Solid-Phase-Supported Chemoenzymatic Synthesis and Analysis of Chondroitin Sulfate Proteoglycan Glycopeptides

Proteoglycans (PGs), consisting of glycosaminoglycans (GAGs) linked with the core protein through a tetrasaccharide linkage region, play roles in many important biological events. The chemical synthesis of PG glycopeptides is extremely challenging. In this work, the enzymes required for synthesis of chondroitin sulfate (CS) PG (CSPG) have been expressed and the suitable sequence of enzymatic reactions has been established. To expedite CSPG synthesis, the peptide acceptor was immobilized on solid phase and the glycan units were directly installed enzymatically onto the peptide. Subsequent enzymatic chain elongation and sulfation led to the successful synthesis of CSPG glycopeptides. The CS dodecasaccharide glycopeptide was the longest homogeneous CS glycopeptide synthesized to date. The enzymatic synthesis was much more efficient than the chemical synthesis of the corresponding CS glycopeptides, which could reduce the total number of synthetic steps by 80 %. The structures of the CS glycopeptides were confirmed by mass spectrometry analysis and NMR studies. In addition, the interactions between the CS glycopeptides and cathepsin G were studied. The sulfation of glycan chain was found to be important for binding with cathepsin G. This efficient chemoenzymatic strategy opens new avenues to investigate the structures and functions of PGs.

Fmoc Solid-Phase Peptide Synthesis

Synthetic peptides are important as drugs and in research. Currently, the method of choice for producing these compounds is solid-phase peptide synthesis. Here, we describe the scope and limitations of Fmoc solid-phase peptide synthesis. Furthermore, we provide a detailed protocol for Fmoc peptide synthesis.

Engineering Nanotrap Hydrogel for Immune Modulation in Wound Healing

Imbalanced immune regulation leads to the abnormal wound healing process, e.g., chronic unhealing wound or hypertrophic scar formation. Thus, the attenuation of the overflowing inflammatory factors is a viable approach to maintain the homeostatic immune regulation to facilitate normal wound healing. A versatile telodendrimer (TD) nanotrap (NT) platform is developed for efficient biomolecular protein binding. The conjugation of TD NT in size-exclusive biocompatible hydrogel resin allows for topical application for cytokine scavenging. Fine-tuning the TD NT density/valency in hydrogel resin controls resin swelling, optimizes molecular diffusion, and improves cytokine capture for effective immune modulation. The hydrogel with reduced TD NT density allows for higher protein/cytokine adsorption capacity with faster kinetics, due to the reduced barrier of TD NT nano-assembly. The positively charged TD NT hydrogel exhibits superior removal of negatively charged proinflammatory cytokines from the lipopolysaccharide (LPS, a potent endotoxin) primed immune cell culture medium. The negatively charged TD NT hydrogel removes positively charged anti-inflammatory cytokines efficiently from cell culture medium. TD NT hydrogel effectively constrains the local inflammation induced by subcutaneous LPS injection in mice. These results indicate the great potential applications of the engineered TD NT hydrogel as topical immune modulatory treatments to attenuate local inflammation.

Attachment of cyclodextrin acids to PEGA resin and study of binding with fluorescence microscopy

Three different cyclodextrin acids, 6^A,6^D-di-O-(prop-2-carboxy-1,3-dienyl)-α-cyclodextrin (1), 6-deoxy-β-cyclodextrin-6-carboxylic acid (2), 6-deoxy-β-cyclodextrin-6-ethylenecarboxylic acid (3), were prepared and attached to amino PEGA resin as amides using coupling conditions with COMU and NEM. Host-guest binding to the resins was studied by fluorescence microscopy using 8-anilinoaphtalene-1-sulfonic acid (ANS) as guest, and was found to follow the equation I_F = I_Fmax*[ANS]/([ANS] + K_d) where F, F_max and K_d are the fluorescence, maximum fluorescence and K_d the dissociation constant for the ANS-cyclodextrin complex, respectively. K_d was 4.4, 2.4 and 4.9 × 10^-4 M for the three resins. Competitive inhibition of ANS binding was performed with 1-adamantanylamine and octyl β-d-glucoside with the latter being selective for the α-cyclodextrin as expected.

A nanotrap improves survival in severe sepsis by attenuating hyperinflammation

Targeting single mediators has failed to reduce the mortality of sepsis. We developed a telodendrimer (TD) nanotrap (NT) to capture various biomolecules via multivalent, hybrid and synergistic interactions. Here, we report that the immobilization of TD-NTs in size-exclusive hydrogel resins simultaneously adsorbs septic molecules, e.g. lipopolysaccharides (LPS), cytokines and damage- or pathogen-associated molecular patterns (DAMPs/PAMPs) from blood with high efficiency (92-99%). Distinct surface charges displayed on the majority of pro-inflammatory cytokines (negative) and anti-inflammatory cytokines (positive) allow for the selective capture via TD NTs with different charge moieties. The efficacy of NT therapies in murine sepsis is both time-dependent and charge-dependent. The combination of the optimized NT therapy with a moderate antibiotic treatment results in a 100% survival in severe septic mice by controlling both infection and hyperinflammation, whereas survival are only 50-60% with the individual therapies. Cytokine analysis, inflammatory gene activation and tissue histopathology strongly support the survival benefits of treatments.

Machine-Driven Enzymatic Oligosaccharide Synthesis by Using a Peptide Synthesizer

For decades, researchers have endeavored to develop a general automated system to synthesize oligosaccharides that is comparable to the preparation of oligonucleotides and oligopeptides by commercially available machines. Inspired by the success of automated oligosaccharide synthesis through chemical glycosylation, a fully automated system is reported for oligosaccharides synthesis through enzymatic glycosylation in aqueous solution. The designed system is based on the use of a thermosensitive polymer and a commercially available peptide synthesizer. This study represents a proof-of-concept demonstration that the enzymatic synthesis of oligosaccharides can be achieved in an automated manner using a commercially available peptide synthesizer.

Sustainable Flow Synthesis of Encoded Beads for Combinatorial Chemistry and Chemical Biology

Monosized beads of polar resins were synthesized for combinatorial chemistry and chemical biology by sustainable microchannel flow synthesis. Regular, biocompatible, and optically encoded beads could be efficiently prepared on large scale and in high yield. In a preparative flow polymerization instrument, taking advantage of a designed T-connector for droplet formation, quality beads were synthesized with accurate size control using a minimal amount of recirculating silicon oil as suspension medium. Bead-size was controlled through shear imposed by the silicon oil flow rate. This process provided 86% yield of ∼500 μm macrobeads beads within a 20 μm size range with no deformities or vacuoles, ideally suited for combinatorial chemistry and protein binding studies. The simple flow equipment consisted of a syringe pump for monomer and initiator delivery, a T-connector, a gear pump for oil recirculation, a long, heated coil of Teflon tubing and a collector syringe. The method was used for preparation of PEGA₁₉₀₀ beads, optically encoded with fluorescent microparticles. The microparticle matrix (MPM) encoded beads were tested in a MPM-decoder showing excellent recognition in bead decoding.

Sortase A-mediated on-resin peptide cleavage and in situ ligation: an efficient one-pot strategy for the synthesis of functional peptides and proteins

A one-pot approach combining Sortase A mediated on-resin peptide cleavage, activation and in situ ligation was developed and was employed to synthesize dual functional peptides, modify peptides with lipid, biotin and PEG, as well as protein N-terminal labeling in high efficiency.

Fmoc Solid-Phase Peptide Synthesis

Synthetic peptides are important as drugs and in research. Currently, the method of choice for producing these compounds is solid-phase peptide synthesis. In this nonspecialist review, we describe the scope and limitations of Fmoc solid-phase peptide synthesis. Furthermore, we provide a detailed protocol for Fmoc peptide synthesis.

A solid-phase affinity labeling method for target-selective isolation and modification of proteins

Solid-phase affinity labeling of a target protein, peanut agglutinin (PNA), with the specifically designed chemical tool 1 selectively and effectively furnished the labeled PNA. Furthermore, this method was applicable to native human carbonic anhydrase II in red blood cell lysate using the chemical tool 2 without the need for tedious manipulations.

Enzymatic reactions on immobilised substrates

This review gives an overview of enzymatic reactions that have been conducted on substrates attached to solid surfaces. Such biochemical reactions have become more important with the drive to miniaturisation and automation in chemistry, biology and medicine. Technical aspects such as choice of solid surface and analytical methods are discussed and examples of enzyme reactions that have been successful on these surfaces are provided.

A new approach for the synthesis of O-glycopeptides through a combination of solid-phase glycosylation and fluorous tagging chemistry (SHGPFT)

A new and efficient hybrid approach has been developed for the synthesis and purification of O-linked glycopeptides with high purity.

Glycosylation efficiencies on different solid supports using a hydrogenolysis-labile linker

Automated oligosaccharide assembly requires suitable linkers to connect the first monosaccharide to a solid support. A new hydrogenolysis-labile linker that is stable under both acidic and basic conditions was designed, synthesized and coupled to different resins. Glycosylation and cleavage efficiencies on these functionalized solid supports were investigated, and restrictions for the choice of solid support for oligosaccharide synthesis were found.

Measuring binding of protein to gel-bound ligands using magnetic levitation

This paper describes the use of magnetic levitation (MagLev) to measure the association of proteins and ligands. The method starts with diamagnetic gel beads that are functionalized covalently with small molecules (putative ligands). Binding of protein to the ligands within the bead causes a change in the density of the bead. When these beads are suspended in a paramagnetic aqueous buffer and placed between the poles of two NbFeB magnets with like poles facing, the changes in the density of the bead on binding of protein result in changes in the levitation height of the bead that can be used to quantify the amount of protein bound. This paper uses a reaction-diffusion model to examine the physical principles that determine the values of rate and equilibrium constants measured by this system, using the well-defined model system of carbonic anhydrase and aryl sulfonamides. By tuning the experimental protocol, the method is capable of quantifying either the concentration of protein in a solution, or the binding affinities of a protein to several resin-bound small molecules simultaneously. Since this method requires no electricity and only a single piece of inexpensive equipment, it may find use in situations where portability and low cost are important, such as in bioanalysis in resource-limited settings, point-of-care diagnosis, veterinary medicine, and plant pathology. It still has several practical disadvantages. Most notably, the method requires relatively long assay times and cannot be applied to large proteins (>70 kDa), including antibodies. The design and synthesis of beads with improved characteristics (e.g., larger pore size) has the potential to resolve these problems.

Toward automated oligosaccharide synthesis

Carbohydrates have been shown to play important roles in biological processes. The pace of development in carbohydrate research is, however, relatively slow due to the problems associated with the complexity of carbohydrate structures and the lack of general synthetic methods and tools available for the study of this class of biomolecules. Recent advances in synthesis have demonstrated that many of these problems can be circumvented. In this Review, we describe the methods developed to tackle the problems of carbohydrate-mediated biological processes, with particular focus on the issue related to the development of the automated synthesis of oligosaccharides. Further applications of carbohydrate microarrays and vaccines to human diseases are also highlighted.

An essential epitope of anti-MUC1 monoclonal antibody KL-6 revealed by focused glycopeptide library

Human serum Krebs von den Lungen-6 (KL-6) antigen, a high-molecular-weight glycoprotein classified as a polymorphic epithelial mucin (MUC1), is a biomarker of diseases such as interstitial pneumonia, lung adenocarcinoma, breast cancer, colorectal adenocarcinoma, and hepatocellular carcinoma. Anti-KL-6 monoclonal antibody (anti-KL-6 MAb) is therefore a potential diagnostic and therapeutic reagent. Although glycosylation at Thr/Ser residues of the tandem-repeating MUC1 peptides appears to determine the disease-associated antigenic structures of KL-6, an essential epitope structure recognized by anti-KL-6 MAb remains unclear. In the present study, a novel compound library of synthetic MUC1 glycopeptides allowed the first rapid and precise evaluation of the specific epitope structure of anti-KL-6 MAb by combined use of a tailored glycopeptides library and common ELISA protocol. We demonstrated that the minimal antigenic structure, an essential epitope, recognized by anti-KL-6 MAb is a heptapeptide sequence Pro-Asp-Thr-Arg-Pro-Ala-Pro (PDTRPAP), in which the Thr residue is modified by Neu5Ac alpha2,3Gal beta1,3GalNAc alpha (2,3-sialyl T antigen, core 1-type O-glycan). Anti-KL-6 MAb did not bind with other tumor-relevant antigens, such as GalNAc alpha (Tn), Neu5Ac alpha2,6GalNAc alpha (STn), and Gal beta1,3GalNAc alpha (T), except for Neu5Ac alpha2,3Gal beta1,3(Neu5Ac alpha2,6)GalNAc alpha (2,3/2,6-disialyl T). However, anti-KL-6 MAb could not differentiate the above minimal antigenic glycopeptide from some core 2-based glycopeptides involving this crucial epitope structure and showed a similar binding affinity toward these compounds, indicating that branching at the O-6 position of GalNAc residue does not influence the interaction of anti-KL-6 MAb with some MUC1 glycoproteins involving an essential epitope. Actually, anti-KL-6 MAb reacts with 2,3/2,6-disialyl T having a 2,3-sialyl T component. This is why anti-KL-6 MAb often reacts with various kinds of tumor-derived MUC1 glycoproteins as well as a clinically important MUC1 glycoprotein biomarker of interstitial pneumonia, namely KL-6, originally discovered as a circulating pulmonary adenocarcinoma-associated antigen. In other words, combined use of anti-KL-6 MAb and some probes that can differentiate the sugars substituted at the O-6 position of the GalNAc residue in MUC1 glycopeptides including the PDTRPAP sequence might be a promising diagnostic protocol for individual disease-specific biomarkers. It was also revealed that glycosylation at neighboring Thr/Ser residues outside the immunodominant PDTRPAP motif strongly influences the interaction between anti-KL-6 MAb and MUC1 glycopeptides involving the identified epitope. Our novel strategy will greatly facilitate the processes for the identification of the tumor-specific and strong epitopes of various known anti-MUC1 MAbs and allow for their practical application in the generation of improved antibody immunotherapeutics, diagnostics, and MUC1-based cancer vaccines.

Resins with identical specifications are not identical. Identifying a useful solid-phase resin

The quality of the most commonly used support for solid-phase syntheses, polystyrene resin cross-linked with 1% of divinylbenzene, differs considerably even among different lots of resin from the same source. Determination of the swelling capacity of resins before carrying out solid-phase syntheses represents a very simple means of nondestructive presynthetic resin characterization.

Kinetics of enzyme attack on substrates covalently attached to solid surfaces: influence of spacer chain length, immobilized substrate surface concentration and surface charge

The use of alpha-chymotrypsin to cleave covalently bound N-acetyl- l-tryptophan (Ac-Trp-OH) from the surfaces of aminopropylated controlled pore glass (CPG) and the polymer PEGA 1,900 was investigated. Oligoglycine spacer chains were used to present the covalently attached Ac-Trp-OH substrate to the aqueous enzyme. In the absence of the oligoglycine spacer chain, the rate of release was relatively slow, especially from the PEGA 1,900. These slow rates reflect the position of the amino group to which Ac-Trp-OH is covalently attached. On the glass there was a clear optimum with a chain of four glycine residues. For PEGA 1,900 there is no real apparent change beyond two glycine residues. The decline in rate beyond these optima are a possible result of changes in oligoglycine structure. Comparing different surface loadings of bound substrate the rate of release of Ac-Trp-OH from CPG with a pore diameter of 1,200 A was optimal when using 83% of the maximum that can be coupled, then fell again at higher loading. The rate of Ac-Trp-OH release from CPG was the same for surface coverages of 0.4 and 1.0. The introduction of permanent surface charges on CPG 1,200 exhibits a distinct influence on enzymatic cleavage with an increase in the rate of biocatalysis at the surface. Optimal presentation of covalently immobilized substrate on different supports by use of appropriate linkers leads to favorable biocatalysis from the support.

Real-Time Imaging of Protease Action on Substrates Covalently Immobilised to Polymer Supports

We report for the first time single bead spatially resolved activity measurements of solid-phase biocatalytic systems followed in real-time. Trypsin cleavage of Bz-Arg-OH and subtilisin cleavage of Z-Gly-Gly-Leu-OH each liberate a free amino group on aminocoumarin covalently immobilised to PEGA(1900) beads [a co-polymer of poly(ethylene glycol) with molecular mass of 1900 cross-linked with acrylamide]. This restores fluorescence which is imaged in optical sections by two-photon microscopy. For trypsin cleavage, fluorescence is restricted initially to surface regions, with more than 1 hour needed before reaction is fully underway in the bead centre, presumably reflecting slow enzyme diffusion. In contrast, for subtilisin cleavage fluorescence develops throughout the bead more quickly.

Galectins - potential targets for cancer therapy

Galectins are a family of galactose binding lectins that have become the focus of attention of cancer biologists due to their numerous regulatory roles in normal cellular metabolism and also because of their altered levels in various cancers. They are reportedly similar to several prominent and established modulators of apoptosis. In this review, we present a brief outline of the advancements in the methodology used to detect and identify them and their therapeutic applications in cancer. Their possible interactions with other glycoconjugates are also discussed and a vision for their future use in diagnosis and therapeutics is provided.

Inhibition and Detection of Galectins

More and more studies report on the roles that galectins play in numerous types of cancer. These roles can be varied, as has been shown particularly for galectin-3. These studies have created the need for inhibitors that can block unwanted effects, and the need to detect galectins in tissues, in order to better understand their role, and aid in diagnosis and prognosis. Since galectins bind beta-galactosides, monovalent galactose-derived inhibitors have been prepared but also peptidic ones have appeared. Since galectins often induce crosslinking and partake in aggregation phenomena, multivalency has been a successful design element in inhibitor development. Currently, there are no cheap and convenient solutions available for the detection of, ideally multiple, galectins in tissue samples, although antibody-based methods such as ELISA and Western blot analysis are being used. Besides these, a chemical probe-based method also shows potential as an alternative.

On-Bead Chemical Synthesis and Display of Phosphopeptides for Affinity Pull-Down Proteomics

We describe a new method for phosphopeptide proteomics based on the solid-phase synthesis of phosphopeptides on beads suitable for affinity pull-down experiments. Peptide sequences containing the Bad Ser112 and Ser136 phosphorylation motifs were used as bait in affinity pull-down experiments to determine their ability to bind 14-3-3 proteins. Support-bound peptides were assembled directly on the solid support (PEGA) by standard solid-phase synthesis through a BAL-type handle. The peptides were varied in length and sequence. This synthetic strategy also allowed introduction of a soft electrophile (aldehyde) at the C terminus for potential activity-based proteomics. The synthetic support-bound Bad phosphopeptides were able to pull down 14-3-3zeta. Furthermore, Bad phosphopeptides bound endogenous 14-3-3 proteins, and all seven members of the 14-3-3 family were identified by mass spectrometry. In control experiments, none of the unphosphorylated Bad peptides bound transfected 14-3-3zeta or endogenous 14-3-3. We conclude that the combined synthesis and display of phosphopeptides on-bead is a fast and efficient method for affinity pull-down proteomics.

Insulins with built-in glucose sensors for glucose responsive insulin release

Derivatization of insulin with phenylboronic acids is described, thereby equipping insulin with novel glucose sensing ability. It is furthermore demonstrated that such insulins are useful in glucose-responsive polymer-based release systems. The preferred phenylboronic acids are sulfonamide derivatives, which, contrary to naïve boronic acids, ensure glucose binding at physiological pH, and simultaneously operate as handles for insulin derivatization at LysB29. The glucose affinities of the novel insulins were evaluated by glucose titration in a competitive assay with alizarin. The affinities were in the range 15-31 mM (K(d)), which match physiological glucose fluctuations. The dose-responsive glucose-mediated release of the novel insulins was demonstrated using glucamine-derived polyethylene glycol polyacrylamide (PEGA) as a model, and it was shown that Zn(II) hexamer formulation of the boronated insulins resulted in steeper glucose sensitivity relative to monomeric insulin formulation. Notably, two of the boronated insulins displayed enhanced insulin receptor affinity relative to native insulin (113%-122%) which is unusual for insulin LysB29 derivatives.

Identification of peptide ligands for malignancy- and growth-regulating galectins using random phage-display and designed combinatorial peptide libraries

Members of the galectin family of endogenous lectins are involved in tumor growth regulation and in establishing characteristics of the malignant phenotype via protein-carbohydrate and protein-protein interactions. To identify peptide ligands with the potential to modulate these tumor-relevant interactions beneficially, complementary screening methods were employed, that is, both phage-display and a combinatorial pentapeptide library with the key YXY tripeptide core. Three representative prototype galectins were selected. The search for high-affinity ligands among phage-displayed random heptamers yielded enrichment after five selection cycles of the nonglycomimetic CQSPSARSC peptide in the case of the chicken homologue of galectin-1 but not the human protein, an indication for specificity. The most active glycomimetic from the combinatorial library of 5832 pentamers was WYKYW. Identification of peptide ligands for galectins with and without glycomimetic properties is thus possible. Our study documents the potential to combine the two library-based approaches for structural optimization of lead peptides.

Solid-supported enzymatic synthesis of pectic oligogalacturonides and their analysis by MALDI-TOF mass spectrometry

Solid-phase biosynthetic reactions, followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis (MALDI-TOF), was used to gain insight into the biosynthesis of pectin oligomers. Sepharose supports bearing long pectic oligogalacturonides (OGAs) anchored through a disulfide-containing cleavable linker, were prepared. The OGAs (degrees of polymerization of 13 and 14) were efficiently immobilized through the reducing end via formation of an oxime linkage. These OGA-derivatized matrices were subsequently employed in novel solid-phase enzymatic reactions, with the pectin biosynthetic enzyme, alpha-1,4-galacturonosyltransferase, GalAT (solubilized from Arabidopsis thaliana) and the glycosyl donor, uridine diphosphate-galacturonic acid (UDP-GalA). Solid-supported biosynthesis was followed by cleavage of the immobilized OGAs and direct analysis of the products released into the liquid phases by MALDI-TOF mass spectrometry. In time course studies conducted with an immobilized (alpha-D-GalA)14 and limiting amounts of the glycosyl donor, the predominant product was an OGA extended by one GalA residue at the non-reducing end (i.e., (GalA)15). When UDP-GalA was added in approximately excess compared to immobilized (GalA)13, OGAs up to the 16-mer were synthesized, confirming the non-processivity of the GalAT in vitro.

Synthesis of novel acceptor substrates for the dolichyl phosphate mannose synthase from yeast

Dolichols are polyisoprenoid lipid components of mammalian membranes consisting of an average of 20 head-to-tail linked isoprene units of which the first isoprene is fully saturated. The unusual size of these lipids is intriguing and poses questions about the role of dolichol structure in biological processes. In order to probe structure and function we have synthesised potential dolichyl analogues that retain only the first two isoprene units and carry a second functional group within the terminal lipid chain. Such analogues were evaluated as substrates for a key enzyme in the dolichyl-dependent pathway of glycan biosynthesis, dolichyl phosphate mannose (Dol-P-Man) synthase. It was shown that some functional groups, including labels such as biotin, could be tolerated. When the synthetic analogues were attached to a solid support they were still substrates for the Dol-P-Man system and thus allowed the enzymatic solid-phase synthesis of glycolipids.

Combining combinatorial chemistry and affinity chromatography: highly selective inhibitors of human betaine: homocysteine S-methyltransferase

A new method to find novel protein targets for ligands of interest is proposed. The principle of this approach is based on affinity chromatography and combinatorial chemistry. The proteins within a crude rat liver homogenate were allowed to interact with a combinatorial library of phosphinic pseudopeptides immobilized on affinity columns. Betaine: homocysteine S-methyltransferase (BHMT) was one of the proteins that was retained and subsequently eluted from these supports. The phosphinic pseudopeptides, which served as immobilized ligands for the isolation of rat BHMT, were then tested for their ability to inhibit human recombinant BHMT in solution. The most potent inhibitor also behaved as a selective ligand for the affinity purification of BHMT from a complex media. Further optimization uncovered Val-Phe-psi[PO(2-)-CH(2)]-Leu-His-NH(2) as a potent BHMT inhibitor that has an IC(50) of about 1 microM.

Dendrimers and hyperbranched polymers as high-loading supports for organic synthesis

Polymeric supports have become a big necessity for automated synthesis and combinatorial chemistry, yet, the loading capacities of most polystyrene resins are very limited (typically < 1.5 mmol x g(-1)). Dendrimers and hyperbranched polymers have been discussed for this application and now became readily available. These soluble polymers can either be used directly as high-loading supports for substrates, reagents, and catalysts or alternatively in hybrid polymers linked to conventional polystyrene resins.