Preparation of carbohydrate arrays by using Diels-Alder reactions with inverse electron demand

Carbohydrate microarrays are an emerging tool for the high-throughput screening of carbohydrate-protein interactions that represent the basis of many biologically and medicinally relevant processes. The crucial step in the preparation of carbohydrate arrays is the attachment of carbohydrate probes to the surface. We examined the Diels-Alder reaction with inverse-electron-demand (DARinv) as an irreversible, chemoselective ligation reaction for that purpose. After having shown the efficiency of the DARinv in solution, we prepared a series of carbohydrate-dienophile conjugates that were printed onto tetrazine-modified glass slides. Binding experiments with fluorescently labeled lectins proved successful and homogeneous immobilization was achieved by the DARinv. For immobilization of nonfunctionalized reducing oligosaccharides we developed a bifunctional chemoselective linker that enabled the attachment of a dienophile tag to the oligosaccharides through oxime ligation. The conjugates obtained were successfully immobilized on glass slides. The presented strategies for the immobilization of both synthetic carbohydrate derivatives and unprotected reducing oligosaccharides facilitate the preparation of high-quality carbohydrate microarrays by means of the chemoselective DARinv. This concept can be readily adapted for the preparation of other biomolecule arrays.     

Three‐Dimensional Arrays Using GlycoPEG Tags: Glycan Synthesis,Purification and Immobilisation

Glycan arrays have become the premier tool for rapidly establishing the binding or substrate specificities of lectins and carbohydrate‐processing enzymes. New approaches for accelerating carbohydrate synthesis to address the enormous complexity of natural glycan structures are necessary. Moreover, optimising glycan immobilisation is key for the development of selective, sensitive and reproducible array‐based assays. We present a tag‐based approach that accelerates the preparation of glycan arrays on all levels by improving the synthesis, the purification and immobilisation of oligosaccharides. Glycan primers were chemically attached to bifunctional polyethyleneglycol (PEG) tags, extended enzymatically with the help of recombinant glycosyltransferases and finally purified by ultrafiltration. When printed directly onto activated glass slides, these glycoPEG tags afforded arrays with exceptionally high sensitivity, low background and excellent spot morphology. Likewise, the conjugation of glycoPEG tags to latex nanoparticles yielded multivalent scaffolds for carbohydrate‐binding assays with very low non‐specific binding.     

Peptide microarrays for the determination of protease substrate specificity

A method is described for the preparation of substrate microarrays that allow for the rapid determination of protease substrate specificity. Peptidyl coumarin substrates, synthesized on solid support using standard techniques, are printed onto glass slides using DNA microarraying equipment. The linkage from the peptide to the slide is formed through a chemoselective reaction, resulting in an array of uniformly displayed fluorogenic substrates. The arrays can be treated with proteases to yield substrate specificity profiles. Standard instrumentation for visualization of microarrays can be used to obtain comparisons of the specificity constants for all of the prepared substrates. The utility of these arrays is demonstrated by the selective cleavage of preferred substrates with trypsin, thrombin, and granzyme B, and by assessing the extended substrate specificity of thrombin using a microarray of 361 different peptidyl coumarin substrates.     

Noncovalent fluorous interactions for the synthesis of carbohydrate microarrays

A surface patterning method based on noncovalent immobilization of fluorous-tagged sugars on fluorous-derivatized glass slides allows the facile fabrication of carbohydrate microarrays. To expand the scope of these arrays, the first syntheses are reported of arabinose, rhamnose, lactose, maltose, and glucosamine tagged with a single C₈F₁₇-tail for ease of purification as well as array formation. Screening of these carbohydrate microarrays against lectins from Triticum vulgaris (WGA) and Arachis hypogaea (PNA) demonstrate that the noncovalent fluorous–fluorous interaction is sufficient to retain not only mono- but also disaccharides under the biological assay conditions.     

Synthesis of β‐1,4‐Linked Galactan Side‐Chains of Rhamnogalacturonan I

The synthesis of linear‐ and (1→6)‐branched β‐(1→4)‐d ‐galactans, side‐chains of the pectic polysaccharide rhamnogalacturonan I is described. The strategy relies on iterative couplings of n‐pentenyl disaccharides followed by a late stage glycosylation of a common hexasaccharide core. Reaction with a covalent linker and immobilization on N‐hydroxysuccinimide (NHS)‐modified glass surfaces allows the generation of carbohydrate microarrays. The glycan arrays enable the study of protein–carbohydrate interactions in a high‐throughput fashion, demonstrated herein with binding studies of mAbs and a CBM.     

Carbohydrate chips for studying high-throughput carbohydrate-protein interactions

Carbohydrate-protein interactions play important biological roles in living organisms. For the most part, biophysical and biochemical methods have been used for studying these biomolecular interactions. Less attention has been given to the development of high-throughput methods to elucidate recognition events between carbohydrates and proteins. In the current effort to develop a novel high-throughput tool for monitoring carbohydrate-protein interactions, we prepared carbohydrate microarrays by immobilizing maleimide-linked carbohydrates on thiol-derivatized glass slides and carried out lectin binding experiments by using these microarrays. The results showed that carbohydrates with different structural features selectively bound to the corresponding lectins with relative binding affinities that correlated with those obtained from solution-based assays. In addition, binding affinities of lectins to carbohydrates were also quantitatively analyzed by determining IC(50) values of soluble carbohydrates with the carbohydrate microarrays. To fabricate carbohydrate chips that contained more diverse carbohydrate probes, solution-phase parallel and enzymatic glycosylations were performed. Three model disaccharides were in parallel synthesized in solution-phase and used as carbohydrate probes for the fabrication of carbohydrate chips. Three enzymatic glycosylations on glass slides were consecutively performed to generate carbohydrate microarrays that contained the complex oligosaccharide, sialyl Le(x). Overall, these works demonstrated that carbohydrate chips could be efficiently prepared by covalent immobilization of maleimide-linked carbohydrates on the thiol-coated glass slides and applied for the high-throughput analyses of carbohydrate-protein interactions.     

Facile preparation of carbohydrate microarrays by site-specific, covalent immobilization of unmodified carbohydrates on hydrazide-coated glass slides

[reaction: see text] A new, simple and efficient immobilization method to attach mono-, di-, oligo-, and polysaccharides to hydrazide-coated glass slides was developed. Protein and cell-binding experiments show that the carbohydrate microarrays prepared by this method are applicable for the rapid analysis of protein-carbohydrate interactions and fast detection of pathogens.     

A generic small-molecule microarray immobilization strategy

Small-molecule microarrays are often limited by the requirement for each compound undergoing immobilization to contain a common functional group or by the need to prepare glass slides containing photo-reactive groups. Herein, we present a generic strategy that allows any compound library to be immobilized. This was achieved by printing a fluorous-tagged photo-reactive 3-aryl-3-trifluoromethyldiazirine, which undergoes non-selective insertion into compounds following UV-activation, onto fluorous-functionalized glass slides. The arrays could be reused following aqueous stripping and re-assessment of the compounds with the same protein or another target of interest.     

Carbohydrate analysis prepares to enter the "Omics" era

In this issue, Houseman and Mrksich describe a carbohydrate array preparation method that can be used to analyze protein-carbohydrate interactions and to characterize the substrate specificity of a carbohydrate-modifying enzyme. Carbohydrate chips were prepared by a novel procedure that allows the covalent attachment of carbohydrate-diene conjugates to a specially engineered monolayer surface. The surface presents a precisely controllable ratio of reactive benzoquinone and inert ethylene glycol groups. Nonspecific adsorption of proteins to the surface is extremely low, and the surface is compatible with popular detection techniques. The immobilization technique was demonstrated to be compatible with recently developed automated solid phase carbohydrate synthesis methods, paving the way for the development of highly complex carbohydrate arrays.     

Rapid glycoconjugation with glycosyl amines

Conjugation of unprotected carbohydrates to surfaces or probes by chemoselective ligation reactions is indispensable for the elucidation of their numerous biological functions. In particular, the reaction with oxyamines leading to the formation of carbohydrate oximes which are in equilibrium with cyclic N-glycosides (oxyamine ligation) has an enormous impact in the field. Although highly chemoselective, the reaction is rather slow. Here, we report that the oxyamine ligation is significantly accelerated without the need for a catalyst when starting with glycosyl amines. Reaction rates are increased up to 500-fold compared to the reaction of the reducing carbohydrate. For comparison, aniline-catalyzed oxyamine ligation is only increased 3.8-fold under the same conditions. Glycosyl amines from mono- and oligosaccharides are easily accessible from reducing carbohydrates via the corresponding azides by using Shoda''s reagent (2-chloro-1,3-dimethylimidazolinium chloride, DMC) and subsequent reduction. Furthermore, glycosyl amines are readily obtained by enzymatic release from N-glycoproteins making the method suited for glycomic analysis of these glycoconjugates which we demonstrate employing RNase B. Oxyamine ligation of glycosyl amines can be carried out at close to neutral conditions which makes the procedure especially valuable for acid-sensitive oligosaccharides.

A new method for carbohydrate-oxyamine ligation starting from glycosyl amines 1 instead of the commonly used reducing sugars 2 results in tremendously increased ligation rates without the need for a catalyst, such as aniline.     

Multivalent Design of Apoptosis‐Inducing Bid‐BH3 Peptide–Oligosaccharides Boosts the Intracellular Activity at Identical Overall Peptide Concentrations

Multivalent peptide–oligosaccharide conjugates were prepared and used to investigate the multivalency effect concerning the activity of Bid‐BH3 peptides in live cells. Dextran oligosaccharides were carboxyethylated selectively in the 2‐position of the carbohydrate units and activated for the ligation of N‐terminally cysteinylated peptides. Ligation through maleimide coupling was found to be superior to the native chemical ligation protocol. Monomeric Bid‐BH3 peptides were virtually inactive, whereas pentameric peptide conjugates induced apoptosis up to 20‐fold stronger at identical peptide concentrations. Comparison of lowly multivalent and highly multivalent peptide dextrans proved a multivalency effect in life cells which was specific for the BH3 peptide sequence.     

Preparation and use of microarrays containing synthetic heparin oligosaccharides for the rapid analysis of heparin-protein interactions

Heparin is a highly sulfated, linear polymer that participates in a plethora of biological processes by interaction with many proteins. The chemical complexity and heterogeneity of this polysaccharide can explain the fact that, despite its widespread medical use as an anticoagulant drug, the structure-function relationship of defined heparin sequences is still poorly understood. Here, we present the chemical synthesis of a library containing heparin oligosaccharides ranging from di- to hexamers of different sequences and sulfation patterns. An amine-terminated linker was placed at the reducing end of the synthetic structures to allow for immobilization onto N-hydroxysuccinimide activated glass slides and creation of heparin microarrays. Key features of this modular synthesis, such as the influence of the amine linker on the glycosidation efficiency, the use of 2-azidoglucose as glycosylating agents for oligosaccharide assembly, and the compatibility of the protecting group strategy with the sulfation-deprotection steps, are discussed. Heparin microarrays containing this oligosaccharide library were constructed using a robotic printer and employed to characterize the carbohydrate binding affinities of three heparin-binding growth factors. FGF-1, FGF-2 and FGF-4 that are implicated in angiogenesis, cell growth and differentiation were studied. These heparin chips aided in the discovery of novel, sulfated sequences that bind FGF, and in the determination of the structural requirements needed for recognition by using picomoles of protein on a single slide. The results presented here highlight the potential of combining oligosaccharide synthesis and carbohydrate microarray technology to establish a structure-activity relationship in biological processes.     

One‐Pot Synthesis of Unprotected Anomeric Glycosyl Thiols in Water for Glycan Ligation Reactions with Highly Functionalized Sugars

Chemical synthesis of oligosaccharide conjugates is essential for studying the functional relevance of carbohydrates, and this task would be facilitated considerably if reliable methods for the anomeric ligation of unprotected sugars in water were available. Here, a method for the preparation of anomeric glycosyl thiols from complex unprotected mono‐, di‐, and oligosaccharides is presented. By exploiting the neighboring‐group effect of the 2‐acetamido‐group, 1,2‐oxazolines are generated and converted into 1‐glycosyl thioesters through treatment with 1‐thioacids. The unprotected anomeric glycosyl thiolates released in situ were conjugated to Michael acceptors, aliphatic halogenides, and aziridines to furnish versatile glycoconjugates. Conjugation of amino acids and proteins was accomplished using the thiol–ene reaction with terminal olefins. This method gives efficient access to anomeric glycosyl thiols and thiolates, which enables anomeric ligations of complex unprotected glycans in water.     

Carbohydrate arrays for the evaluation of protein binding and enzymatic modification

This paper reports a chemical strategy for preparing carbohydrate arrays and utilizes these arrays for the characterization of carbohydrate-protein interactions. Carbohydrate chips were prepared by the Diels-Alder-mediated immobilization of carbohydrate-cyclopentadiene conjugates to self-assembled monolayers that present benzoquinone and penta(ethylene glycol) groups. Surface plasmon resonance spectroscopy showed that lectins bound specifically to immobilized carbohydrates and that the glycol groups prevented nonspecific protein adsorption. Carbohydrate arrays presenting ten monosaccharides were then evaluated by profiling the binding specificities of several lectins. These arrays were also used to determine the inhibitory concentrations of soluble carbohydrates for lectins and to characterize the substrate specificity of beta-1,4-galactosyltransferase. Finally, a strategy for preparing arrays with carbohydrates generated on solid phase is shown. This surface engineering strategy will permit the preparation and evaluation of carbohydrate arrays that present diverse and complex structures.     

糖芯片合成中的固定化策略*

近年来,糖芯片作为一种强有力的生化分析工具在糖生物学的研究中获得了越来越广泛的应用。在糖芯片制备过程中,糖探针在基板表面的固定是最重要也是最难的一步,它不仅要能牢固的固定在芯片基板上,还必须具有足够的生物活性,因此糖芯片在制备过程中制定合适的糖探针固定化策略一直是一个难点,也是极具挑战性的研究热点。本文首先概述了近几年糖芯片作为一种强有力的生化分析工具在糖生物学研究中的应用。详尽介绍了三种将糖探针固定在固相基片表面的策略：（1）非位点特异性、非共价的方式;（2）位点特异性、非共价的方式;（3）位点特异性、共价的方式。并对糖芯片固定化策略的发展进行了展望。     

Regio- and chemoselective covalent immobilization of proteins through unnatural amino acids

A general approach was developed for the regio- and chemoselective covalent immobilization of soluble proteins on glass surfaces through an unnatural amino acid created by post-translationally modifying the cysteine residue in a CaaX recognition motif with functional groups suitable for "click" chemistry or a Staudinger ligation. Farnesyl diphosphate analogues bearing omega-azide or omega-alkyne moieties were attached to the cysteine residue in Cys-Val-Ile-Ala motifs at the C-termini of engineered versions of green fluorescent protein (GFP) and glutathione S-transferase (GST) by protein farnesyltransferase. The derivatized proteins were attached to glass slides bearing linkers containing azide ("click" chemistry) or phosphine (Staudinger ligation) groups. "Click"-immobilized proteins were detected by fluorescently labeled antibodies and remained attached to the slide through two cycles of stripping under stringent conditions at 80 degrees C. GFP immobilized by a Staudinger ligation was detected by directly imagining the GFP fluorophore over a period of 6 days. These methods for covalent immobilization of proteins should be generally applicable. CaaX recognition motifs can easily be appended to the C-terminus of a cloned protein by a simple modification of the corresponding gene, and virtually any soluble protein or peptide bearing a CaaX motif is a substrate for protein farnesyltransferase.     

A Modular Method for the High‐Yield Synthesis of Site‐Specific Protein–Polymer Therapeutics

A versatile method is described to engineer precisely defined protein/peptide–polymer therapeutics by a modular approach that consists of three steps: 1) fusion of a protein/peptide of interest with an elastin‐like polypeptide that enables facile purification and high yields; 2) installation of a clickable group at the C terminus of the recombinant protein/peptide with almost complete conversion by enzyme‐mediated ligation; and 3) attachment of a polymer by a click reaction with near‐quantitative conversion. We demonstrate that this modular approach is applicable to various protein/peptide drugs and used it to conjugate them to structurally diverse water‐soluble polymers that prolong the plasma circulation duration of these proteins. The protein/peptide–polymer conjugates exhibited significantly improved pharmacokinetics and therapeutic effects over the native protein/peptide upon administration to mice. The studies reported here provide a facile method for the synthesis of protein/peptide–polymer conjugates for therapeutic use and other applications.     

Formation and characterization of DNA microarrays at silicon nitride substrates

A versatile method for direct, covalent attachment of DNA microarrays at silicon nitride layers, previously deposited by chemical vapor deposition at silicon wafer substrates, is reported. Each microarray fabrication process step, from silicon nitride substrate deposition, surface cleaning, amino-silanation, and attachment of a homobifunctional cross-linking molecule to covalent immobilization of probe oligonucleotides, is defined, characterized, and optimized to yield consistent probe microarray quality, homogeneity, and probe-target hybridization performance. The developed microarray fabrication methodology provides excellent (high signal-to-background ratio) and reproducible responsivity to target oligonucleotide hybridization with a rugged chemical stability that permits exposure of arrays to stringent pre- and posthybridization wash conditions through many sustained cycles of reuse. Overall, the achieved performance features compare very favorably with those of more mature glass based microarrays. It is proposed that this DNA microarray fabrication strategy has the potential to provide a viable route toward the successful realization of future integrated DNA biochips.     

Peptide-Directed Attachment of Hydroxylamines to Specific Lysines of IgG Antibodies for Bioconjugations with Acylboronates

The role of monoclonal antibodies as vehicles to deliver payloads has evolved as a powerful tool in cancer therapy in recent years. The clinical development of therapeutic antibody conjugates with precise payloads holds great promise for targeted therapeutic interventions. The use of affinity-peptide mediated functionalization of native off-the-shelf antibodies offers an effective approach to selectively modify IgG antibodies with a drug–antibody ratio (DAR) of 2. Here, we report the traceless, peptide-directed attachment of two hydroxylamines to native IgGs followed by chemoselective potassium acyltrifluoroborate (KAT) ligation with quinolinium acyltrifluoroborates (QATs), which provide enhanced ligation rates with hydroxylamines under physiological conditions. By applying KAT ligation to the modified antibodies, conjugation of small molecules, proteins, and oligonucleotides to off-the-shelf IgGs proceeds efficiently, in good yields, and with simultaneous cleavage of the affinity peptide-directing moiety.     

Covalent immobilization of carbohydrates on sol-gel-coated microplates

Carbohydrate microarrays have attracted increasing attention in recent years because of their ability to monitor biologically important protein-carbohydrate interactions in a high-throughput manner. Here we have developed an effective approach to immobilizing intact carbohydrates directly on polystyrene microtiter plates coated with amine-functionalized sol-gel monolayers. Lectin binding was monitored by fluorescence spectroscopy using these covalent arrays of carbohydrates that contained six mono- and di-saccharides on the microplates. In addition, binding affinities of lectin to carbohydrates were also quantitatively analyzed by determining IC(50) values of lectin-specific antibody with these arrays. Our results indicate that microplate-based carbohydrate arrays can be efficiently fabricated by covalent immobilization of intact carbohydrates on sol-gel-coated microplates. The microplate-based carbohydrate arrays can be applied for screening of protein-carbohydrate interactions in a high-throughput manner.