Exploiting Uniformly 13C-Labeled Carbohydrates for Probing Carbohydrate-Protein Interactions by NMR Spectroscopy

Automated Synthesis of Algal Fucoidan Oligosaccharides

Fucoidan, a sulfated polysaccharide found in algae, plays a central role in marine carbon sequestration and exhibits a wide array of bioactivities. However, the molecular diversity and structural complexity of fucoidan hinder precise structure-function studies. To address this, we present an automated method for generating well-defined linear and branched α-fucan oligosaccharides. Our syntheses include oligosaccharides with up to 20 cis-glycosidic linkages, diverse branching patterns, and 11 sulfate monoesters. In this study, we demonstrate the utility of these oligosaccharides by (i) characterizing two endo-acting fucoidan glycoside hydrolases (GH107), (ii) utilizing them as standards for NMR studies to confirm suggested structures of algal fucoidans, and (iii) developing a fucoidan microarray. This microarray enabled the screening of the molecular specificity of four monoclonal antibodies (mAb) targeting fucoidan. It was found that mAb BAM4 has cross-reactivity to β-glucans, while mAb BAM2 has reactivity to fucoidans with 4-O-sulfate esters. Knowledge of the mAb BAM2 epitope specificity provided evidence that a globally abundant marine diatom, Thalassiosira weissflogii, synthesizes a fucoidan with structural homology to those found in brown algae. Automated glycan assembly provides access to fucoidan oligosaccharides. These oligosaccharides provide the basis for molecular level investigations into fucoidan's roles in medicine and carbon sequestration.

Metabolic labeling of hyaluronan: Biosynthesis and quantitative analysis of 13C,15N-enriched hyaluronan by NMR and MS-based methods

Hyaluronan (HA), a member of the GAG family of glycans, has many diverse biological functions that vary a lot depending on the length of the HA chain and its concentration. A better understanding of the structure of different-sized HA at the atomic level is therefore crucial to decipher these biological functions. NMR is a method of choice for conformational studies of biomolecules, but there are limitations due to the low natural abundance of the NMR active nuclei ¹³C and ¹⁵N. We describe here the metabolic labeling of HA using the bacterium Streptococcus equi subsp. Zooepidemicus and the subsequent analysis by NMR and mass spectrometry. The level of ¹³C and ¹⁵N isotope enrichment at each position was determined quantitatively by NMR spectroscopy and was further confirmed by high-resolution mass spectrometry analysis. This study provides a valid methodological approach that can be applied to the quantitative assessment of isotopically labeled glycans and will help improve detection capabilities and facilitate future structure-function relationship analysis of complex glycans.

Exploring multivalent carbohydrate-protein interactions by NMR

Nuclear Magnetic Resonance (NMR) has been widely employed to assess diverse features of glycan-protein molecular recognition events. Different types of qualitative and quantitative information at different degrees of resolution and complexity can be extracted from the proper application of the available NMR-techniques. In fact, affinity, structural, kinetic, conformational, and dynamic characteristics of the binding process are available. Nevertheless, except in particular cases, the affinity of lectin-sugar interactions is weak, mostly at the low mM range. This feature is overcome in biological processes by using multivalency, thus augmenting the strength of the binding. However, the application of NMR methods to monitor multivalent lectin-glycan interactions is intrinsically challenging. It is well known that when large macromolecular complexes are formed, the NMR signals disappear from the NMR spectrum, due to the existence of fast transverse relaxation, related to the large size and exchange features. Indeed, at the heart of the molecular recognition event, the associated free-bound chemical exchange process for both partners takes place in a particular timescale. Thus, these factors have to be considered and overcome. In this review article, we have distinguished, in a subjective manner, the existence of multivalent presentations in the glycan or in the lectin. From the glycan perspective, we have also considered whether multiple epitopes of a given ligand are presented in the same linear chain of a saccharide (i.e., poly-LacNAc oligosaccharides) or decorating different arms of a multiantennae scaffold, either natural (as in multiantennae N-glycans) or synthetic (of dendrimer or polymer nature). From the lectin perspective, the presence of an individual binding site at every monomer of a multimeric lectin may also have key consequences for the binding event at different levels of complexity.

Atom-economical synthesis of 1,2-bis(phosphine oxide)ethanes from calcium carbide with straightforward access to deuterium- and 13C-labeled bidentate phosphorus ligands and metal complexes

Straightforward access to bidentate phosphorus ligands and bis(phosphineoxide)ethanes is described based on atom-economic addition reaction. A practical approach was developed to incorporate 2H and 13C labels using easily available reagents.

Synthetic Approaches to Break the Chemical Shift Degeneracy of Glycans

NMR spectroscopy is the leading technique for determining glycans' three-dimensional structure and dynamic in solution as well as a fundamental tool to study protein-glycan interactions. To overcome the severe chemical shift degeneracy of these compounds, synthetic probes carrying NMR-active nuclei (e. g., ¹³ C or ¹⁹ F) or lanthanide tags have been proposed. These elegant strategies permitted to simplify the complex NMR analysis of unlabeled analogues, shining light on glycans' conformational aspects and interaction with proteins. Here, we highlight some key achievements in the synthesis of specifically labeled glycan probes and their contribution towards the fundamental understanding of glycans.

Hydrofluoromethylation of alkenes with fluoroiodomethane and beyond

A process for the direct hydrofluoromethylation of alkenes is reported for the first time. This straighforward silyl radical-mediated reaction utilises CH₂FI as a non-ozone depleting reagent, traditionally used in electrophilic, nucleophilic and carbene-type chemistry, but not as a CH₂F radical source. By circumventing the challenges associated with the high reduction potential of CH₂FI being closer to CH₃I than CF₃I, and harnessing instead the favourable bond dissociation energy of the C–I bond, we demonstrate that feedstock electron-deficient alkenes are converted into products resulting from net hydrofluoromethylation with the intervention of (Me₃Si)₃SiH under blue LED activation. This deceptively simple yet powerful methodology was extended to a range of (halo)methyl radical precursors including ICH₂I, ICH₂Br, ICH₂Cl, and CHBr₂F, as well as CH₃I itself; this latter reagent therefore enables direct hydromethylation. This versatile chemistry was applied to ¹⁸F-, ¹³C-, and D-labelled reagents as well as complex biologically relevant alkenes, providing facile access to more than fifty products for applications in medicinal chemistry and positron emission tomography.

Herein, we report the direct hydro(halo)methylation of alkenes from a variety of (halo)methyl iodides (including F-18, C-13, D-2 isotopologues), enabling the incorporation of a plethora of C-1 fragments into complex biologically active molecules.

What is the Sugar Code?

A code is defined by the nature of the symbols, which are used to generate information‐storing combinations (e. g. oligo‐ and polymers). Like nucleic acids and proteins, oligo‐ and polysaccharides are ubiquitous, and they are a biochemical platform for establishing molecular messages. Of note, the letters of the sugar code system (third alphabet of life) excel in coding capacity by making an unsurpassed versatility for isomer (code word) formation possible by variability in anomery and linkage position of the glycosidic bond, ring size and branching. The enzymatic machinery for glycan biosynthesis (writers) realizes this enormous potential for building a large vocabulary. It includes possibilities for dynamic editing/erasing as known from nucleic acids and proteins. Matching the glycome diversity, a large panel of sugar receptors (lectins) has developed based on more than a dozen folds. Lectins ‘read’ the glycan‐encoded information. Hydrogen/coordination bonding and ionic pairing together with stacking and C−H/π‐interactions as well as modes of spatial glycan presentation underlie the selectivity and specificity of glycan‐lectin recognition. Modular design of lectins together with glycan display and the nature of the cognate glycoconjugate account for the large number of post‐binding events. They give an entry to the glycan vocabulary its functional, often context‐dependent meaning(s), hereby building the dictionary of the sugar code.

Selective 13 C-Labels on Repeating Glycan Oligomers to Reveal Protein Binding Epitopes through NMR: Polylactosamine Binding to Galectins

A combined chemo-enzymatic synthesis/NMR-based methodology is presented to identify, in unambiguous manner, the distinctive binding epitope within repeating sugar oligomers when binding to protein receptors. The concept is based on the incorporation of 13 C-labels at specific monosaccharide units, selected within a repeating glycan oligomeric structure. No new chemical tags are added, and thus the chemical entity remains the same, while the presence of the 13 C-labeled monosaccharide breaks the NMR chemical shift degeneracy that occurs in the non-labeled compound and allows the unique identification of the different components of the oligomer. The approach is demonstrated by a proof-of-concept study dealing with the interaction of a polylactosamine hexasaccharide with five different galectins that display distinct preferences for these entities.

Conformational and Structural characterization of carbohydrates and their interactions studied by NMR

Carbohydrates, either free or as glycans conjugated with other biomolecules, participate in many essential biological processes. Their apparent simplicity in terms of chemical functionality hides an extraordinary diversity and structural complexity. Deeply deciphering at the atomic level their structures is essential to understand their biological function and activities, but it is still a challenging task in need of complementary approaches and no generalized procedures are available to address the study of such complex, natural glycans. The versatility of Nuclear Magnetic Resonance spectroscopy (NMR) often makes it the preferred choice to study glycans and carbohydrates in solution media. The most basic NMR parameters, namely chemical shifts, coupling constants and nuclear Overhauser effects, allow defining short or repetitive chain sequences and characterize their structures and local geometries either in the free state or when interacting with other biomolecules, rendering additional information on the molecular recognition processes. The increased accessibility to carbohydrate molecules extensively or selectively labeled with 13C boosts the resolution and detail that analyzed glycan structures can reach. In turn, structural information derived from NMR, complemented with molecular modeling and theoretical calculations can also provide dynamic information on the conformational flexibility of carbohydrate structures. Furthermore, using partially oriented media or paramagnetic perturbations, it has been possible to introduce additional long-range observables rendering structural information on longer and branched glycan chains. In this review, we provide examples of these studies and an overview of the recent and most relevant NMR applications in the glycobiology field.

A general strategy for the structural determination of carbohydrates by multi-dimensional NMR spectroscopies

Two-dimensional NMR spectroscopies are one of the most frequently used techniques for the structural determination of carbohydrates. However, the data analysis is challenging because of the signal overlap in the ¹H homonuclear correlation spectra. We attempted to explore a general strategy for the structural determination of carbohydrates by combined multi-dimensional spectroscopies. The strategy was applied to a human milk oligosaccharide lacto-N-difucohexaose I, that has been previously studied by conventional two-dimensional NMR spectroscopy. Assignment of the intra-residue resonances of the hexasaccharide using the three-dimensional spectrum was straightforward. Consequently, data analysis of the multi-dimensional spectra was significantly simplified, leading to a quicker determination of the intra- and inter-residue connections in the hexasaccharide. Application of the NMR strategy to chondroitin sulfate from bovine cartilage revealed two repeating disaccharide regions of the A and C units of chondroitin sulfate, indicating the high potential of this technique for the structural determination of complex polysaccharides.

Structural Characterization of N-Linked Glycans in the Receptor Binding Domain of the SARS-CoV-2 Spike Protein and their Interactions with Human Lectins

The glycan structures of the receptor binding domain of the SARS-CoV2 spike glycoprotein expressed in human HEK293F cells have been studied by using NMR. The different possible interacting epitopes have been deeply analysed and characterized, providing evidence of the presence of glycan structures not found in previous MS-based analyses. The interaction of the RBD 13 C-labelled glycans with different human lectins, which are expressed in different organs and tissues that may be affected during the infection process, has also been evaluated by NMR. In particular, 15 N-labelled galectins (galectins-3, -7 and -8 N-terminal), Siglecs (Siglec-8, Siglec-10), and C-type lectins (DC-SIGN, MGL) have been employed. Complementary experiments from the glycoprotein perspective or from the lectin's point of view have permitted to disentangle the specific interacting epitopes in each case. Based on these findings, 3D models of the interacting complexes have been proposed.

A detailed picture of a protein-carbohydrate hydrogen-bonding network revealed by NMR and MD simulations

Cyanovirin-N (CV-N) is a cyanobacterial lectin with antiviral activity towards HIV and several other viruses. Here, we identify mannoside hydroxyl protons that are hydrogen bonded to the protein backbone of the CV-N domain B binding site, using NMR spectroscopy. For the two carbohydrate ligands Manα(1→2)ManαOMe and Manα(1→2) Manα(1→6)ManαOMe five hydroxyl protons are involved in hydrogen-bonding networks. Comparison with previous crystallographic results revealed that four of these hydroxyl protons donate hydrogen bonds to protein backbone carbonyl oxygens in solution and in the crystal. Hydrogen bonds were not detected between the side chains of Glu41 and Arg76 with sugar hydroxyls, as previously proposed for CV-N binding of mannosides. Molecular dynamics simulations of the CV-N/Manα(1→2)Manα(1→6)ManαOMe complex confirmed the NMR-determined hydrogen-bonding network. Detailed characterization of CV-N/mannoside complexes provides a better understanding of lectin-carbohydrate interactions and opens up to the use of CV-N and similar lectins as antiviral agents.

Synthesis of type 1 Lewis b hexasaccharide antigen structures featuring flexible incorporation of l-[U-13C6]-fucose for NMR binding studies

While 13C-labelled proteins are common tools in NMR studies, lack of access to 13C-labelled carbohydrate structures has restricted their use. l-Fucose is involved in a wide range of physiological and pathophysiological processes in mammalian organisms. Here, l-[U-13C6]-Fuc labelled type I Lewis b (Leb) structures have been synthesised for use in NMR binding studies with the Blood-group Antigen Binding Adhesin (BabA), a membrane-bound protein from the bacterium Helicobacter pylori. As part of this work, an efficient synthesis of a benzylated l-[U-13C6]-Fuc thioglycoside donor from l-[U-13C6]-Gal has been developed. The design and synthesis of an orthogonally protected tetrasaccharide precursor enabled controlled introduction of one or two 13C-labelled or non-labelled fucosyl residues prior to global deprotection. NMR analysis showed that it is straightforward to assign the anomeric centres as well as the H-5 positions to the individual fucosyl residues which are relevant for NMR binding studies.

Glycan structures and their interactions with proteins. A NMR view

Carbohydrate molecules are essential actors in key biological events, being involved as recognition points for cell-cell and cell-matrix interactions related to health and disease. Despite outstanding advances in cryoEM, X-ray crystallography and NMR still remain the most employed techniques to unravel their conformational features and to describe the structural details of their interactions with biomolecular receptors. Given the intrinsic flexibility of saccharides, NMR methods are of paramount importance to deduce the extent of motion around their glycosidic linkages and to explore their receptor-bound conformations. We herein present our particular view on the latest advances in NMR methodologies that are permitting to magnify their applications for deducing glycan conformation and dynamics and understanding the recognition events in which there are involved.

Novel NMR Avenues to Explore the Conformation and Interactions of Glycans

This perspective article is focused on the presentation of the latest advances in NMR methods and applications that are behind the exciting achievements in the understanding of glycan receptors in molecular recognition events. Different NMR-based methodologies are discussed along with their applications to scrutinize the conformation and dynamics of glycans as well as their interactions with protein receptors.

Harnessing 13C-labeled myo-inositol to interrogate inositol phosphate messengers by NMR

The analysis of inositol poly- and pyrophosphates, an important group of eukaryotic messengers, is enabled by applying ¹³C-labeled inositol.

Inositol poly- and pyrophosphates (InsPs and PP-InsPs) are an important group of metabolites and mediate a wide range of processes in eukaryotic cells. To elucidate the functions of these molecules, robust techniques for the characterization of inositol phosphate metabolism are required, both at the biochemical and the cellular level. Here, a new tool-set is reported, which employs uniformly ¹³C-labeled compounds ([¹³C₆]myo-inositol, [¹³C₆]InsP₅, [¹³C₆]InsP₆, and [¹³C₆]5PP-InsP₅), in combination with commonly accessible NMR technology. This approach permitted the detection and quantification of InsPs and PP-InsPs within complex mixtures and at physiological concentrations. Specifically, the enzymatic activity of IP6K1 could be monitored in vitro in real time. Metabolic labeling of mammalian cells with [¹³C₆]myo-inositol enabled the analysis of cellular pools of InsPs and PP-InsPs, and uncovered high concentrations of 5PP-InsP₅ in HCT116 cells, especially in response to genetic and pharmacological perturbation. The reported method greatly facilitates the analysis of this otherwise spectroscopically silent group of molecules, and holds great promise to comprehensively analyze inositol-based signaling molecules under normal and pathological conditions.

Use of Circular Statistics To Model αMan-(1→2)-αMan and αMan-(1→3)-α/βMan O-Glycosidic Linkage Conformation in 13C-Labeled Disaccharides and High-Mannose Oligosaccharides

A new experimental method, MA' AT analysis, has been applied to investigate the conformational properties of O-glycosidic linkages in several biologically important mannose-containing di- and oligosaccharides. Methyl α-d-mannopyranosyl-(1→2)-α-d-mannopyranoside (2), methyl α-d-mannopyranosyl-(1→3)-α-d-mannopyranoside (3), and methyl α-d-mannopyranosyl-(1→3)-β-d-mannopyranoside (4) were prepared with selective ¹³C-enrichment to enable the measurement of NMR scalar couplings across their internal O-glycosidic linkages. Density functional theory (DFT) was used to parameterize equations for J_CH and J_CC values in 2-4 that are sensitive to phi (ϕ) and psi (ψ). The experimental J-couplings and parameterized equations were treated using a circular statistics algorithm encoded in the MA' AT program. Conformations about ϕ and ψ treated using single-state von Mises models gave excellent fits to the ensembles of redundant J-couplings. Mean values and circular standard deviations (CSDs) for each linkage torsion angle ϕ (CSD) and ψ (CSD) in 2, -29° (25°) and 20° (22°); in 3, -36° (36°) and 8° (27°); in 4, -37° (34°) and 10° (26°); ϕ = H1'-C1'-O1'-CX and ψ = C1'-O1'-CX-HX (CX = aglycone carbon) were compared to histograms obtained from 1 μs aqueous molecular dynamics (MD) simulations and X-ray database statistical analysis. MA' AT-derived models of ψ were in very good agreement with the MD and X-ray data, but not those of ϕ, suggesting a need for force field revision. The effect of structural context on linkage conformation was also investigated in four selectively ¹³C-labeled homomannose tri- and tetrasaccharides using the MA' AT method. In the cases examined, context effects were found to be small.

The recognition of glycans by protein receptors. Insights from NMR spectroscopy

Carbohydrates (glycans, saccharides, sugars) are everywhere. In fact, glycan-protein interactions are involved in many essential processes of life and disease. The understanding of the key structural details at the atomic and molecular level is of paramount importance to effectively design molecules for therapeutic purposes. Different approximations may be employed to decipher these molecular recognition processes with high resolution. Advances in cryo-electron microscopy are providing exquisite details on different biological mechanisms involving sugars, while better and better protocols for structural refinement in the application of X-ray methods for protein-sugar complexes and glycoproteins are also permitting fantastic advances in the glycoscience arena. Alternatively, NMR spectroscopy remains as one of the most rewarding techniques to explore protein-carbohydrate interactions. In fact, given the intrinsic dynamic nature of saccharides, NMR can afford exquisite structural information at the atomic detail, not accessible by other techniques. However, the access to this information is sometimes intricate, and requires careful analysis and well-defined strategies. In this review, we have highlighted these issues and presented an overview of different modern NMR approaches with a focus on the latest developments and challenges.

Solid-State NMR of highly 13C-enriched cholesterol in lipid bilayers

Cholesterol (Chol) is vital for cell function as it is essential to a myriad of biochemical and biophysical processes. The atomistic details of Chol's interactions with phospholipids and proteins is therefore of fundamental interest, and NMR offers unique opportunities to interrogate these properties at high resolution. Towards this end, here we describe approaches for examining the structure and dynamics of Chol in lipid bilayers using high levels of ¹³C enrichment in combination with magic-angle spinning (MAS) methods. We quantify the incorporation levels and demonstrate high sensitivity and resolution in 2D ¹³C-¹³C and ¹H-¹³C spectra, enabling de novo assignments and site-resolved order parameter measurements obtained in a fraction of the time required for experiments with natural abundance sterols. We envision many potential future applications of these methods to study sterol interactions with drugs, lipids and proteins.

Direct Observation of Carbohydrate Hydroxyl Protons in Hydrogen Bonds with a Protein

Hydroxyl proton resonances of uniformly ¹³C-labeled Manα(1-2)Manα(1-2)ManαOMe (Man₃) bound to cyanovirin-N (CV-N) were detected at ambient temperature in aqueous solution by NMR spectroscopy. The directions of the hydroxyl groups were determined on the basis of NOEs, and a previously unknown hydrogen-bonding network between Man₃ and CV-N was discovered. This is the first report on detecting hydroxyl protons of a protein-bound carbohydrate in aqueous solution by NMR. Approaches such as those presented here may open the door for accurately determining intermolecular hydrogen bonds in carbohydrate-protein complexes.