Analysis of Density‐Dependent Binding of Glycans by Lectins Using Carbohydrate Microarrays

To investigate the density‐dependent binding of glycans by lectins using carbohydrate microarrays, a number of C‐terminal hydrazide‐conjugated neoglycopeptides with various valences and different spatial arrangements of the sugar ligands were prepared on a solid support. The synthetic strategy includes (1) assembly of alkyne‐linked peptides possessing C‐terminal hydrazide on a solid support, (2) coupling of azide‐linked, unprotected sugars to the alkyne‐linked peptides on the solid support utilizing click chemistry, and (3) release of the neoglycopeptides from the solid support. By using this synthetic methodology, sixty five neoglycopeptides with a valency ranging from 1 to 4 and different spatial arrangements of the carbohydrate ligands were generated. Carbohydrate microarrays were constructed by immobilizing the prepared neoglycopeptides on epoxide‐derivatized glass slides and were used to analyze the density‐dependent binding of glycans by lectins. The results of binding property determinations show that lectin binding is highly dependent on the surface glycan density.     

Minimizing the Entropy Penalty for Ligand Binding: Lessons from the Molecular Recognition of the Histo Blood‐Group Antigens by Human Galectin‐3

Ligand conformational entropy plays an important role in carbohydrate recognition events. Glycans are characterized by intrinsic flexibility around the glycosidic linkages, thus in most cases, loss of conformational entropy of the sugar upon complex formation strongly affects the entropy of the binding process. By employing a multidisciplinary approach combining structural, conformational, binding energy, and kinetic information, we investigated the role of conformational entropy in the recognition of the histo blood‐group antigens A and B by human galectin‐3, a lectin of biomedical interest. We show that these rigid natural antigens are pre‐organized ligands for hGal‐3, and that restriction of the conformational flexibility by the branched fucose (Fuc) residue modulates the thermodynamics and kinetics of the binding process. These results highlight the importance of glycan flexibility and provide inspiration for the design of high‐affinity ligands as antagonists for lectins.     

Quantitative analysis of carbohydrate-protein interactions using glycan microarrays: determination of surface and solution dissociation constants

Carbohydrate-protein interactions on surface and in solution were quantitatively measured by a glycan microarray. Assessing carbohydrate affinities is typically difficult due to weak affinities and limited sources of structurally complex glycans. We described here a sensitive, high-throughput, and convenient glycan microarray technology for the simultaneous determination of a wide variety of parameters in a single experiment using small amounts of materials. Assay systems based on this technology were developed to analyze multivalent interactions and determine the surface dissociation constant (KD,surf) for surface-coated mannose derivatives with mannose binding lectins and antibodies. Competition experiments that employed monovalent ligands in solution yielded KD and Ki values in solution similar to equilibrium binding constants obtained in titration microcalorimetry and surface plasmon resonance experiments.     

Multivalent Gold Glycoclusters: High Affinity Molecular Recognition by Bacterial Lectin PA‐IL

Multivalent protein‐carbohydrate interactions are involved in the initial stages of many fundamental biological and pathological processes through lectin–carbohydrate binding. The design of high affinity ligands is therefore necessary to study, inhibit and control the processes governed through carbohydrate recognition by their lectin receptors. Carbohydrate‐functionalised gold nanoclusters (glyconanoparticles, GNPs) show promising potential as multivalent tools for studies in fundamental glycobiology research as well as biomedical applications. Here we present the synthesis and characterisation of galactose functionalised GNPs and their effectiveness as binding partners for PA‐IL lectin from Pseudomonas aeruginosa. Interactions were evaluated by hemagglutination inhibition (HIA), surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) assays. Results show that the gold nanoparticle platform displays a significant cluster glycoside effect for presenting carbohydrate ligands with almost a 3000‐fold increase in binding compared with a monovalent reference probe in free solution. The most effective GNP exhibited a dissociation constant (K_d) of 50 nM per monosaccharide, the most effective ligand of PA‐IL measured to date; another demonstration of the potential of glyco‐nanotechnology towards multivalent tools and potent anti‐adhesives for the prevention of pathogen invasion. The influence of ligand presentation density on their recognition by protein receptors is also demonstrated.     

Fluorinated Carbohydrates as Lectin Ligands: Dissecting Glycan–Cyanovirin Interactions by Using 19F NMR Spectroscopy

NMR spectroscopy and isothermal titration calorimetry (ITC) are powerful methods to investigate ligand–protein interactions. Here, we present a versatile and sensitive fluorine NMR spectroscopic approach that exploits the ¹⁹F nucleus of ¹⁹F‐labeled carbohydrates as a sensor to study glycan binding to lectins. Our approach is illustrated with the 11 kDa Cyanovirin‐N, a mannose binding anti‐HIV lectin. Two fluoro‐deoxy sugar derivatives, methyl 2‐deoxy‐2‐fluoro‐α‐D ‐mannopyranosyl‐(1→2)‐α‐D ‐mannopyranoside and methyl 2‐deoxy‐2‐fluoro‐α‐D ‐mannopyranosyl‐(1→2)‐α‐D ‐mannopyranosyl‐(1→2)‐α‐D ‐mannopyranoside were utilized. Binding was studied by ¹⁹F NMR spectroscopy of the ligand and ¹H–¹⁵N HSQC NMR spectroscopy of the protein. The NMR data agree well with those obtained from the equivalent reciprocal and direct ITC titrations. Our study shows that the strategic design of fluorinated ligands and fluorine NMR spectroscopy for ligand screening holds great promise for easy and fast identification of glycan binding, as well as for their use in reporting structural and/or electronic perturbations that ensue upon interaction with a cognate lectin.     

Synthesis of Benzaldehyde‐Functionalized Glycans: A Novel Approach Towards Glyco‐SAMs as a Tool for Surface Plasmon Resonance Studies

In recent years the interest in tools for investigating carbohydrate–protein (CPI) and carbohydrate‐carbohydrate interactions (CCI) has increased significantly. For the investigation of CPI and CCI, several techniques employing different linking methods are available. Surface plasmon resonance (SPR) imaging is a most appropriate tool for analyzing the formation of self‐assembled monolayers (SAM) of carbohydrate derivatives, which can mimic the glycocalyx. In contrast to the SPR imaging methods used previously to analyze CPI and CCI, the novel approach reported herein allows a facile and rapid synthesis of linker spacers and carbohydrate derivatives and enhances the binding event by controlling the amount and orientation of ligand. For immobilization on biorepulsive amino‐functionalized SPR chips by reductive amination, diverse aldehyde‐functionalized glycan structures (glucose, galactose, mannose, glucosamine, cellobiose, lactose, and lactosamine) have been synthesized in several facile steps that include olefin metathesis. Effective immobilization and the first binding studies are presented for the lectin concanavalin A.     

Acute‐phase proteins investigation based on lectins affinity capture prior to 2‐DE separation: Application to serum from multiple sclerosis patients

Plasma acute‐phase proteins (APPs) glyco‐isoforms are important biomarkers of inflammatory processes such as those occurring in multiple sclerosis (MS). Specific analysis of these proteins is often hampered by sample biochemical complexity. The aim of our study was to set up a method to accurately visualize, identify and quantify APPs glyco‐isoforms in human serum. An enrichment strategy based on affinity chromatography using the carbohydrate‐binding proteins concanavalin A (ConA) and erythrina cristagalli lectin (ECL) was applied to pooled serum samples from 15 patients and 9 healthy individuals. Image analysis of 2‐DE detected 30 spots with a fold change higher than 1.5. A total of 14 were statistically significant (p value<0.05): 7 up‐regulated and 7 down‐regulated in MS samples. ESI LC‐Nanospray IT mass spectrometry analysis confirmed that all of them were APPs isoforms supporting the idea that the accurate analysis of differential glycosylation profiles in these biomarkers is instrumental to distinguish between MS patients and healthy subjects. Additionally, overlaps in ConA/ECL maps protein patterns suggest how the used lectins are able to bind sugars harbored by the same oligosaccharide structure. Among identified proteins, the presence of complex and/or hybrid type N‐linked sugar structures is well known. Performing galectin‐3 binding and Western blotting, we were able to demonstrate a correlation between hybrid type glyco‐isoforms of β‐haptoglobin and MS. In conclusion, although the patho‐physiological role of the identified species still remains unclear and further validations are needed, these findings may have a relevant impact on disease‐specific marker identification approaches.     

Glyco-macroligand microarray with controlled orientation and glycan density

We report a new type of glycan microarray, namely, oriented and density-controlled glyco-macroligand microarray based on end-point immobilization of glycopolymer that was accompanied with boronic acid (BA) ligands in different sizes as detachable "temporary molecular spacers". Briefly, an O-cyanate chain-end functionalized lactose-containing glycopolymer was pre-complexed with polyacrylamide-BA, lysozyme-BA, and bovine serum albumin (BSA)-BA conjugates as macromolecular spacers first and then immobilized onto an amine-functionalized glass slide via isourea bond formation both at pH 10.3, respectively. Subsequently, the macromolecular spacers were detached from the immobilized glycopolymers at pH 7.4 so as to afford the oriented and density controlled glycopolymer microarrays. The spaced glycopolymer microarray showed enhanced lectin (Arachis hypogaea) binding compared to a non-spaced one. Among them, the polyacrylamide-BA spaced glycopolymer showed the highest level of lectin binding compared to lysozyme-BA- and BSA-BA-spaced glycopolymers. Furthermore, SPR results confirmed the same trend of density-dependent lectin binding as the glycoarray. This glyco-macroligand microarray platform permits variations of glycan density in the polymer, glycopolymer density and its orientation on the microarray surface and thus will provide a versatile tool for profiling glycan recognition for both basic biological research and practical applications.     

Boronate‐Affinity Glycan‐Oriented Surface Imprinting: A New Strategy to Mimic Lectins for the Recognition of an Intact Glycoprotein and Its Characteristic Fragments

Lectins possess unique binding properties and are of particular value in molecular recognition. However, lectins suffer from several disadvantages, such as being hard to prepare and showing poor storage stability. Boronate‐affinity glycan‐oriented surface imprinting was developed as a new strategy for the preparation of lectin‐like molecularly imprinted polymers (MIPs). The prepared MIPs could specifically recognize an intact glycoprotein and its characteristic fragments, even within a complex sample matrix. Glycan‐imprinted MIPs could thus prove to be powerful tools for important applications such as proteomics, glycomics, and diagnostics.     

Synthetic Mucin‐Like Glycopeptides as Versatile Tools to Measure Effects of Glycan Structure/Density/Position on the Interaction with Adhesion/Growth‐Regulatory Galectins in Arrays

Functional pairing of cellular glycoconjugates with tissue lectins is a highly selective process, whose determinative factors have not yet been fully delineated. Glycan structure and modes of presentation, that is, its position and density, can contribute to binding, as different members of a lectin family can regulate degrees of responsiveness to these factors. Using a peptide repeat sequence motif of the glycoprotein mucin‐1, the principle of introducing synthetic (glyco)peptides with distinct variations in these three parameters to an array‐based screening of tissue lectins is illustrated. Interaction profiles of seven adhesion/growth‐regulatory galectins cover the range from intense signals with core 2 pentasaccharides and core 1 binding for galectins‐3 and ‐5 to a lack of binding for galectin‐1 and also the galectin‐related protein, which was included as a negative control. Remarkably, the two tandem‐repeat‐type galectins‐4 and ‐8 were distinguished by core 1 sialylation, as the two separated domains were. These results encourage further synthetic elaboration of the glycopeptide library and testing of the network of natural galectins and rationally engineered variants of the lectins.     

Residue‐centric modeling and design of saccharide and glycoconjugate structures

The RosettaCarbohydrate framework is a new tool for modeling a wide variety of saccharide and glycoconjugate structures. This report describes the development of the framework and highlights its applications. The framework integrates with established protocols within the Rosetta modeling and design suite, and it handles the vast complexity and variety of carbohydrate molecules, including branching and sugar modifications. To address challenges of sampling and scoring, RosettaCarbohydrate can sample glycosidic bonds, side‐chain conformations, and ring forms, and it utilizes a glycan‐specific term within its scoring function. Rosetta can work with standard PDB, GLYCAM, and GlycoWorkbench (.gws ) file formats. Saccharide residue‐specific chemical information is stored internally, permitting glycoengineering and design. Carbohydrate‐specific applications described herein include virtual glycosylation, loop‐modeling of carbohydrates, and docking of glyco‐ligands to antibodies. Benchmarking data are presented and compared to other studies, demonstrating Rosetta's ability to predict glyco‐ligand binding. The framework expands the tools available to glycoscientists and engineers. © 2016 Wiley Periodicals, Inc.     

SEAL by NMR: Glyco‐Based Selenium‐Labeled Affinity Ligands Detected by NMR Spectroscopy

We report a method for the screening of interactions between proteins and selenium‐labeled carbohydrate ligands. SEAL by NMR is demonstrated with selenoglycosides binding to lectins where the selenium nucleus serves as an NMR‐active handle and reports on binding through ⁷⁷Se NMR spectroscopy. In terms of overall sensitivity, this nucleus is comparable to ¹³C NMR, while the NMR spectral width is ten times larger, yielding little overlap in ⁷⁷Se NMR spectroscopy, even for similar compounds. The studied ligands are singly selenated bioisosteres of methyl glycosides for which straightforward preparation methods are at hand and libraries can readily be generated. The strength of the approach lies in its simplicity, sensitivity to binding events, the tolerance to additives and the possibility of having several ligands in the assay. This study extends the increasing potential of selenium in structure biology and medicinal chemistry. We anticipate that SEAL by NMR will be a beneficial tool for the development of selenium‐based bioactive compounds, such as glycomimetic drug candidates.     

Sampling of Glycan‐Bound Conformers by the Anti‐HIV Lectin Oscillatoria agardhii agglutinin in the Absence of Sugar

Lectins from different sources have been shown to interfere with HIV infection by binding to the sugars of viral‐envelope glycoproteins. Three‐dimensional atomic structures of a number of HIV‐inactivating lectins have been determined, both as free proteins and in glycan‐bound forms. However, details on the mechanism of recognition and binding to sugars are elusive. Herein we focus on the anti‐HIV lectin OAA from Oscillatoria agardhii: We show that in the absence of sugars in solution, both the sugar‐free and sugar‐bound protein conformations that were observed in the X‐ray crystal structures exist as conformational substates. Our results suggest that glycan recognition occurs by conformational selection within the ground state; this model differs from the popular “excited‐state” model. Our findings provide further insight into molecular recognition of the major receptor on the HIV virus by OAA. These details can potentially be used for the optimization and/or development of preventive anti‐HIV therapeutics.     

Iron(III)‐Quantity‐Dependent Aggregation–Dispersion Conversion of Functionalized Gold Nanoparticles

Developing gold nanoparticles (AuNPs) with well‐designed functionality is highly desirable for boosting the performance and versatility of inorganic–organic hybrid materials. In an attempt to achieve ion recognition with specific signal expressions, we present here 4‐piperazinyl‐1,8‐naphthalimide‐functionalized AuNPs for the realization of quantitative recognition of Fe^III ions with dual (colorimetric and fluorescent) output. The research takes advantage of 1) quantity‐controlled chelation‐mode transformation of the piperazinyl moiety on the AuNPs towards Fe^III, thereby resulting in an aggregation–dispersion conversion of the AuNPs in solution, and 2) photoinduced electron transfer of a naphthaimide fluorophore on the AuNPs, thus leading to reversible absorption and emission changes. The functional AuNPs are also responsive to pH variations. This strategy for realizing the aggregation–dispersion conversion of AuNPs with returnable signal output might exhibit application potential for advanced nanoscale chemosensors.     

Multi-mannosides based on a carbohydrate scaffold: synthesis, force field development, molecular dynamics studies, and binding affinities for lectin Con A

A short and efficient strategy for the synthesis of multi-valent mannosides based on a selectively functionalized carbohydrate scaffold was reported involving (i) direct regioselective azidation of unprotected commercial saccharides, (ii) acetylation, (iii) grafting of the mannosyl ligands by click chemistry, and (iv) deacetylation. New glycoclusters with a valency ranging from 1 to 4 and different spatial arrangements of the epitopes were obtained. Binding affinities of the new glycoclusters toward concanavalin A (Con A) lectin were investigated by an enzyme-linked lectin essay (ELLA). The synthetic multi-valent compounds exhibited a remarkable cluster effect with a relative potency per mannoside residue ranging from 8.1 to 9.1 depending on the structures. ELLA experiments were in agreement with the establishment of favorable interactions between triazole ring and Con A, increasing the binding affinity. A new force field topology database was developed in agreement with the GLYCAM 2004 force field. Molecular dynamics performed on representative glyco-conjugates revealed interesting structural features such as rigidity of the scaffold for a well-defined presentation of the ligands and highly flexible mannose counterparts. The new glycoconjugates reported may be promising tools as probes or effectors of biological processes involving lectins.     

Sequence‐Defined Introduction of Hydrophobic Motifs and Effects in Lectin Binding of Precision Glycomacromolecules

This study investigates the influence of an increasingly hydrophobic backbone of multivalent glycomimetics based on sequence‐defined oligo(amidoamines) on their resulting affinity toward bacterial lectins. Glycomacromolecules are obtained by stepwise assembly of tailor‐made building blocks on solid support, using both hydrophobic aliphatic and aromatic building blocks to enable a gradual change in hydrophobicity of the backbone. Their binding behavior toward model lectin Concanavalin A (ConA) is evaluated using isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR) showing higher affinities for glycomacromolecules with higher content of hydrophobic and aromatic moieties in the backbone. Finally, glycomacromolecules are tested in a bacterial adhesion inhibition study against Escherichia coli where more hydrophobic backbones yield higher inhibitory potentials most likely due to additional secondary interactions with hydrophobic regions of the protein receptor as well as a change in conformation exposing carbohydrate ligands for increased binding. Overall, the results highlight the influence and thereby importance of the polymer backbone itself on the resulting properties of polymeric biomimetics.     

Promotion of sugar-lectin recognition through the multiple sugar presentation offered by regioselectively addressable functionalized templates (RAFT): a QCM-D and SPR study

The investigation of recognition events between carbohydrates and proteins, especially the understanding of how spatial factors and binding avidity are correlated, remains a great interest for glycobiology. In this context we have investigated by nanogravimetry (QCM-D) and surface plasmon resonance (SPR), the kinetics and thermodynamics of the interaction between concanavalin A (Con A) and various neoglycopeptide ligands of low molecular weight. Regioselectively addressable functionalized templates (RAFT) have been used as scaffolds for the design of multivalent neoglycopeptides bearing thiol or biotin functions for their anchoring on transducer surfaces. Although these multivalent neoglycopeptide ligands cannot span multiple binding sites within the same Con A protein, they have increased activities relative to their monovalent counterpart. Our results emphasize that the multivalent RAFT ligands function by clustering several lectins, which leads to enhanced affinities.     

Synthesis of Multivalent Carbohydrate‐Centered Glycoclusters as Nanomolar Ligands of the Bacterial Lectin LecA from Pseudomonas aeruginosa

A family of fifteen glycoclusters based on a cyclic oligo‐(1→6)‐β‐D ‐glucosamine core has been designed as potential inhibitors of the bacterial lectin LecA with various valencies (from 2 to 4) and linkers. Evaluation of their binding properties towards LecA has been performed by a combination of hemagglutination inhibition assays (HIA), enzyme‐linked lectin assays (ELLA), and isothermal titration microcalorimetry (ITC). Divalent ligands displayed dissociation constants in the sub‐micromolar range and tetravalent ligands displayed low nanomolar affinities for this lectin. The influence of the linker could also be demonstrated; aromatic moieties are the best scaffolds for binding to the lectin. The affinities observed in vitro were then correlated with molecular models to rationalize the possible binding modes of these glycoclusters with the bacterial lectin.     

Glycopeptide Mimetics Recapitulate High‐Mannose‐Type Oligosaccharide Binding and Function

High‐mannose‐type glycans (HMTGs) decorating viral spike proteins are targets for virus neutralization. For carbohydrate‐binding proteins, multivalency is important for high avidity binding and potent inhibition. To define the chemical determinants controlling multivalent interactions we designed glycopeptide HMTG mimetics with systematically varied mannose valency and spacing. Using the potent antiviral lectin griffithsin (GRFT) as a model, we identified by NMR spectroscopy, SPR, analytical ultracentrifugation, and microcalorimetry glycopeptides that fully recapitulate the specificity and kinetics of binding to Man₉GlcNAc₂Asn and a synthetic nonamannoside. We find that mannose spacing and valency dictate whether glycopeptides engage GRFT in a face‐to‐face or an intermolecular binding mode. Surprisingly, although face‐to‐face interactions are of higher affinity, intermolecular interactions are longer lived. These findings yield key insights into mechanisms involved in glycan‐mediated viral inhibition.     

Quantitative evaluation of lectin‐reactive glycoforms of α1‐acid glycoprotein using lectin affinity capillary electrophoresis with fluorescence detection

α₁‐Acid glycoprotein (AGP) was previously shown to be a marker candidate of disease progression and prognosis of patients with malignancies by analysis of its glycoforms via lectins. Herein, affinity capillary electrophoresis of fluorescein‐labeled AGP using lectins with the aid of laser‐induced fluorescence detection was developed for quantitative evaluation of the fractional ratios of concanavalin A‐reactive or Aleuria aurantia lectin‐reactive AGP. Labeled AGP was applied at the anodic end of a fused‐silica capillary (50 μm id, 360 μm od, 27 cm long) coated with linear polyacryloyl‐β‐alanyl‐β‐alanine, and electrophoresis was carried out for about 10 min in 60 mM 3‐morpholinopropane‐1‐sulfonic acid‐NaOH buffer (pH 7.35). Addition of the lectins to the anode buffer resulted in the separation of lectin‐reactive glycoform peaks from lectin‐non‐reactive glycoform peaks. Quantification of the peak area of each group revealed that the percent of lectin‐reactive AGP is independent of a labeling ratio ranging from 0.4 to 1.5 mol fluorescein/mol AGP, i.e. the standard deviation of 0.5% for an average of 59.9% (n=3). In combination with a facile procedure for micro‐purification of AGP from serum, the present procedure, marking the reactivity of AGP with lectins, should be useful in determining the prognosis for a large number of patients with malignancies.