Conversion into the corresponding azide followed by copper‐catalyzed azide–alkyne cycloaddition afforded multivalent glycoconjugates of Gb3 for further investigation as anti‐cancer therapeutics.     

Natural glycoconjugates with antitumor activity

Cancer is one of the major causes of death worldwide. As a consequence, many different therapeutic approaches, including the use of glycosides as anticancer agents, have been developed. Various glycosylated natural products exhibit high activity against a variety of microbes and human tumors. In this review we classify glycosides according to the nature of their aglycone (non-saccharidic) part. Among them, we describe anthracyclines, aureolic acids, enediyne antibiotics, macrolide and glycopeptides presenting different strengths and mechanisms of action against human cancers. In some cases, the glycosidic residue is crucial for their activity, such as in anthracycline, aureolic acid and enediyne antibiotics; in other cases, Nature has exploited glycosylation to improve solubility or pharmacokinetic properties, as in the glycopeptides. In this review we focus our attention on natural glycoconjugates with anticancer properties. The structure of several of the carbohydrate moieties found in these conjugates and their role are described. The structure–activity relationship of some of these compounds, together with the structural features of their interaction with the biological targets, are also reported. Taken together, all this information is useful for the design of new potential anti-tumor drugs.     

Synergistic DNA- and Protein-Based Recognition Promote an RNA-Templated Bio-orthogonal Reaction

Biomolecular assemblies composed of proteins and oligonucleotides play a central role in biological processes. While in nature, oligonucleotides and proteins usually assemble via non-covalent interactions, synthetic conjugates have been developed which covalently link both modalities. The resulting peptide-oligonucleotide conjugates have facilitated novel biological applications as well as the design of functional supramolecular systems and materials. However, despite the importance of concerted protein/oligonucleotide recognition in nature, conjugation approaches have barely utilized the synergistic recognition abilities of such complexes. Herein, the structure-based design of peptide-DNA conjugates that bind RNA through Watson-Crick base pairing combined with peptide-mediated major groove recognition is reported. Two distinct conjugate families with tunable binding characteristics have been designed to adjacently bind a particular RNA sequence. In the resulting ternary complex, their peptide elements are located in proximity, a feature that was used to enable an RNA-templated click reaction. The introduced structure-based design approach opens the door to novel functional biomolecular assemblies.     

Applications of Carbohydrate‐Gold Nanoparticles for Volumetric Flow Measurements Using an Opto‐Acoustic Technique

Gold nanoparticles with carbohydrate ligands attached on their surface have been synthesized and characterized with various techniques. The new nanoparticle conjugates have shown great potentials as a contrast agent for opto‐acoustic imaging. Hemocompatibility measurements of human blood for the carbohydrate‐gold nanoparticles have shown that the conjugates are feasible for in vivo testing. Preliminary quantitative flow measurements using the conjugates were also studied in this work based on the indicator‐dilution theory. In vitro phantom experiments were designed and conducted, and results were discussed.     

Mapping protein: carbohydrate interactions

Many biologically important interactions occur between proteins and carbohydrates. The examination of these interactions at the atomic level is critical not only in understanding the nature of these interactions and their biological role, but also in the design of effective modulators of these interactions. While experimentally obtained structural information is preferred, quite often this information is unavailable. In order to address this, several methods have been developed to probe the interactions between protein and carbohydrate in the absence of structural data. These methods map the interactions between protein and carbohydrate, and identify the groups involved, both at the carbohydrate and protein level. Here, we review these developments, and examine the strengths, weaknesses, and pitfalls of these methods.     

Recent progress in the solid-phase synthesis of glycopeptide

The recent understanding of the biological role of glycoproteins has brought about a demand for the highly homogeneous glycopeptides as the functional model for glycoproteins. Thus, much efforts have been made to establish easy and efficient method for glycopeptide synthesis. In this paper, we briefly review the recent advances in the synthesis of O- and N-linked glycopeptide based on the solid-phase method. In O-glycopeptide section, the preparation of glycosylated amino acid units with mucin type and other O-linked carbohydrate chains and their use for solid-phase synthesis are summarized. Other approaches, such as the glycosylation of resin bound peptide are also overviewed. In N-glycopeptide section, the synthesis using glycosylated amino acid units as well as other methods are described.     

Indanoyl amino acid conjugates: tunable elicitors of plant secondary metabolism

The unassuming nature of plants belies their viciously effective defensive strategies in the face of herbivore attack. Under the direction of, among others, octadecanoid hormones, plants respond by producing phytoalexins, bitter and toxic alkaloids, protease inhibitors, and even volatile compounds that call predatory insects to the herbivores. A rational design of 4-oxoindanoyl amino acid conjugates based on the phytotoxin, coronatine, as a structural guide resulted in a series of highly active compounds which turn on defensive systems in much the same way as octadecanoid hormones. The developments in the syntheses of indanoyl amino acid conjugates have created easy access to substantial amounts of a variety of such compounds. When these compounds were tested in biological systems, they showed abilities to induce defensive responses that surpassed octadecanoid hormones. In addition, small changes in the structures of these compounds resulted in large differences in the particular defensive systems that were activated. Indanoyl amino acid conjugates are promising tools in photoaffinity approaches towards the macromolecular targets of octadecanoids and their subcellular localization. Owing to the strong activation of plant defense or their efficient induction of fruit abscission which facilitates mechanical harvest, the compounds are promising candidates for future application in agriculture.     

Mass spectrometry in coupling with affinity capture-release and isotope-coded affinity tags for quantitative protein analysis

Affinity capture-release electrospray ionization mass spectrometry (ACESIMS) and isotope-coded affinity tags (ICAT) are two recently introduced techniques for the quantitation of protein activity and content with applications to clinical enzymology and functional proteomics, respectively. One common feature of these methods is that they use biotinylated tags that function as molecular handles for highly selective and reversible affinity capture of conjugates from complex biological mixtures such as cell homogenates and sub-cellular organelles. ACESIMS uses synthetic substrate conjugates specifically to target cellular enzymes that, when deficient, are the cause of genetic diseases. Multiplex determination of enzyme activities is used for the diagnosis of lysosomal storage diseases. The ICAT method relies on selective conjugation of cysteine thiol groups in proteins, followed by enzymatic digestion and quantitative analysis of peptide conjugates by mass spectrometry. Another common feature of the ACESIMS and ICAT approaches is that both use conjugates labeled with stable heavy isotopes as internal standards for quantitation. Selected applications of the ACESIMS and ICAT techniques are presented that include molecular-level diagnosis of genetic diseases in children and quantitative determination of protein expression in cells.     

Carbohydrate post-glycosylational modifications

Carbohydrate modification is a common phenomenon in nature. Many carbohydrate modifications such as some epimerization, O-acetylation, O-sulfation, O-methylation, N-deacetylation, and N-sulfation, take place after the formation of oligosaccharide or polysaccharide backbones. These modifications can be categorized as carbohydrate post-glycosylational modifications (PGMs). Carbohydrate PGMs further extend the complexity of the structures and the synthesis of carbohydrates and glycoconjugates. They also increase the capacity of the biological regulation that is achieved by finely tuning the structures of carbohydrates. Developing efficient methods to obtain structurally defined naturally occurring oligosaccharides, polysaccharides, and glycoconjugates with carbohydrate PGMs is essential for understanding the biological significance of carbohydrate PGMs. Combined with high-throughput screening methods, synthetic carbohydrates with PGMs are invaluable probes in structure-activity relationship studies. We illustrate here several classes of carbohydrates with PGMs and their applications. Recent progress in chemical, enzymatic, and chemoenzymatic syntheses of these carbohydrates and their derivatives are also presented.     

Stereoselective Synthesis of C-Glycosides by Suzuki Cross-coupling Reaction

Carbohydrates and their conjugates have been recognized to play a wide variety of metabolic roles in numerous biological processes.[1] Various modified sugars and analogues have been recently synthesized for further investigation of glycosidase reactions and for the development of specific glycosidase inhibitors.[2] As one of the most important carbohydrate mimics, C-glycosides have attracted great attention due to their stability to chemical or enzymatic hydrolysis of the glycosidic linkage. A number of methodologies for the preparation of C-glycosides have been extensively investigated.[3] We have recently reported the syntheses of novel C-glycosyl amino acids and amino-C-disaccharides possessing a ketose form via the stereoselective 1,3-dipolar cycloaddition of exo-methylenesugars (1) and nitrones.[4,5] As a continuation of our research on the synthesis of C-glycosides using exo-methylenesugar as the precursor, we wish to describe here a stereoselective synthesis of C-glycosides by Suzuki cross-coupling reaction.     

5-Formyluracil targeted biochemical reactions with proteins inhibit DNA replication,induce mutations and interference gene expression in living cells

Covalent DNA–protein cross-links are toxic DNA lesions that interfere with essential biological processes, which can cause serious biological consequences, such as genomic instability and protein misexpression. 5-Formyluracil (5fU) as an important modification in DNA, which is mainly from oxidative damage, exists in a variety of cells and tissues. We have reported that 5fU mediated DNA–protein conjugates could exist in human cells [Zhou et al. CCS Chem. 2 (2020) 54–63]. We now aimed to explore its potential biological effects in vitro and in vivo. In this paper, we firstly reported that 5fU intermediated DNA–peptide or DNA–protein conjugates (both were called DPCs) could inhibit different polymerases bypass or cause mutations. Then we further investigated the functional impacts caused by 5fU-mediated DPCs, which appeared in different gene expression components [in the promoter sequence or 5′-untranslated regions (UTR)]. These results together may contribute to a broader understanding of DNA–protein interactions as well as the biological functions associated with 5fU.     

Family Business: Multiple Members of Major Phytohormone Classes Orchestrate Plant Stress Responses

Low‐molecular‐weight compounds such as jasmonic, abscisic and salicylic acids are commonly thought to be regulators of plant stress responses. However, it is becoming clear that these molecules, often referred to as phytohormones, are only a part of bigger groups of compounds with biological activity. We propose that the concept of “hormone families” may help to better understand plant physiological responses by taking into account not only the alleged main regulators, but also their precursors, conjugates and catabolites. Novel approaches to profile potentially active compounds in plants are discussed.     

Advances in polymer and polymeric nanostructures for protein conjugation

Linear polymers have been considered the best molecular structures for the formation of efficient protein conjugates due to their biological advantages, synthetic convenience and ease of functionalization. In recent years, much attention has been dedicated to develop synthetic strategies that produce the most control over protein conjugation utilizing linear polymers as scaffolds. As a result, different conjugate models, such as semitelechelic, homotelechelic, heterotelechelic and branched or star polymer conjugates, have been obtained that take advantage of these well-controlled synthetic strategies. Development of protein conjugates using nanostructures and the formation of said nanostructures from protein–polymer bioconjugates are other areas in the protein bioconjugation field. Although several polymer–protein technologies have been developed from these discoveries, few review articles have focused on the design and function of these polymers and nanostructures. This review will highlight some recent advances in protein-linear polymer technologies that employ protein covalent conjugation and successful protein-nanostructure bioconjugates (covalent conjugation as well) that have shown great potential for biological applications.     

Chemical Synthesis of N-Aryl Glycosides

Along with the O- and C-aryl glycosides, N-aryl glycosides represent an important class of carbohydrate and heterocyclic aryl conjugates that possess diverse applications and implications of biological interest. However, most of the synthetic efforts have been directed toward the preparation of O- and C-aryl glycosides. This review focuses on the various strategies that have been employed to synthesize N-aryl glycosides, most of which developed in the past 20 years. Besides having their unique applications, these N-aryl glycosides can also be treated as the analogs of O- and C-aryl glycosides. Wide ranges of reaction conditions are discussed for the optimum conditions.     

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.     

Tuning Achiral to Chiral Supramolecular Helical Superstructures

The design and synthesis of achiral organic functional molecules which can assemble into a chiral with selective handedness in the absence of chiral substances is an important in understanding the role chirality plays within these systems. In this review, we described general approaches towards supramolecular chiral molecules the synthesis and self‐assembly of achiral molecule to active chiral molecules to investigate controlled supramolecular chiral nanostructures with their photoluminescent properties for rapid, sensitive and selective detection of analytes of choice. Various small molecules have been discussed for achiral to chiral along with induction of chirality and controlled chiral helical structures in detail. We discussed few examples where stimuli used to control the chirality such as temperature, pH etc. Finally, we will also explore on the photo responsive helicity properties of the aggregation induced emission active molecule such as tetraphenylethene conjugates.