Recent progress in the field of glycopeptide synthesis

Chemical synthesis and functional evaluation of glycopeptides and glycoproteins containing rare glycosyl amino acid linkages

Covering: 1987 to 2023Naturally existing glycoproteins through post-translational protein glycosylation are highly heterogeneous, which not only impedes the structure-function studies, but also hinders the development of their potential medical usage. Chemical synthesis represents one of the most powerful tools to provide the structurally well-defined glycoforms. Being the key step of glycoprotein synthesis, glycosylation usually takes place at serine, threonine, and asparagine residues, leading to the predominant formation of the O- and N-glycans, respectively. However, other amino acid residues containing oxygen, nitrogen, sulfur, and nucleophilic carbon atoms have also been found to be glycosylated. These diverse glycoprotein linkages, occurring from microorganisms to plants and animals, play also pivotal biological roles, such as in cell-cell recognition and communication. The availability of these homogenous rare glycopeptides and glycoproteins can help decipher the glyco-code for developing therapeutic agents. This review highlights the chemical approaches for assembly of the functional glycopeptides and glycoproteins bearing these "rare" carbohydrate-amino acid linkages between saccharide and canonical amino acid residues and their derivatives.

Protein cysteine S-glycosylation: oxidative hydrolysis of protein S-glycosidic bonds in aqueous alkaline environments

Some glycoproteins contain carbohydrates S-linked to cysteine (Cys) residues. However, relatively few S-glycosylated proteins have been detected, due to the lack of an effective research methodology. This work outlines a general concept for the detection of S-glycosylation sites in proteins. The approach was verified by exploratory experiments on a model mixture of β-S-glucosylated polypeptides obtained by the chemical transformation of lysozyme P00698. The model underwent two processes: (1) oxidative hydrolysis of S-glycosidic bonds under alkaline conditions to expose the thiol group of Cys residues; (2) thiol S-alkylation leading to thiol S-adduct formation at the former S-glycosylation sites. Oxidative hydrolysis was conducted in aqueous urea, dimethyl sulfoxide, or trifluoroethanol, with silver nitrate as the reaction promoter, in the presence of triethylamine and/or pyridine. The concurrent formation of stable protein silver thiolates, gluconic acid, and silver nanoclusters was observed. The essential de-metalation of protein silver thiolates using dithiothreitol preceded the S-labeling of Cys residues with 4-vinyl pyridine or a fluorescent reagent. The S-labeled model was sequenced by tandem mass spectrometry to obtain data on the modifications and their distribution over the protein chains. This enabled the efficiency of both S-glycosidic bonds hydrolysis and S-glycosylation site labeling to be evaluated. Suggestions are also given for testing this novel strategy on real proteomic samples.

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.

Design and Synthesis of Mucin-Inspired Glycopolymers

Mucins are bottlebrush biopolymers that are glycoproteins on the surfaces of cells and as hydrogels secreted inside and outside the body. Mucin function in biology includes cell-cell recognition, signaling, protection, adhesion, and lubrication. Because of their attractive and diverse properties, mucins have recently become the focus of synthetic efforts by researchers who hope to understand and emulate these biomaterials. This review is focused on the development of methodologies for preparing mucin-inspired synthetic oligomers and glycopolymers, including solid-phase synthesis, polymerization of glycosylated monomers, and post-polymerization grafting of glycans to polymer chains. How these synthetic mucins have been used in health applications is discussed. Natural mucins are formed from a conserved set of monomers that are combined into chains of different sequences and lengths to achieve materials with widely diverse properties. Adopting this design paradigm from natural mucins could lead to next-generation bioinspired synthetic materials.

Parallel Glyco-SPOT Synthesis of Glycopeptide Libraries

Glycan recognition is typically studied using free glycans, but glycopeptide presentations represent more physiological conditions for glycoproteins. To facilitate studies of glycopeptide recognition, we developed Glyco-SPOT synthesis, which enables the parallel production of diverse glycopeptide libraries at microgram scales. The method uses a closed system for prolonged reactions required for coupling Fmoc-protected glycoamino acids, including O-, N-, and S-linked glycosides, and release conditions to prevent side reactions. To optimize reaction conditions and sample reaction progress, we devised a biopsy testing method. We demonstrate the efficient utilization of such microscale glycopeptide libraries to determine the specificity of glycan-recognizing antibodies (e.g., CTD110.6) using microarrays, enzyme specificity on-array and in-solution (e.g., ST6GalNAc1, GCNT1, and T-synthase), and binding kinetics using fluorescence polarization. We demonstrated that the glycosylation on these peptides can be expanded using glycosyltransferases both in-solution and on-array. This technology will promote the discovery of biological functions of peptide modifications by glycans.

Glycoprotein Mimics with Tunable Functionalization through Global Amino Acid Substitution and Copper Click Chemistry

Glycoproteins and their mimics are challenging to produce because of their large number of polysaccharide side chains that form a densely grafted protein-polysaccharide brush architecture. Herein a new approach to protein bioconjugate synthesis is demonstrated that can approach the functionalization densities of natural glycoproteins through oligosaccharide grafting. Global amino acid substitution is used to replace the methionine residues in a methionine-enriched elastin-like polypeptide with homopropargylglycine (HPG); the substitution was found to replace 93% of the 41 methionines in the protein sequence as well as broaden and increase the thermoresponsive transition. A series of saccharides were conjugated to the recombinant protein backbones through copper(I)-catalyzed alkyne-azide cycloaddition to determine reactivity trends, with 83-100% glycosylation of HPGs. Only an acetyl-protected sialyllactose moiety showed a lower level of 42% HPG glycosylation that is attributed to steric hindrance. The recombinant glycoproteins reproduced the key biofunctional properties of their natural counterparts such as viral inhibition and lectin binding.

Glycoconjugate synthesis using chemoselective ligation

Chemoselective ligation of carbohydrates and polypeptides was achieved using an adipic acid dihydrazide cross-linker. The reducing end of a carbohydrate is efficiently attached to peptides in two steps, constructing a glycoconjugate in high yield and with high regioselectivity, enabling the production of homogeneous glycoconjugates.

Solvent- and catalyst-free transamidations of unprotected glycosyl carboxamides

New green and atom efficient transamidation reactions of various glycosyl carboxamides with primary and secondary amines are described.

Stepwise triple-click functionalization of synthetic peptides

The increasing popularity of peptides as promising molecular scaffolds for biomedical applications and as valuable biochemical probes makes new methods allowing for their modification highly desirable. We describe herein an optimized protocol based on a sequence of CuAAC click reactions and selective deprotection steps, which leads to an efficient multi-functionalization of synthetic peptides. The methodology has been successfully applied to the construction of defined heteroglycopeptides and fluorophore-quencher-containing probes for proteases. The developed chemistry thus represents an important addition to the available toolbox of methods enabling efficient postsynthetic modification of peptides. The commercial availability of numerous azide probes further greatly extends the application potential of the described methodology.

Using Chemical Synthesis To Study and Apply Protein Glycosylation

Protein glycosylation is one of the most common post-translational modifications and can influence many properties of proteins. Abnormal protein glycosylation can lead to protein malfunction and serious disease. While appreciation of glycosylation's importance is growing in the scientific community, especially in recent years, a lack of homogeneous glycoproteins with well-defined glycan structures has made it difficult to understand the correlation between the structure of glycoproteins and their properties at a quantitative level. This has been a significant limitation on rational applications of glycosylation and on optimizing glycoprotein properties. Through the extraordinary efforts of chemists, it is now feasible to use chemical synthesis to produce collections of homogeneous glycoforms with systematic variations in amino acid sequence, glycosidic linkage, anomeric configuration, and glycan structure. Such a technical advance has greatly facilitated the study and application of protein glycosylation. This Perspective highlights some representative work in this research area, with the goal of inspiring and encouraging more scientists to pursue the glycosciences.

Introduction: General Aspects of the Chemical Biology of Glycoproteins

This chapter is meant to serve as an introduction to the remainder of the book by providing general background on the chemical biology of glycoproteins as well as a brief review of the chapters that follow. The purpose here is to introduce some basic concepts common to many forms of glycosylation for those readers who may be unfamiliar with the field. We begin with a discussion of the strategies and methods used to study protein glycosylation. During the overview, an effort is made to highlight a few relevant aspects of chemical glycobiology, including glycoprotein biosynthesis and a brief description of the synthesis and function of glycoproteins. Finally, we have a summary of the contributions from chemical biology over the years. It is our hope that, after reading this introductory chapter, the reader will have a broad view of the chemical glycobiology field as it currently stands and a deeper appreciation for some of the unique ideas that chemical biology brings to the field.

Obstacles and solutions for chemical synthesis of syndecan-3 (53-62) glycopeptides with two heparan sulfate chains

Proteoglycans play critical roles in many biological events. Due to their structural complexities, strategies towards synthesis of this class of glycopeptides bearing well-defined glycan chains are urgently needed. In this work, we give the full account of the synthesis of syndecan-3 glycopeptide (53-62) containing two different heparan sulfate chains. For assembly of glycans, a convergent 3+2+3 approach was developed producing two different octasaccharide amino acid cassettes, which were utilized towards syndecan-3 glycopeptides. The glycopeptides presented many obstacles for post-glycosylation manipulation, peptide elongation, and deprotection. Following screening of multiple synthetic sequences, a successful strategy was finally established by constructing partially deprotected single glycan chain containing glycopeptides first, followed by coupling of the glycan-bearing fragments and cleavage of the acyl protecting groups.

Tailored Synthesis of 162-Residue S-Monoglycosylated GM2-Activator Protein (GM2AP) Analogues that Allows Facile Access to a Protein Library

A synthetic protocol for the preparation of 162-residue S-monoglycosylated GM2-activator protein (GM2AP) analogues bearing various amino acid substitutions for Thr69 has been developed. The facile incorporation of the replacements into the protein was achieved by means of a one-pot/N-to-C-directed sequential ligation strategy using readily accessible middle N-sulfanylethylanilide (SEAlide) peptides each consisting of seven amino acid residues. A kinetically controlled ligation protocol was successfully applied to the assembly of three peptide segments covering the GM2AP. The native chemical ligation (NCL) reactivities of the SEAlide peptides can be tuned by the presence or absence of phosphate salts. Furthermore, NCL of the alkyl thioester fragment [GM2AP (1-31)] with the N-terminal cysteinyl prolyl thioester [GM2AP (32-67)] proceeded smoothly to yield the 67-residue prolyl thioester, with the prolyl thioester moiety remaining intact. This newly developed strategy enabled the facile synthesis of GM2AP analogues. Thus, we refer to this synthetic protocol as "tailored synthesis" for the construction of a GM2AP library.

N-Linked Glycosyl Auxiliary-Mediated Native Chemical Ligation on Aspartic Acid: Application towards N-Glycopeptide Synthesis

A practical approach towards N-glycopeptide synthesis using an auxiliary-mediated dual native chemical ligation (NCL) has been developed. The first NCL connects an N-linked glycosyl auxiliary to the thioester side chain of an N-terminal aspartate oligopeptide. This intermediate undergoes a second NCL with a C-terminal thioester oligopeptide. Mild cleavage provides the desired N-glycopeptide.

Glycosylation, an effective synthetic strategy to improve the bioavailability of therapeutic peptides

Glycosylation of peptides is a promising strategy for modulating the physicochemical properties of peptide drugs and for improving their absorption through biological membranes. This review highlights various methods for the synthesis of glycoconjugates and recent progress in the development of glycosylated peptide therapeutics. Furthermore, the impacts of glycosylation in overcoming the existing barriers that restrict oral and brain delivery of peptides are described herein.

Applications of Chemical Ligation in Peptide Synthesis via Acyl Transfer

The utility of native chemical ligation (NCL) in the solution or solid phase synthesis of peptides, cyclic peptides, glycopeptides, and neoglycoconjugates is reviewed. In addition, the mechanistic details of inter- or intra-molecular NCLs are discussed from experimental and computational points of view.

Chemical and chemoenzymatic synthesis of glycoproteins for deciphering functions

Glycoproteins are an important class of biomolecules involved in a number of biological recognition processes. However, natural and recombinant glycoproteins are usually produced as mixtures of glycoforms that differ in the structures of the pendent glycans, which are difficult to separate in pure glycoforms. As a result, synthetic homogeneous glycopeptides and glycoproteins have become indispensable probes for detailed structural and functional studies. A number of elegant chemical and biological strategies have been developed for synthetic construction of tailor-made, full-size glycoproteins to address specific biological problems. In this review, we highlight recent advances in chemical and chemoenzymatic synthesis of homogeneous glycoproteins. Selected examples are given to demonstrate the applications of tailor-made, glycan-defined glycoproteins for deciphering glycosylation functions.

Chemical assembly of N-glycoproteins: a refined toolbox to address a ubiquitous posttranslational modification

Incremental developments in the chemistry of peptides, proteins and carbohydrates have enabled researchers to assemble entire glycoproteins with high precision. Based on sophisticated ligation chemistries pure glycoproteins bearing a single glycosylation pattern have become available. The impact of N-glycosylation on the function of glycoproteins is generally recognized but not well understood. Based on the recent advances in the synthesis of glycoproteins by chemical methods researchers can finally start to elucidate the various roles of carbohydrates in complex biomolecules in detail.

Enhanced epimerization of glycosylated amino acids during solid-phase peptide synthesis

Glycopeptides are extremely useful for basic research and clinical applications, but access to structurally defined glycopeptides is limited by the difficulties in synthesizing this class of compounds. In this study, we demonstrate that many common peptide coupling conditions used to prepare O-linked glycopeptides result in substantial amounts of epimerization at the α position. In fact, epimerization resulted in up to 80% of the non-natural epimer, indicating that it can be the major product in some reactions. Through a series of mechanistic studies, we demonstrate that the enhanced epimerization relative to nonglycosylated amino acids is due to a combination of factors, including a faster rate of epimerization, an energetic preference for the unnatural epimer over the natural epimer, and a slower overall rate of peptide coupling. In addition, we demonstrate that use of 2,4,6-trimethylpyridine (TMP) as the base in peptide couplings produces glycopeptides with high efficiency and low epimerization. The information and improved reaction conditions will facilitate the preparation of glycopeptides as therapeutic compounds and vaccine antigens.

Native N-glycopeptide thioester synthesis through N→S acyl transfer

Peptide thioesters are important tools for the total synthesis of proteins using native chemical ligation (NCL). Preparation of glycopeptide thioesters, that enable the assembly of homogeneously glycosylated proteins, is complicated by the perceived fragile nature of the sugar moiety. Herein, we demonstrate the compatibility of thioester formation via N→S acyl transfer with native N-glycopeptides and report observations that will aid in their preparation.

On-resin convergent synthesis of a glycopeptide from HIV gp120 containing a high mannose type N-linked oligosaccharide

This chapter describes a rapid and efficient approach for the solid-phase synthesis of N-linked glycopeptides that utilizes on-resin glycosylamine coupling to produce N-linked glycosylation sites. In this method, the full-length nonglycosylated peptide is first synthesized on a solid-phase support using standard Fmoc chemistry. The glycosylation site is then introduced through an orthogonally protected 2-phenylisopropyl (PhiPr) aspartic acid (Asp) residue. After selective deprotection of the Asp residue, a high mannose type oligosaccharide glycosylamine is coupled on-resin to the free Asp side chain to form a N-glycosidic bond. Subsequent protecting group removal and peptide cleavage from the resin ultimately yields the desired glycopeptide. This strategy provides an effective route for conducting glycosylation reactions on a solid-phase support, simplifies the process of glycopeptide purification relative to solution-phase glycopeptide synthesis strategies, and enables the recovery of potentially valuable, un-reacted oligosaccharides. This approach has been applied to the solid-phase synthesis of the N-linked high mannose glycosylated form of peptide T (ASTTTNYT), a fragment of the HIV-1 envelope glycoprotein gp120.

Synthesis of small glycopeptides by decarboxylative condensation and insight into the reaction mechanism

The chemical synthesis of homogeneous glycoproteins and glycopeptides facilitates progress toward understanding the functional role of carbohydrates attached to proteins and is important in the preparation of glycopeptide-based therapeutics. A series of protected and unprotected glycosyl dipeptides, glycopeptide I, which contained the alpha-ketoacid moiety at the C-terminus, were synthesized and ligated with a series of O-tert-butyl-protected N-hydroxylamino acids to afford O-tert-butyl-protected glycosyl tripeptides, glycopeptide II. The reactions were carried out under both anhydrous and aqueous conditions at neutral pH to produce glycopeptide products in yields ranging from 15% to 86% depending on the amino acids present at the ligation junction. The best yields were obtained when both the alpha-ketoacid and the N-hydroxylamino acid contained medium-sized side chains. In addition to the expected tripeptide product, 2,5-substituted oxazoles were isolated when O-tert-butyl protected N-hydroxylamines of glycine were employed in the reaction. The formation of the oxazole is believed to result from an intramolecular cyclization of the O-tert-butyl ester on a nitrilium ion intermediate followed by aromatization. A decarboxylative condensation between O(18)-labeled phenyl pyruvic acid and N-hydroxyphenethylamine oxalate salt resulted in amide products lacking the O(18)-label, providing further support for the nitrilium ion in the reaction pathway.

Chemical synthesis of homogeneous glycopeptides and glycoproteins

Oligosaccharides linked to proteins are known to play important roles in several biological events. However, oligosaccharides are heterogeneous, which has hindered detailed elucidation of oligosaccharide functions. In order to solve this problem, glycoproteins having homogeneous oligosaccharides have long been required. For this purpose, an efficient preparative method of complex-type oligosaccharides has been investigated from a natural source and this method was found to afford over 24 kinds of diverse complex-type oligosaccharides by use of chemical methods and branch-specific sequential glycosidase digestion. The sufficient amount of homogeneous complex type oligosaccharides obtained enabled us to examine the synthesis of homogeneous glycopeptides as well as glycoproteins by use of solid phase glycopeptide synthetic method and native chemical ligation. This review describes recent progress related to the efficient method of oligosaccharide preparation and synthesis of glycoproteins including bioactive erythropoietin.

Study of on-resin convergent synthesis of N-linked glycopeptides containing a large high mannose N-linked oligosaccharide

Here we present a convergent on-resin glycosylamine coupling strategy for solid phase N-linked glycopeptide synthesis, and apply it to the synthesis of high mannose containing glycopeptides. In this strategy, the 2-phenylisopropyl protecting group is used as an orthogonal handle to create glycosylation sites on-resin after synthesis of nonglycosylated peptides. In addition to allowing selective deprotection of aspartic acid residues for creation of glycosylation sites, the 2-phenylisopropyl protecting group also efficiently suppresses aspartimide formation during peptide synthesis. The key step of on-resin glycosylamine coupling to an aspartic acid residue was first optimized for a small sugar, N-acetylglucosamine, and then applied to a much larger high mannose oligosaccharide, Man(8)GlcNAc(2). Satisfying coupling yields were obtained for both small and large sugars. The use of on-resin glycosylamine coupling simplifies purification of N-linked glycopeptides, and also allows convenient recovery of unreacted valuable large oligosaccharides. This approach was applied to the solid phase synthesis of glycosylated forms of the 34 amino acid HIV-1 gp41 C34 glycopeptide, which is an HIV-1 entry inhibitor. The HIV-1 entry inhibition assay of synthesized glycopeptides showed the retention of bioactivity of high mannose Man(8)GlcNAc(2)-C34.

Expressed protein ligation: a resourceful tool to study protein structure and function

This review outlines the use of expressed protein ligation (EPL) to study protein structure, function and stability. EPL is a chemoselective ligation method that allows the selective ligation of unprotected polypeptides from synthetic and recombinant origin for the production of semi-synthetic protein samples of well-defined and homogeneous chemical composition. This method has been extensively used for the site-specific introduction of biophysical probes, unnatural amino acids, and increasingly complex post-translational modifications. Since it was introduced 10 years ago, EPL applications have grown increasingly more sophisticated in order to address even more complex biological questions. In this review, we highlight how this powerful technology combined with standard biochemical analysis techniques has been used to improve our ability to understand protein structure and function.

Efficient substitution reaction from cysteine to the serine residue of glycosylated polypeptide: repetitive peptide segment ligation strategy and the synthesis of glycosylated tetracontapeptide having acid labile sialyl-T(N) antigens

This paper reports the synthesis of a 40-residue glycopeptide having two antigenic sialyl-T(N) (NeuAc-alpha-(2,6)-GalNAc-Thr) residues in the MUC1 sequence. This target glycopeptide is a tandem repeat form of 20-residue glycopeptides. For the synthesis of this large molecule, native chemical ligation (NCL) at the serine site was used ((Cys)NCL(Ser)). The concept of (Cys)NCL(Ser) relies on the following: (1) conventional NCL between peptide-alpha-thioester and the cysteine residue of another peptide segment; (2) methylation of the thiol that was used for NCL; (3) acidic CNBr conversion of the cysteine residue to the serine residue forming an O-ester linkage; and (4) an O- to N-acyl shift to couple the two glycopeptides through a native amide bond. To synthesize glycopeptide having an acid-labile sugar moiety, a 20-residue glycopeptide-alpha-thioester and 20-residue glycopeptide having a cysteine residue at the N-terminal were synthesized by solid phase glycopeptide synthesis, and then coupled by (Cys)NCL(Ser). As the result of extensive investigation, CNBr activation with an additional acid (trifluoroacetic acid) was found to be essential to obtain good reactivity and yield, and this condition afforded a tandem repeat form of 40-residue sialylglycopeptide having two sialyl-T(N) residues. In addition to this, it was demonstrated that the cysteine thiol protected by the acetoamidomethyl (Acm) group did not react with the CNBr reagent, and therefore (Cys)NCL(Ser) can be used for repetitive native chemical ligation in the presence of a protecting N-terminal cysteine residue with an Acm group.

Emerging methods for the production of homogeneous human glycoproteins

Most circulating human proteins exist as heterogeneously glycosylated variants (glycoforms) of an otherwise homogeneous polypeptide. Though glycan heterogeneity is most likely important to glycoprotein function, the preparation of homogeneous glycoforms is important both for the study of the consequences of glycosylation and for therapeutic purposes. This review details selected approaches to the production of homogeneous human N- and O-linked glycoproteins with human-type glycans. Particular emphasis is placed on recent developments in the engineering of glycosylation pathways within yeast and bacteria for in vivo production, and on the in vitro remodeling of glycoproteins by enzymatic means. The future of this field is very exciting.