Carbohydrate recognition by boronolectins, small molecules, and lectins

Synergistic Boronic Acid and Photoredox Catalysis: Synthesis of C-Branched Saccharides via Selective Alkylation of Unprotected Saccharides

Here we present a regio- and stereoselective alkylation approach for unprotected saccharides using synergistic boronic acid and photoredox catalysis. Targeting the equatorial C-H bond of the cis-1,2-diol motif, this method employs MeB(OH)2 as a catalyst. Mechanistic investigations indicate that the formation of a tetracoordinate boron species, resulting from the interaction between the cyclic boronic diol ester and a free hydroxyl group in the saccharide, is critical to this transformation. Notably, this method enables efficient late-stage modification of complex carbohydrates, such as raffinose and the drug digoxin, expanding opportunities for carbohydrate functionalization.

Boron enabled bioconjugation chemistries

Novel bioconjugation reactions have been heavily pursued for the past two decades. A myriad of conjugation reactions have been developed for labeling molecules of interest in their native context as well as for constructing multifunctional molecular entities or stimuli-responsive materials. A growing cluster of bioconjugation reactions were realized by tapping into the unique properties of boron. As a rare element in human biology, boronic acids and esters exhibit remarkable biocompatibility. A number of organoboron reagents have been evaluated for bioconjugation, targeting the reactivity of either native biomolecules or those incorporating bioorthogonal functional groups. Owing to the dynamic nature of B-O and B-N bond formation, a significant portion of the boron-enabled bioconjugations exhibit rapid reversibility and accordingly have found applications in the development of reversible covalent inhibitors. On the other hand, stable bioconjugations have been developed that display fast kinetics and significantly expand the repertoire of bioorthogonal chemistry. This contribution presents a summary and comparative analysis of the recently developed boron-mediated bioconjugations. Importantly, this article seeks to provide an in-depth discussion of the thermodynamic and kinetic profiles of these boron-enabled bioconjugations, which reveals structure-reactivity relationships and provides guidelines for bioapplications.

Effective enrichment of glycated proteome using ultrasmall gold nanoclusters functionalized with boronic acid

Glycated proteins play a crucial role in various biological pathways and the pathogenesis of human diseases. A comprehensive analysis of glycated proteins is essential for understanding their biological significance. However, their low abundance and heterogeneity in complex biological samples necessitate an enrichment procedure prior to their detection. Current enrichment strategies primarily rely on the boronic acid (BA) affinity method combined with functional nanoparticles; however, the effectiveness of these approaches is often suboptimal. In this study, a novel nanocluster (NC)-based enrichment material was synthesized for the first time, characterized as Au22SG18 functionalized with 24 BA groups, in which SG is glutathione. The functionalized BA established a reversible covalent bond with the cis-dihydroxy group through pH adjustment, enabling selective enrichment of glycated peptides. After the optimization of the enrichment protocol, we demonstrated highly sensitive and selective enrichment of standard glycopeptides using the NC-based enrichment material, exhibiting excellent reusability. Efficient enrichment was also demonstrated for the glycated proteome from human serum. These results highlight the potential of the atomically well-defined ultrasmall Au NCs as a powerful tool for high-throughput analysis of glycated peptides.

Towards Biomimetic Recognition of Glycans by Synthetic Receptors

Carbohydrates are abundant in Nature, where they are mostly assembled within glycans as free polysaccharides or conjugated to a variety of biological molecules such as proteins and lipids. Glycans exert several functions, including protein folding, stability, solubility, resistance to proteolysis, intracellular traffic, antigenicity, and recognition by carbohydrate-binding proteins. Interestingly, misregulation of their biosynthesis that leads to changes in glycan structures is frequently recognized as a mark of a disease state. Because of glycan ubiquity, carbohydrate binding agents (CBAs) targeting glycans can lead to a deeper understanding of their function and to the development of new diagnostic and prognostic strategies. Synthetic receptors selectively recognizing specific carbohydrates of biological interest have been developed over the past three decades. In addition to the success obtained in the effective recognition of monosaccharides, synthetic receptors recognizing more complex guests have also been developed, including di- and oligosaccharide fragments of glycans, shedding light on the structural and functional requirements necessary for an effective receptor. In this review, the most relevant achievements in molecular recognition of glycans and their fragments will be summarized, highlighting potentials and future perspectives of glycan-targeting synthetic receptors.

Medical Relevance, State-of-the-Art and Perspectives of "Sweet Metacode" in Liquid Biopsy Approaches

This review briefly introduces readers to an area where glycomics meets modern oncodiagnostics with a focus on the analysis of sialic acid (Neu5Ac)-terminated structures. We present the biochemical perspective of aberrant sialylation during tumourigenesis and its significance, as well as an analytical perspective on the detection of these structures using different approaches for diagnostic and therapeutic purposes. We also provide a comparison to other established liquid biopsy approaches, and we mathematically define an early-stage cancer based on the overall prognosis and effect of these approaches on the patient's quality of life. Finally, some barriers including regulations and quality of clinical validations data are discussed, and a perspective and major challenges in this area are summarised.

Palladium-Catalyzed ipso-Borylation of Aryl Halides Promoted by Lewis Acid-Mediated Electrophilic Activation of Aryl(halo)palladium(II) Complex

Palladium-catalyzed ipso-borylation of aryl halides, well-known as Miyaura borylation, is one of the reliable synthetic methods for organoborons. This reaction involves base-mediated nucleophilic activation of diboron that enables transmetalation of an aryl(halo)palladium(II) intermediate with a diboron. As an alternative, herein, we have established Lewis acid-mediated conditions for borylating (pseudo)haloarenes that require no external base. The electrophilic activation of the aryl(halo)palladium(II) intermediate via dehalogenation with Lewis acidic zinc complexes promotes the borylation.

Genetically Encoded Boronolectin as a Specific Red Fluorescent UDP-GlcNAc Biosensor

There is great interest in developing boronolectins that are synthetic lectin mimics containing a boronic acid functional group for reversible recognition of diol-containing molecules, such as glycans and ribonucleotides. However, it remains a significant challenge to gain specificity. Here, we present a genetically encoded boronolectin which is a hybrid protein consisting of a noncanonical amino acid (ncAA) p-boronophenylalanine (pBoF), natural-lectin-derived peptide sequences, and a circularly permuted red fluorescent protein (cpRFP). The genetic encodability permitted a straightforward protein engineering process to derive a red fluorescent biosensor that can specifically bind uridine diphosphate N-acetylglucosamine (UDP-GlcNAc), an important nucleotide sugar involved in metabolic sensing and cell signaling. We further characterized the resultant boronic acid- and peptide-assisted UDP-GlcNAc sensor (bapaUGAc) both in vitro and in live mammalian cells. Because UDP-GlcNAc in the endoplasmic reticulum (ER) and Golgi apparatus plays essential roles in glycosylating biomolecules in the secretory pathway, we genetically expressed bapaUGAc in the ER and Golgi and validated the sensor for its responses to metabolic disruption and pharmacological inhibition. In addition, we combined bapaUGAc with UGAcS, a recently reported green fluorescent UDP-GlcNAc sensor based on an alternative sensing mechanism, to monitor UDP-GlcNAc level changes in the ER and cytosol simultaneously. We expect our work to facilitate the future development of specific boronolectins for carbohydrates. In addition, this newly developed genetically encoded bapaUGAc sensor will be a valuable tool for studying UDP-GlcNAc and glycobiology.

Enlightening the Path to Protein Engineering: Chemoselective Turn-On Probes for High-Throughput Screening of Enzymatic Activity

Many successful stories in enzyme engineering are based on the creation of randomized diversity in large mutant libraries, containing millions to billions of enzyme variants. Methods that enabled their evaluation with high throughput are dominated by spectroscopic techniques due to their high speed and sensitivity. A large proportion of studies relies on fluorogenic substrates that mimic the chemical properties of the target or coupled enzymatic assays with an optical read-out that assesses the desired catalytic efficiency indirectly. The most reliable hits, however, are achieved by screening for conversions of the starting material to the desired product. For this purpose, functional group assays offer a general approach to achieve a fast, optical read-out. They use the chemoselectivity, differences in electronic and steric properties of various functional groups, to reduce the number of false-positive results and the analytical noise stemming from enzymatic background activities. This review summarizes the developments and use of functional group probes for chemoselective derivatizations, with a clear focus on screening for enzymatic activity in protein engineering.

Cycloalkyl Groups as Building Blocks of Artificial Carbohydrate Receptors: Studies with Macrocycles Bearing Flexible Side-Arms

The cyclopentyl group was expected to act as a building block for artificial carbohydrate receptors and to participate in van der Waals contacts with the carbohydrate substrate in a similar way as observed for the pyrrolidine ring of proline in the crystal structures of protein-carbohydrate complexes. Systematic binding studies with a series of 1,3,5-trisubstituted 2,4,6-triethylbenzenes bearing various cycloalkyl groups as recognition units provided indications of the involvement of these groups in the complexation process and showed the influence of the ring size on the receptor efficiency. Representatives of compounds that exhibit a macrocyclic backbone and flexible side arms were now chosen as further model systems to investigate whether the previously observed effects represent a general trend. Binding studies with these macrocycles towards β-D-glucopyranoside, an all-equatorial substituted carbohydrate substrate, included 1H NMR spectroscopic titrations and microcalorimetric investigations. The performed studies confirmed the previously observed tendency and showed that the compound bearing cyclohexyl groups displays the best binding properties.

Bis-Boronic Acid Liposomes for Carbohydrate Recognition and Cellular Delivery

Liposomes are effective therapeutic delivery nanocarriers due to their ability to encapsulate and enhance the pharmacokinetic properties of a wide range of drugs and diagnostic agents. A primary area in which improvement is needed for liposomal drug delivery is to enhance the delivery of these nanocarriers to cells. Cell membrane glycans provide exciting targets for liposomal delivery since they are often densely clustered on cell membranes and glycan overabundance and aberrant glycosylation patterns are a common feature of diseased cells. Herein, we report a liposome platform incorporating bis-boronic acid lipids (BBALs) to increase valency in order to achieve selective saccharide sensing and enhance cell surface binding interactions based on carbohydrate binding interactions. In order to vary properties, multiple BBALs ( 1a-d ) with variable linkers in between the binding units were designed and synthesized. Fluorescence-based microplate screening of carbohydrate binding showed that these compounds exhibit varying binding properties depending on their structures. Additionally, fluorescence microscopy experiments indicated enhancements in cellular association when BBALs were incorporated in liposomes. These results demonstrate that multivalent BBALs serve as an exciting glycan binding liposome system for targeted liposome delivery.

Chiral Assemblies of Planar and Achiral meta-Arylene Ethynylene Macrocycles Induced by Saccharide Recognition

We created chiral assemblies of planar and achiral macrocycles by saccharide recognition. To achieve this, we synthesized stackable meta-arylene ethynylene macrocycles consisting of pyridine-acetylene-phenol and pyridine-acetylene-aniline units. ¹H NMR, absorption, and fluorescence emission spectroscopy indicated that these macrocycles formed 1:1 and 2:1 complexes with lipophilic alkyl glycosides. The 2:1 complex of the pyridine-acetylene-phenol macrocycle showed induced circular dichroism (ICD) bands, meaning that two achiral macrocycles are arranged in an asymmetrically twisted manner. CD spectroscopy revealed that the helical sense was affected by the chirality of guest saccharides. On the other hand, strong CD bands were observed after solid-liquid extraction of native saccharides into lipophilic solvents using the pyridine-acetylene-aniline macrocycle.

Unique On-Site Spinning Sampling of Highly Water-Soluble Organics Using Functionalized Monolithic Sorbents

Water utilities encounter unpredictable odor issues that cannot be explained by routine water parameters during spring runoff, even in the summer and fall. Highly water-soluble organics (e.g., amino acids and saccharides) have been reported to form odorous disinfection byproducts during disinfection, but the lack of simple and practical on-site sampling techniques hampers their routine monitoring at trace levels in source water. Therefore, we have created two functionalized nested-in-sponge silica monoliths (NiS-SMs) using a one-pot synthesis method and demonstrated their application for extracting highly soluble organics in water. The NiS-SMs functionalized with the sulfonic group and phenylboronic moiety selectively extracted amino acids and monosaccharides, respectively. We further developed a spinning sampling technique using the composites and evaluated its robust performance under varying water conditions. The spinning sampling coupled to high-performance liquid chromatography tandem mass spectrometry analysis provided limits of detection for amino acids at 0.038-0.092 ng L^-1 and monosaccharides at 0.036-0.14 ng L^-1. Using the pre-equilibrium sampling-rate calibration, we demonstrated the applicability of the spinning sampling technique for on-site sampling and monitoring of amino acids and monosaccharides in river water. The new composite materials and rapid on-site sampling technique are unique and efficient tools for monitoring highly soluble organics in water sources.

Strategies and Tactics for the Development of Selective Glycan-Binding Proteins

The influences of glycans impact all biological processes, disease states, and pathogenic interactions. Glycan-binding proteins (GBPs), such as lectins, are decisive tools for interrogating glycan structure and function because of their ease of use and ability to selectively bind defined carbohydrate epitopes and glycosidic linkages. GBP reagents are prominent tools for basic research, clinical diagnostics, therapeutics, and biotechnological applications. However, the study of glycans is hindered by the lack of specific and selective protein reagents to cover the massive diversity of carbohydrate structures that exist in nature. In addition, existing GBP reagents often suffer from low affinity or broad specificity, complicating data interpretation. There have been numerous efforts to expand the GBP toolkit beyond those identified from natural sources through protein engineering, to improve the properties of existing GBPs or to engineer novel specificities and potential applications. This review details the current scope of proteins that bind carbohydrates and the engineering methods that have been applied to enhance the affinity, selectivity, and specificity of binders.

Regiochemical Effects on the Carbohydrate Binding and Selectivity of Flexible Synthetic Carbohydrate Receptors with Indole and Quinoline Heterocyclic Groups

Synthetic carbohydrate receptors (SCRs) that bind cell-surface carbohydrates could be used for disease detection, drug-delivery, and therapeutics, or for the site-selective modification of complex carbohydrates but their potential has not been realized because of remaining challenges associated with binding affinity and substrate selectivity. We have reported recently a series of flexible SCRs based upon a biaryl core with four pendant heterocyclic groups that bind glycans selectively through noncovalent interactions. Here we continue to explore the role of heterocycles on substrate selectivity by expanding our library to include a series of indole and quinoline heterocycles that vary in their regiochemistry of attachment to the biaryl core. The binding of these SCRs to a series of biologically-relevant carbohydrates was studied by 1H NMR titrations in CD2Cl2 and density-functional theory calculations. We find SCR030, SCR034 and SCR037 are selective, SCR031, SCR032, and SCR039 are strong binders, and SCR033, SCR035, SCR036, and SCR038 are promiscuous and bind weakly. Computational analysis reveals the importance of C-H⋯π and H-bonding interactions in defining the binding properties of these new receptors. By combining these data with those obtained from our previous studies on this class of flexible SCRs, we develop a series of design rules that account for the binding of all SCRs of this class and anticipate the binding of future, not-yet imagined tetrapodal SCRs.

Iridium-Catalyzed Enantioconvergent Allylation of a Boron-Stabilized Organozinc Reagent

An iridium-catalyzed enantioconvergent coupling of the versatile boron-stabilized organozinc reagent BpinCH₂ZnI with a racemic branched allylic carbonate has been developed here, which differs from our previous work by using 1,1-bisborylmethane through the kinetic resolution process. The reaction has a broad substrate scope, and various chiral homoallylic organoboronic esters could be obtained in good yields with excellent enantioselectivities. The synthetic practicability of the products was demonstrated by their conversion to other useful families of compounds.

Effective Enrichment Strategy Using Boronic Acid-Functionalized Mesoporous Graphene-Silica Composites for Intact N- and O-Linked Glycopeptide Analysis in Human Serum

The heterogeneity and low abundance of protein glycosylation present challenging barriers to the analysis of intact glycopeptides, which is key to comprehensively understanding the role of glycosylation in an organism. Efficient and specific enrichment of intact glycopeptides could help greatly with this problem. Here, we propose a new enrichment strategy using a boronic acid (BA)-functionalized mesoporous graphene-silica composite (denoted as GO@mSiO₂-GLYMO-APB) for isolating intact glycopeptides from complex biological samples. The merits of this composite, including high surface area and synergistic effect from size exclusion functionality of mesoporous material, hydrophilic interaction of silica, and the reversible covalent binding with BA, enable the effective and specific enrichment of both intact N- and O-glycopeptides. The results from the enrichment performance of the strategy evaluated by standard glycoproteins and the application to global N- and O-glycosylation analyses in human serum indicate the robustness and potential of the strategy for intact glycopeptide analysis.

Molecular Boronic Acid-Based Saccharide Sensors

Boronic acids can reversibly bind diols, a molecular feature that is ubiquitous within saccharides, leading to their use in the design and implementation of sensors for numerous saccharide species. There is a growing understanding of the importance of saccharides in many biological processes and systems; while saccharide or carbohydrate sensing in medicine is most often associated with detection of glucose in diabetes patients, saccharides have proven to be relevant in a range of disease states. Herein the relevance of carbohydrate sensing for biomedical applications is explored, and this review seeks to outline how the complexity of saccharides presents a challenge for the development of selective sensors and describes efforts that have been made to understand the underpinning fluorescence and binding mechanisms of these systems, before outlining examples of how researchers have used this knowledge to develop ever more selective receptors.

Current and future advances in fluorescence-based visualization of plant cell wall components and cell wall biosynthetic machineries

Plant cell wall-derived biomass serves as a renewable source of energy and materials with increasing importance. The cell walls are biomacromolecular assemblies defined by a fine arrangement of different classes of polysaccharides, proteoglycans, and aromatic polymers and are one of the most complex structures in Nature. One of the most challenging tasks of cell biology and biomass biotechnology research is to image the structure and organization of this complex matrix, as well as to visualize the compartmentalized, multiplayer biosynthetic machineries that build the elaborate cell wall architecture. Better knowledge of the plant cells, cell walls, and whole tissue is essential for bioengineering efforts and for designing efficient strategies of industrial deconstruction of the cell wall-derived biomass and its saccharification. Cell wall-directed molecular probes and analysis by light microscopy, which is capable of imaging with a high level of specificity, little sample processing, and often in real time, are important tools to understand cell wall assemblies. This review provides a comprehensive overview about the possibilities for fluorescence label-based imaging techniques and a variety of probing methods, discussing both well-established and emerging tools. Examples of applications of these tools are provided. We also list and discuss the advantages and limitations of the methods. Specifically, we elaborate on what are the most important considerations when applying a particular technique for plants, the potential for future development, and how the plant cell wall field might be inspired by advances in the biomedical and general cell biology fields.

Hollow MnFe2O4@C@APBA Nanospheres with Size Exclusion and pH Response for Efficient Enrichment of Endogenous Glycopeptides

Enrichment and detection of glycopeptides are an important clinical measure for the diagnosis of complex diseases. Enrichment materials play a key role in this process; they must have an effective sample-screening ability to eliminate the interference of nonglycopeptides. In this work, novel hollow MnFe₂O₄@C@APBA nanospheres (HMCAs) with magnetic and pH responsiveness were prepared for glycopeptide enrichment. The as-prepared composites have a suitable hollow structure and large specific surface area, and the boron hydroxyl group in their cavities can fix or disconnect the hydrophilic groups of the glycopeptides at different pH, so the glycopeptides can be adsorbed or desorbed in a controllable way. Enrichment results showed that the HMCAs exhibited an excellent enrichment performance: ultralow limit of detection (approximately 0.5 fmol μL^-1), perfect size-exclusion effect (HRP/BSA, 1:800, w/w), favorable universality (HRP, IgG, and RNase B), and high binding capacity (150 mg/g). In order to verify the application of materials in practice, the HMCAs were used for the analysis of complex samples and it was found that 474 glycopeptides were identified from 210 glycoproteins in three replicate analyses of 2 μL of human serum. The results showed that the HMCAs could be used as a promising enrichment material for glycopeptide characterization in MS-based glycoproteomics and related fields.

A Pyridine-Acetylene-Aniline Oligomer: Saccharide Recognition and Influence of this Recognition Array on the Activity as Acylation Catalyst

In order to create new functions of foldamer-type hosts, various kinds of recognition arrays are expected to be developed. Here, a pyridine-acetylene-aniline unit is presented as a new class of a saccharide recognition array. The conformational stabilities of this array were analyzed by DFT calculation, and suggested that a pyridine-acetylene-aniline oligomer tends to form a helical structure. An oligomer of this array was synthesized, and its association for octyl β-D-glucopyranoside was confirmed by ¹ H NMR measurements. UV/Vis, circular dichroism, and fluorescence titration experiments revealed its high affinity for octyl glycosides in apolar solvents (K_a =10⁴ to 10⁵  M^-1 ). This oligomer was relatively stable under basic conditions, and therefore this array was expected to be applied to the derivatization of saccharides. A 4-(dialkylamino)pyridine attached pyridine-acetylene-aniline oligomer proved to catalyze the acylation of the octyl glucoside.

Flexible Synthetic Carbohydrate Receptors as Inhibitors of Viral Attachment

Carbohydrate-receptor interactions are often involved in the docking of viruses to host cells, and this docking is a necessary step in the virus life cycle that precedes infection and, ultimately, replication. Despite the conserved structures of the glycans involved in docking, they are still considered "undruggable", meaning these glycans are beyond the scope of conventional pharmacological strategies. Recent advances in the development of synthetic carbohydrate receptors (SCRs), small molecules that bind carbohydrates, could bring carbohydrate-receptor interactions within the purview of druggable targets. Here we discuss the role of carbohydrate-receptor interactions in viral infection, the evolution of SCRs, and recent results demonstrating their ability to prevent viral infections in vitro. Common SCR design strategies based on boronic ester formation, metal chelation, and noncovalent interactions are discussed. The benefits of incorporating the idiosyncrasies of natural glycan-binding proteins-including flexibility, cooperativity, and multivalency-into SCR design to achieve nonglucosidic specificity are shown. These studies into SCR design and binding could lead to new strategies for mitigating the grave threat to human health posed by enveloped viruses, which are heavily glycosylated viroids that are the cause of some of the most pressing and untreatable diseases, including HIV, Dengue, Zika, influenza, and SARS-CoV-2.

Synthetic lectins for selective binding of glycoproteins in water

Although synthetic mimics of lectins can be extremely useful in biological and biomedical research, molecular recognition of carbohydrates has been hampered by their strong solvation in water and subtle structural differences among analogues. Molecularly imprinted nanoparticle receptors were prepared with glycans directly cleaved from glycoproteins. Functionalized with boroxole groups in the binding sites, these water-soluble synthetic lectins bound the parent glycoproteins selectively in water with an association constant of Ka = 104-105 M-1. The strong binding enabled the receptors to protect the targeted glycans from enzymatic cleavage. When clicked onto magnetic nanoparticles, the receptors enabled facile isolation of glycoproteins from a mixture.

Graphene Hybrid Materials for Controlling Cellular Microenvironments

Cellular microenvironments are known as key factors controlling various cell functions, including adhesion, growth, migration, differentiation, and apoptosis. Many materials, including proteins, polymers, and metal hybrid composites, are reportedly effective in regulating cellular microenvironments, mostly via reshaping and manipulating cell morphologies, which ultimately affect cytoskeletal dynamics and related genetic behaviors. Recently, graphene and its derivatives have emerged as promising materials in biomedical research owing to their biocompatible properties as well as unique physicochemical characteristics. In this review, we will highlight and discuss recent studies reporting the regulation of the cellular microenvironment, with particular focus on the use of graphene derivatives or graphene hybrid materials to effectively control stem cell differentiation and cancer cell functions and behaviors. We hope that this review will accelerate research on the use of graphene derivatives to regulate various cellular microenvironments, which will ultimately be useful for both cancer therapy and stem cell-based regenerative medicine.

Selective Binding of Complex Glycans and Glycoproteins in Water by Molecularly Imprinted Nanoparticles

Synthetic receptors to recognize biological glycans are in great need for modern glycoscience and technology, but their design and synthesis have been a daunting challenge due to strong solvation of carbohydrates in water and structural complexity of the guest. Molecular imprinting in surfactant micelles with amide cross-linkers provides a convenient one-pot method to prepare nanoparticle receptors for glycosides, glycans, and glycoproteins, taking advantage of hydrogen-bonding interactions near the surfactant/water interface. Biologically competitive micromolar binding affinities were obtained in water and subtle structural differences of glycans could be distinguished.

Paving the Way for Practical Use of Sugar-Binding Natural Products as Lectin Mimics in Glycobiological Research

Pradimicins (PRMs) constitute an exceptional class of natural products that show Ca²⁺ -dependent recognition of d-mannose (Man). In addition to therapeutic uses as antifungal drugs, the application of PRMs as lectin mimics for glycobiological research has been attracting considerable interest, since the emerging biological roles of Man-containing glycans have been highlighted. However, only a few attempts have been made to use PRMs for glycobiological purposes. The limited use of PRMs is primarily due to the early assumption that the readily modifiable carboxyl group of PRMs is involved in Ca²⁺ binding, and thus, not available to prepare research tools. Recently, this assumption has been disproved by structural elucidation of the Ca²⁺ complex of PRMs, which paves the way for designing carboxyl group modified derivatives of PRMs for research use. This article outlines studies related to Ca²⁺ -mediated Man binding of PRMs and discusses their application for glycobiology.

Selective glucose sensing in complex media using a biomimetic receptor

Glucose is a key biomedical analyte, especially relevant to the management of diabetes. Current methods for glucose determination rely on the enzyme glucose oxidase, requiring specialist instrumentation and suffering from redox-active interferents. In a new approach, a powerful and highly selective achiral glucose receptor is mixed with a sample, l-glucose is added, and the induced CD spectrum is measured. The CD signal results from competition between the enantiomers, and is used to determine the d-glucose content. The involvement of l-glucose doubles the signal range from the CD spectrometer and allows sensitivity to be adjusted over a wide dynamic range. It also negates medium effects, which must be equal for both enantiomers. The method has been demonstrated with human serum, pre-filtered to remove proteins, giving results which closely match the standard biochemical procedures, as well as a cell culture medium and a beer sample containing high (70 mM) and low (0.4 mM) glucose concentrations respectively.

Current Status of Carbohydrates Information in the Protein Data Bank

Carbohydrates are well known for their physicochemical, biological, functional, and therapeutic characteristics. Unfortunately, their chemical nature imposes severe challenges for the structural elucidation of these phenomena, impairing not only the depth of our understanding of carbohydrates but also the development of new biotechnological and therapeutic applications based on these molecules. In the recent past, the amount of structural information, obtained mainly from X-ray crystallography, has increased progressively, as well as its quality. In this context, the current work presents a global analysis of the carbohydrate information available in the Protein Data Bank (PDB). From high quality structures, it is clear that most of the data are highly concentrated on a few sets of residue types, on their monosaccharidic forms, and connected by a small diversity of glycosidic linkages. The geometries of these linkages can be mostly associated with the types of linkages instead of residues, while the level of puckering distortion was characterized, quantified, and located in a pseudorotational equilibrium landscape, not only to local minima but also to transitional states. These qualitative and quantitative analyses offer a global picture of the carbohydrate structural content in the PDB, potentially supporting the building of new models for carbohydrate-related biological phenomena at the atomistic level, including new developments on force field parameters.

A Preorganized Hydrogen-Bonding Motif for the Molecular Recognition of Carbohydrates

The choice between adaptive and preorganized architectures, or of the most effective hydrogen bonding groups to be selected, are dilemmas that supramolecular chemists must address in designing synthetic receptors for such a challenging guest as carbohydrates. In this paper, structurally related architectures featuring two alternative hydrogen bonding motifs were compared to ascertain the structural and functional origin of their binding differences and the advantages that can be expected in monosaccharide recognition. A set of structurally related macrocyclic receptors were prepared, and their binding properties were measured by NMR and ITC techniques in chloroform vs a common saccharidic target, namely, the β-octyl glycoside of D-glucose. Results showed that the diaminocarbazolic motif, recently reported as the constituting unit of highly effective receptors for saccharides in water, is a superior hydrogen bonding motif compared to the previously described diaminopyrrolic motif, which was successfully employed in molecular recognition of carbohydrates in polar organic solvents, due to intrinsic structural and functional factors, rather than to hydrophobic contributions. In addition, the occurrence of a rare example of a thermodynamic template effect exerted by the beta-glucoside has been ascertained, enhancing the synthesis outcome of the otherwise low yielding preparation of the described macrocyclic receptors.

Copper-Catalyzed Triboration: Straightforward, Atom-Economical Synthesis of 1,1,1-Triborylalkanes from Terminal Alkynes and HBpin

A convenient and efficient one-step synthesis of 1,1,1-triborylalkanes was achieved via sequential dehydrogenative borylation and double hydroborations of terminal alkynes with HBpin (HBpin=pinacolborane) catalyzed by inexpensive and readily available Cu(OAc)2 . This process proceeds under mild conditions, furnishing 1,1,1-tris(boronates) with wide substrate scope, excellent selectivity, and good functional-group tolerance, and is applicable to gram-scale synthesis without loss of yield. The 1,1,1-triborylalkanes can be used in the preparation of α-vinylboronates and borylated cyclic compounds, which are valuable but previously rare compounds. Different alkyl groups can be introduced stepwise via base-mediated deborylative alkylation to produce racemic tertiary alkyl boronates, which can be readily transformed into useful tertiary alcohols.

Selective Sugar Recognition by Anthracene-Type Boronic Acid Fluorophore/Cyclodextrin Supramolecular Complex Under Physiological pH Condition

We synthesized novel PET (photoinduced electron transfer)-type fluorescence glucose probe 1 [(4-(anthracen-2-yl-carbamoyl)-3-fluorophenyl)boronic acid], which has a phenylboronic acid (PBA) moiety as the recognition site and anthracene as the fluorescent part. Although the PBA derivatives dissociate and bind with sugar in the basic condition, our new fluorescent probe can recognize sugars in the physiological pH by introducing an electron-withdrawing fluorine group into the PBA moiety. As a result, the pK _a value of this fluorescent probe was lowered and the probe was able to recognize sugars at the physiological pH of 7.4. The sensor was found to produce two types of fluorescent signals, monomer fluorescence and dimer fluorescence, by forming a supramolecular 2:1 complex of 1 with glucose inside a γ-cyclodextrin (γ-CyD) cavity. Selective ratiometric sensing of glucose by the 1/γ-CyD complex was achieved in water at physiological pH.

Global and site-specific analysis of protein glycosylation in complex biological systems with Mass Spectrometry

Protein glycosylation is ubiquitous in biological systems and plays essential roles in many cellular events. Global and site-specific analysis of glycoproteins in complex biological samples can advance our understanding of glycoprotein functions and cellular activities. However, it is extraordinarily challenging because of the low abundance of many glycoproteins and the heterogeneity of glycan structures. The emergence of mass spectrometry (MS)-based proteomics has provided us an excellent opportunity to comprehensively study proteins and their modifications, including glycosylation. In this review, we first summarize major methods for glycopeptide/glycoprotein enrichment, followed by the chemical and enzymatic methods to generate a mass tag for glycosylation site identification. We next discuss the systematic and quantitative analysis of glycoprotein dynamics. Reversible protein glycosylation is dynamic, and systematic study of glycoprotein dynamics helps us gain insight into glycoprotein functions. The last part of this review focuses on the applications of MS-based proteomics to study glycoproteins in different biological systems, including yeasts, plants, mice, human cells, and clinical samples. Intact glycopeptide analysis is also included in this section. Because of the importance of glycoproteins in complex biological systems, the field of glycoproteomics will continue to grow in the next decade. Innovative and effective MS-based methods will exponentially advance glycoscience, and enable us to identify glycoproteins as effective biomarkers for disease detection and drug targets for disease treatment. © 2019 Wiley Periodicals, Inc. Mass Spec Rev 9999: XX-XX, 2019.

Poly(ionic liquid)s as a distinct receptor material to create a highly-integrated sensing platform for efficiently identifying numerous saccharides

A highly-integrated sphere-based sensing platform for directly identifying numerous saccharides very efficiently is developed.

Saccharides have strong hydrophilicities, and are complex molecular structures with subtle structure differences, and tremendous structural variations. The creation of one sensing platform capable of efficiently identifying such target systems presents a huge challenge. Using the integration of unique multiple noncovalent interactions simultaneously occurring in poly(ionic liquid)s (PILs) with multiple signaling channels, in this research an aggregation-induced emission (AIE)-doped photonic structured PIL sphere is constructed. It is found that such a sphere can serve as a highly integrated platform to provide abundant fingerprints for directly sensing numerous saccharides with an unprecedented efficiency. As a demonstration, 23 saccharides can be conveniently identified using only one sphere. More importantly, by using simple ion-exchanges of PIL receptors or/and increasing the AIE signaling channels, this platform is able to perform, on demand, different sensing tasks very efficiently. This is demonstrated by using it for the detection of difficult targets, such as greatly extended saccharides as well as mixed targets, in real-life examples on one or two spheres. The findings show that this new class of platform is very promising for addressing the challenges of identifying saccharides.

Modeling Boronic Acid Based Fluorescent Saccharide Sensors: Computational Investigation of d-Fructose Binding to Dimethylaminomethylphenylboronic Acid

Designing organic saccharide sensors for use in aqueous solution is a nontrivial endeavor. Incorporation of hydrogen bonding groups on a sensor's receptor unit to target saccharides is an obvious strategy but not one that is likely to ensure analyte-receptor interactions over analyte-solvent or receptor-solvent interactions. Phenylboronic acids are known to reversibly and covalently bind saccharides (diols in general) with highly selective affinity in aqueous solution. Therefore, recent work has sought to design such sensors and understand their mechanism for allowing fluorescence with bound saccharides. In past work, binding orientations of several saccharides were determined to dimethylaminomethylphenylboronic acid (DMPBA) receptors with an anthracene fluorophore; however, the binding orientation of d-fructose to such a sensor could not be determined. In this work, we investigate the potential binding modes by generating 20 possible bidentate and six possible tridentate modes between fructose and DMPBA, a simplified receptor model. Gas phase and implicit solvent geometry optimizations, with a myriad functional/basis set pairs, were carried out to identify the lowest energy bidentate and tridentate binding modes of d-fructose to DMPBA. An interesting hydrogen transfer was observed during selected bidentate gas phase optimizations; this transfer suggests a strong sharing of the hydrogen atom between the boronate hydroxyl and amine nitrogen.

Recognition and protection of glycosphingolipids by synthetic nanoparticle receptors

Nanoparticle receptors were synthesized through micellar imprinting to bind glycosphingolipids with 20-140 μM binding affinities, meanwhile distinguishing glycan composition, the number of acyl chains, and hydroxylation of acyl chains in the lipids. The strong binding enabled the receptors to protect their target glycolipids dispersed in lipid membranes from enzymatic degradation.

Silencing glycosaminoglycan functions in mouse embryonic stem cells with small molecule antagonists

Glycosylation is a ubiquitous post-translational modification that decorates proteins and lipids with glycans. These glycans can play critical roles in regulating biological events, and therefore, the discovery of strategies that target these molecules represent an important advancement toward understanding and controlling glycan-mediated cellular phenotypes. We describe the use of a small molecule, surfen, to temporarily silence the functions mediated by heparan sulfate glycosaminoglycans in mouse embryonic stem cells. Surfen binds heparan sulfate to antagonize growth factor interactions, thereby inhibiting signal transduction events that lead to differentiation. The strategies outlined in this chapter allow the characterization of resulting antagonistic effects caused by glycan-small molecule binding events toward maintaining embryonic stem cell pluripotency, curbing differentiation, and inhibiting signaling events.

Synthesis and Evaluation of Protein-Phenylboronic Acid Conjugates as Lectin Mimetics

Glycan-binding molecules, such as lectins, are very important tools for characterizing, imaging, or targeting glycans and are often involved in either physiological or pathological processes. However, their availability is far less compared to the diversity of native glycans. Therefore, development of lectin mimetics with desired specificity and affinity is in high demand. Boronic acid reacts with 1,2- and 1,3-diols of saccharides in aqueous media through reversible boronate ester formation and are regarded as synthetic lectin mimetics. In this study, bovine serum albumin (BSA)-phenylboronic acid (PBA) conjugates were synthesized in a density-controlled manner by targeting both aspartic and glutamic acids to afford lectin mimetics with multivalent PBA, as multivalency is a key factor for glycan recognition in both specificity and affinity. The resultant BSA-PBA conjugates were characterized by sodium dodecyl sulfate polyacrylamide gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. Their macrophage cell surface glycan-binding capacity was characterized by a competitive lectin-binding assay examined by flow cytometry, and 3-(4,5-di-methylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay showed biocompatibility. These novel lectin mimetics will find a broad range of applications as they can be wittingly modified, altering binding specificity and capacity.

Automated Chemical Oligosaccharide Synthesis: Novel Approach to Traditional Challenges

Advances in carbohydrate chemistry have certainly made common oligosaccharides much more accessible. However, many current methods still rely heavily upon specialized knowledge of carbohydrate chemistry. The application of automated technologies to chemical and life science applications such as genomics and proteomics represents a vibrant field. These automated technologies also present opportunities for their application to organic synthesis, including that of the synthesis of oligosaccharides. However, application of automated methods to the synthesis of carbohydrates is an underdeveloped area as compared to other classes of biomolecules. The overarching goal of this review article is to present the advances that have been made at the interface of carbohydrate chemistry and automated technology.

Boronic acid liposomes for cellular delivery and content release driven by carbohydrate binding

Boronic acid liposomes enable triggered content release and cell delivery driven by carbohydrate binding. Dye release assays using hydrophilic and hydrophobic fluorophores validate dose-dependent release upon carbohydrate treatment. Microscopy results indicate dramatic enhancements in cell delivery, showcasing the prospects of boronic acid lipids for drug delivery.