Chemoenzymatic modular assembly of O-GalNAc glycans for functional glycomics

Recent progress in chemoenzymatic synthesis of human glycans

Glycan is an essential cell component that usually exists in either a free form or a glycoconjugated form. Glycosylation affects the regulatory function of glycoconjugates in health and disease development, indicating the key role of glycan in organisms. Because of the complexity and diversity of glycan structures, it is challenging to prepare structurally well-defined glycans, which hinders the investigation of biological functions at the molecular level. Chemoenzymatic synthesis is an attractive approach for preparing complex glycans, because it avoids tedious protecting group manipulations in chemical synthesis and ensures high regio- and stereo-selectivity of glucosides during glycan assembly. Herein, enzymes, such as glycosyltransferases (GTs) and glycosidases (GHs), and sugar donors involved in the chemoenzymatic synthesis of human glycans are initially discussed. Many state-of-the-art chemoenzymatic methodologies are subsequently displayed and summarized to illustrate the development of synthetic human glycans, for example, N- and O-linked glycans, human milk oligosaccharides, and glycosaminoglycans. Thus, we provide an overview of recent chemoenzymatic synthetic designs and applications for synthesizing complex human glycans, along with insights into the limitations and perspectives of the current methods.

Divergent synthesis of amino acid-linked O-GalNAc glycan core structures

O-GalNAc glycans, also known as mucin-type O-glycans, are primary constituents of mucins on various mucosal sites of the body and also ubiquitously expressed on cell surface and secreted proteins. They have crucial roles in a wide range of physiological and pathological processes, including tumor growth and progression. In addition, altered expression of O-GalNAc glycans is frequently observed during different disease states. Research dedicated to unraveling the structure-function relationships of O-GalNAc glycans has led to the discovery of disease biomarkers and diagnostic tools and the development of O-glycopeptide-based cancer vaccines. Many of these efforts require amino acid-linked O-GalNAc core structures as building blocks to assemble complex O-glycans and glycopeptides. There are eight core structures (cores one to eight), from which all mucin-type O-glycans are derived. In this protocol, we describe the first divergent synthesis of all eight cores from a versatile precursor in practical scales. The protocol involves (i) chemical synthesis of the orthogonally protected precursor (3 days) from commercially available materials, (ii) chemical synthesis of five unique glycosyl donors (1-2 days for each donor) and (iii) selective deprotection of the precursor and assembly of the eight cores (2-4 days for each core). The procedure can be adopted to prepare O-GalNAc cores linked to serine, threonine and tyrosine, which can then be utilized directly for solid-phase glycopeptide synthesis or chemoenzymatic synthesis of complex O-glycans. The procedure empowers researchers with fundamental organic chemistry skills to prepare gram scales of any desired O-GalNAc core(s) or all eight cores concurrently.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2021-2022

The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well-established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.

Genetic and functional diversity of β-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis

β-N-Acetylgalactosamine-containing glycans play essential roles in several biological processes, including cell adhesion, signal transduction, and immune responses. β-N-Acetylgalactosaminidases hydrolyze β-N-acetylgalactosamine linkages of various glycoconjugates. However, their biological significance remains ambiguous, primarily because only one type of enzyme, exo-β-N-acetylgalactosaminidases that specifically act on β-N-acetylgalactosamine residues, has been documented to date. In this study, we identify four groups distributed among all three domains of life and characterize eight β-N-acetylgalactosaminidases and β-N-acetylhexosaminidase through sequence-based screening of deep-sea metagenomes and subsequent searching of public protein databases. Despite low sequence similarity, the crystal structures of these enzymes demonstrate that all enzymes share a prototype structure and have diversified their substrate specificities (oligosaccharide-releasing, oligosaccharide/monosaccharide-releasing, and monosaccharide-releasing) through the accumulation of mutations and insertional amino acid sequences. The diverse β-N-acetylgalactosaminidases reported in this study could facilitate the comprehension of their structures and functions and present evolutionary pathways for expanding their substrate specificity.

Highly stereoselective α-glycosylation with GalN3 donors enabled collective synthesis of mucin-related tumor associated carbohydrate antigens

Mucin-related tumor-associated carbohydrate antigens (TACAs) are important and interesting targets for cancer vaccine therapy. However, efficient access to a library of mucin-related TACAs remains a challenging task. One of the key issues is the challenging construction of α-GalNAc linkages. Here, we report highly stereoselective α-glycosylation with GalN3N-phenyl trifluoroacetimidate donors, which features excellent yields, outstanding stereoselectivities, broad substrate scope and mild reaction conditions. This method is successfully applied to highly stereoselective synthesis of GalN3-α-O-Ser, which served as the common intermediate for collective synthesis of a wide range of TACAs including TN antigen, STN antigen, 2,6 STF antigen, 2,3 STF antigen, glycophorin and cores 1-8 mucin-type O-glycans. In particular, the rationale for this highly stereoselective α-glycosylation is provided for the first time using DFT calculations and mechanistic studies, highlighting the crucial roles of reagent combinations (TMSI and Ph3PO) and the H-bonding directing effect of the N3 group.

Serum antibody screening using glycan arrays

Humans and other animals produce a diverse collection of antibodies, many of which bind to carbohydrate chains, referred to as glycans. These anti-glycan antibodies are a critical part of our immune systems' defenses. Whether induced by vaccination or natural exposure to a pathogen, anti-glycan antibodies can provide protection against infections and cancers. Alternatively, when an immune response goes awry, antibodies that recognize self-glycans can mediate autoimmune diseases. In any case, serum anti-glycan antibodies provide a rich source of information about a patient's overall health, vaccination history, and disease status. Glycan microarrays provide a high-throughput platform to rapidly interrogate serum anti-glycan antibodies and identify new biomarkers for a variety of conditions. In addition, glycan microarrays enable detailed analysis of the immune system's response to vaccines and other treatments. Herein we review applications of glycan microarray technology for serum anti-glycan antibody profiling.

Integrated analysis of natural glycans using a versatile pyrazolone-type heterobifunctional tag ANPMP

Glycans mediate various biological processes through carbohydrate-protein interactions, and glycan microarrays have become indispensable tools for understanding these mechanisms. However, advances in functional glycomics are hindered by the absence of convenient and universal methods for obtaining natural glycan libraries with diverse structures from glycoconjugates. To address this challenge, we have developed an integrative approach that enables one-pot release and simultaneously capture, separation, structural characterization, and functional analysis of N/O-glycans. Using this approach, glycoconjugates are incubated with a pyrazolone-type heterobifunctional tag-ANPMP to obtain glycan-2ANPMP conjugates, which are then converted to glycan-AEPMP conjugates. We prepared a tagged glycan library from porcine gastric mucin, soy protein, human milk oligosaccharides, etc. Following derivatization by N-acetylation and permethylation, glycans were subjected to detailed structural characterization by ESI-MSn analysis, which revealed >83 highly pure glycan-AEPMPs containing various natural glycan epitopes. A shotgun microarray is constructed to study the fine details of glycan-bindings by proteins and antisera.

Recent advances in enzymatic and chemoenzymatic synthesis of N- and O-glycans

Glycosylation is one of the most common post-translational modifications of proteins, which plays essential roles in regulating the biological functions of proteins. Efficient and versatile methods for the synthesis of homogeneous and well-defined N- and O-glycans remain an urgent need for biological studies and biomedical applications. Despite their structural complexity, tremendous progress has been made in the synthesis of N- and O-glycans in recent years. This review discusses some recent advances in the enzymatic and chemoenzymatic synthesis of N- and O-glycans.

Glycosyltransferases as versatile tools to study the biology of glycans

All cells are decorated with complex carbohydrate structures called glycans that serve as ligands for glycan-binding proteins (GBPs) to mediate a wide range of biological processes. Understanding the specific functions of glycans is key to advancing an understanding of human health and disease. However, the lack of convenient and accessible tools to study glycan-based interactions has been a defining challenge in glycobiology. Thus, the development of chemical and biochemical strategies to address these limitations has been a rapidly growing area of research. In this review, we describe the use of glycosyltransferases (GTs) as versatile tools to facilitate a greater understanding of the biological roles of glycans. We highlight key examples of how GTs have streamlined the preparation of well-defined complex glycan structures through chemoenzymatic synthesis, with an emphasis on synthetic strategies allowing for site- and branch-specific display of glyco-epitopes. We also describe how GTs have facilitated expansion of glyco-engineering strategies, on both glycoproteins and cell surfaces. Coupled with advancements in bioorthogonal chemistry, GTs have enabled selective glyco-epitope editing of glycoproteins and cells, selective glycan subclass labeling, and the introduction of novel biomolecule functionalities onto cells, including defined oligosaccharides, antibodies, and other proteins. Collectively, these approaches have contributed great insight into the fundamental biological roles of glycans and are enabling their application in drug development and cellular therapies, leaving the field poised for rapid expansion.

Protein glycosylation and glycoinformatics for novel biomarker discovery in neurodegenerative diseases

Glycosylation is a common post-translational modification of brain proteins including cell surface adhesion molecules, synaptic proteins, receptors and channels, as well as intracellular proteins, with implications in brain development and functions. Using advanced state-of-the-art glycomics and glycoproteomics technologies in conjunction with glycoinformatics resources, characteristic glycosylation profiles in brain tissues are increasingly reported in the literature and growing evidence shows deregulation of glycosylation in central nervous system disorders, including aging associated neurodegenerative diseases. Glycan signatures characteristic of brain tissue are also frequently described in cerebrospinal fluid due to its enrichment in brain-derived molecules. A detailed structural analysis of brain and cerebrospinal fluid glycans collected in publications in healthy and neurodegenerative conditions was undertaken and data was compiled to create a browsable dedicated set in the GlyConnect database of glycoproteins (https://glyconnect.expasy.org/brain). The shared molecular composition of cerebrospinal fluid with brain enhances the likelihood of novel glycobiomarker discovery for neurodegeneration, which may aid in unveiling disease mechanisms, therefore, providing with novel therapeutic targets as well as diagnostic and progression monitoring tools.

Abnormal glycosylation in glioma: related changes in biology, biomarkers and targeted therapy

Glioma is a rapidly growing and aggressive primary malignant tumor of the central nervous system that can diffusely invade the brain tissue around, and the prognosis of patients is not significantly improved by traditional treatments. One of the most general posttranslational modifications of proteins is glycosylation, and the abnormal distribution of this modification in gliomas may shed light on how it affects biological behaviors of glioma cells, including proliferation, migration, and invasion, which may be produced by regulating protein function, cell-matrix and cell‒cell interactions, and affecting receptor downstream pathways. In this paper, from the perspective of regulating protein glycosylation changes and abnormal expression of glycosylation-related proteins (such as glycosyltransferases in gliomas), we summarize how glycosylation may play a crucial role in the discovery of novel biomarkers and new targeted treatment options for gliomas. Overall, the mechanistic basis of abnormal glycosylation affecting glioma progression remains to be more widely and deeply explored, which not only helps to inspire researchers to further explore related diagnostic and prognostic markers but also provides ideas for discovering effective treatment strategies and improving glioma patient survival and prognosis.

Convergent chemoenzymatic synthesis of O-GalNAc rare cores 5, 7, 8 and their sialylated forms

All O-GalNAc glycans are derived from 8 cores with 2 or 3 monosaccharides linked via α- or β-glycosidic bonds. While chemical and chemoenzymatic syntheses of β-linked cores 1-4 and 6 and derived glycans have been well developed, the preparation of α-linked rare cores 5, 7, and 8 is challenging due to the presence of this 1,2-cis linkage. Meanwhile, the biosynthesis and functional roles of these structures are poorly understood. Herein, we synthesize 3 α-linked rare cores with exclusive α-configuration from a versatile precursor through multifaceted chemical modulations. Efficient regioselective α2-6sialylion of the rare cores was then achieved by Photobacterium damselae α2-6sialyltransferase-catalyzed reactions. These structures, together with β-linked cores 1-4 and 6, and their sialylated forms, were fabricated into a comprehensive O-GalNAc core microarray to profile the binding of clinically important GalNAc-specific lectins. It is found that only Tn, (sialyl-)core 5, and core 7 are the binders of WFL, VVL, and SBA, while DBA only recognized (sialyl-)core 5, and Jacalin is the only lectin that binds core 8. In addition, activity assays of human α-N-acetylgalactosaminide α2-6sialyltransferases (ST6GalNAcTs) towards the cores suggested that ST6GalNAc1 may be involved in the biosynthesis of previously identified sialyl-core 5 and sialyl-core 8 glycans. In conclusion, we provide efficient routes to access α-linked O-GalNAc rare cores and derived structures, which are valuable tools for functional glycomics studies of mucin O-glycans.

Systematic synthesis of bisected N-glycans and unique recognitions by glycan-binding proteins

Bisected N-glycans represent a unique class of protein N-glycans that play critical roles in many biological processes. Herein, we describe the systematic synthesis of these structures. A bisected N-glycan hexasaccharide was chemically assembled with two orthogonal protecting groups attached at the C2 of the branching mannose residues, followed by sequential installation of GlcNAc and LacNAc building blocks to afford two asymmetric bisecting "cores". Subsequent enzymatic modular extension of the "cores" yielded a comprehensive library of biantennary N-glycans containing the bisecting GlcNAc and presenting 6 common glycan determinants in a combinatorial fashion. These bisected N-glycans and their non-bisected counterparts were used to construct a distinctive glycan microarray to study their recognition by a wide variety of glycan-binding proteins (GBPs), including plant lectins, animal lectins, and influenza A virus hemagglutinins. Significantly, the bisecting GlcNAc could bestow (PHA-L, rDCIR2), enhance (PHA-E), or abolish (ConA, GNL, anti-CD15s antibody, etc.) N-glycan recognition of specific GBPs, and is tolerated by many others. In summary, synthesized compounds and the unique glycan microarray provide ideal standards and tools for glycoanalysis and functional glycomic studies. The microarray data provide new information regarding the fine details of N-glycan recognition by GBPs, and in turn improve their applications.

Integrated Chemoenzymatic Approach to Streamline the Assembly of Complex Glycopeptides in the Liquid Phase

Glycosylation of proteins is a complicated post-translational modification. Despite the significant progress in glycoproteomics, accurate functions of glycoproteins are still ambiguous owing to the difficulty in obtaining homogeneous glycopeptides or glycoproteins. Here, we describe a streamlined chemoenzymatic method to prepare complex glycopeptides by integrating hydrophobic tag-supported chemical synthesis and enzymatic glycosylations. The hydrophobic tag is utilized to facilitate peptide chain elongation in the liquid phase and expeditious product separation. After removal of the tag, a series of glycans are installed on the peptides via efficient glycosyltransferase-catalyzed reactions. The general applicability and robustness of this approach are exemplified by efficient preparation of 16 well-defined SARS-CoV-2 O-glycopeptides, 4 complex MUC1 glycopeptides, and a 31-mer glycosylated glucagon-like peptide-1. Our developed approach will open up a new range of easy access to various complex glycopeptides of biological importance.

Small tools for sweet challenges: advances in microfluidic technologies for glycan synthesis

Glycans, including oligosaccharides and glycoconjugates, play an integral role in modulating the biological functions of macromolecules. Many physiological and pathological processes are mediated by interactions between glycans, which has led to the use of glycans as biosensors for pathogen and biomarker detection. Elucidating the relationship between glycan structure and biological function is critical for advancing our understanding of the impact glycans have on human health and disease and for expanding the repertoire of glycans available for bioanalysis, especially for diagnostics. Such efforts have been limited by the difficulty in obtaining sufficient quantities of homogenous glycan samples needed to resolve the exact relationships between glycan structure and their structural or modulatory functions on a given glycoconjugate. Synthetic strategies offer a viable route for overcoming these technical hurdles. In recent years, microfluidics have emerged as powerful tools for realizing high-throughput and reproducible syntheses of homogenous glycans for the potential use in functional studies. This critical review provides readers with an overview of the microfluidic technologies that have been developed for chemical and enzymatic glycan synthesis. The advantages and limitations associated with using microreactor platforms to improve the scalability, productivity, and selectivity of glycosylation reactions will be discussed, as well as suggested future work that can address certain pitfalls.

Structural insights into host-microbe glycointeractions

Despite their ubiquitous presence in biological systems, glycans have historically received less attention than they deserved. Investigations in recent years have featured important findings about the role of glycans in regulating the human gut microbiota. Here, we present a brief overview of current trends that shape future directions of computational and experimental research approaches and add to our understanding of host-microbe glycointeractions.

LectinOracle: A Generalizable Deep Learning Model for Lectin-Glycan Binding Prediction

Ranging from bacterial cell adhesion over viral cell entry to human innate immunity, glycan-binding proteins or lectins are abound in nature. Widely used as staining and characterization reagents in cell biology and crucial for understanding the interactions in biological systems, lectins are a focal point of study in glycobiology. Yet the sheer breadth and depth of specificity for diverse oligosaccharide motifs has made studying lectins a largely piecemeal approach, with few options to generalize. Here, LectinOracle, a model combining transformer-based representations for proteins and graph convolutional neural networks for glycans to predict their interaction, is presented. Using a curated data set of 564,647 unique protein-glycan interactions, it is shown that LectinOracle predictions agree with literature-annotated specificities for a wide range of lectins. Using a range of specialized glycan arrays, it is shown that LectinOracle predictions generalize to new glycans and lectins, with qualitative and quantitative agreement with experimental data. It is further demonstrated that LectinOracle can be used to improve lectin classification, accelerate lectin directed evolution, predict epidemiological outcomes in the context of influenza virus, and analyze whole lectomes in host-microbe interactions. It is envisioned that the herein presented platform will advance both the study of lectins and their role in (glyco)biology.

General Tolerance of Galactosyltransferases toward UDP-galactosamine Expands Their Synthetic Capability

Accessing large numbers of structurally diverse glycans and derivatives is essential to functional glycomics. We showed a general tolerance of galactosyltransferases toward uridine-diphosphate-galactosamine (UDP-GalN), which is not a commonly used sugar nucleotide donor. The property was harnessed to develop a two-step chemoenzymatic strategy for facile synthesis of novel and divergent N-acetylgalactosamine (GalNAc)-glycosides and derivatives in preparative scales. The discovery and the application of the new property of existing glycosyltransferases expand their catalytic capabilities in generating novel carbohydrate linkages, thus prompting the synthesis of diverse glycans and glycoconjugates for biological studies.