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Geert-Jan Boons

Publications and source records attributed to Geert-Jan Boons.

At least 19 recordsLinked to original sources
PubMed2006

Synthesis and antigenic analysis of the BclA glycoprotein oligosaccharide from the Bacillus anthracis exosporium.

The glycoprotein BclA is an important constituent of the exosporium of Bacillus anthracis spores. This glycoprotein is substituted with an oligosaccharide composed of a beta-L-rhamnoside substituted with the previously unknown terminal saccharide, 2-O-methyl-4-(3-hydroxy-3-methylbutanamido)-4,6-dideoxy-D-glucopyranose, also referred to as anthrose. Anthrose has not been found in spores of B. cereus and B. thuringiensis, making it a potential species-specific marker for B. anthracis. In order to study the antigenicity of anthrose, efficient syntheses of an anthrose-containing trisaccharide and a series of structurally related analogues were developed. The analogues lacked either the methyl ether at C-2 or contained modified C-4 amino functionalities of anthrose. The synthetic compounds were equipped with an aminopropyl spacer to facilitate conjugation to the carrier proteins mariculture Keyhole Limpet Hemocyanin (mcKLH) and bovine serum albumin (BSA). Serum antibodies of rabbits immunized with live or irradiated spores of B. anthracis Sterne 34F(2) were able to recognize the synthetic trisaccharide-mcKLH conjugate. The specificity of the interaction was confirmed by competitive inhibition with the free- and BSA-conjugated trisaccharides. Inhibition using the trisaccharide analogues demonstrated that the isovaleric acid moiety of anthrose is an important structural motif for antibody recognition. These data demonstrate that 1) anthrose is a specific antigenic determinant of the B. anthracis Sterne spore; 2) this antigen is presented to the immune system of rabbits receiving the anthrax live-spore vaccine; 3) synthetic analogues of the oligosaccharide retain the antigenic structure; and 4) the antigenic region is localized to specific terminal groups of the oligosaccharide. Collectively these data provide an important proof-of-concept step in the synthesis and development of spore-specific reagents for detection and targeting of non-protein structures in B. anthracis.

Animals↗
PubMed2006

Synthesis of glyco(lipo)peptides by liposome-mediated native chemical ligation.

Although native chemical ligation (NCL) is emerging as a powerful method for the assembly of (glyco)peptide building blocks, its applicability is reduced when peptide segments are poorly soluble in aqueous buffer. We have found that incorporating reactants in liposomes allows NCL of lipophilic peptides and lipopeptides. Furthermore, the reaction rates of liposome-mediated NCL are higher than traditional reaction conditions resulting in improved yields. [reaction: see text]

Amino Acid Sequence↗
PubMed2006

Modification of the structure of peptidoglycan is a strategy to avoid detection by nucleotide-binding oligomerization domain protein 1.

Nucleotide-binding oligomerization domain (NOD) protein 1 (NOD1) and NOD2 are pathogen recognition receptors that sense breakdown products of peptidoglycan (PGN) (muropeptides). It is shown that a number of these muropeptides can induce tumor necrosis factor alpha (TNF-alpha) gene expression without significant TNF-alpha translation. This translation block is lifted when the muropeptides are coincubated with lipopolysaccharide (LPS), thereby accounting for an apparently synergistic effect of the muropeptides with LPS on TNF-alpha protein production. The compounds that induced synergistic effects were also able to activate NF-kappaB in a NOD1- or NOD2-dependent manner, implicating these proteins in synergistic TNF-alpha secretion. It was found that a diaminopimelic acid (DAP)-containing muramyl tetrapeptide could activate NF-kappaB in a NOD1-dependent manner, demonstrating that an exposed DAP is not essential for NOD1 sensing. The activity was lost when the alpha-carboxylic acid of iso-glutamic acid was modified as an amide. However, agonists of NOD2, such as muramyl dipeptide and lysine-containing muramyl tripeptides, were not affected by amidation of the alpha-carboxylic acid of iso-glutamic acid. Many pathogens modify the alpha-carboxylic acid of iso-glutamic acid of PGN, and thus it appears this is a strategy to avoid recognition by the host innate immune system. This type of immune evasion is in particular relevant for NOD1.

Cell Line↗
PubMed2006

Practical approach for the stereoselective introduction of beta-arabinofuranosides.

A practical approach for the stereoselective introduction of beta-arabinofuranosides has been developed on the basis of locking an arabinosyl donor in a conformation in which nucleophilic attack from the beta face is favored. The new glycosyl donor was designed by analyzing optimized geometries of low-energy conformers of the arabinofuranosyl oxacarbenium ion. The Newman projection of the E(3) conformer indicated that nucleophilic attack from the alpha face is disfavored because an eclipsed H-2 will be encountered. On the other hand, an approach from the beta face was expected to be more favorable, because it will experience only staggered substituents. The arabinofuranosyl oxacarbenium ion could be locked in the E(3) conformation by employing a 3,5-O-di-tert-butylsilane protecting group, which places C-5 and O-3 in a pseudoequatorial orientation, resulting in a perfect chair conformation of the protecting group. The new glycosyl donor gave excellent beta selectivities in a range of glycosylations with glycosyl acceptors having primary and secondary alcohols. The attractiveness of the new methodology was demonstrated by the chemical synthesis of a fragment of arabinogalactan, which is an important constituent of the primary plant cell wall.

Arabinose↗
PubMed2006

Trypanosoma brucei UDP-galactose-4'-epimerase in ternary complex with NAD+ and the substrate analogue UDP-4-deoxy-4-fluoro-alpha-D-galactose.

The structure of the NAD-dependent oxidoreductase UDP-galactose-4'-epimerase from Trypanosoma brucei in complex with cofactor and the substrate analogue UDP-4-deoxy-4-fluoro-alpha-D-galactose has been determined using diffraction data to 2.7 A resolution. Despite the high level of sequence and structure conservation between the trypanosomatid enzyme and those from humans, yeast and bacteria, the binding of the 4-fluoro-alpha-D-galactose moiety is distinct from previously reported structures. Of particular note is the observation that when bound to the T. brucei enzyme, the galactose moiety of this fluoro-derivative is rotated approximately 180 degrees with respect to the orientation of the hexose component of UDP-glucose when in complex with the human enzyme. The architecture of the catalytic centre is designed to effectively bind different orientations of the hexose, a finding that is consistent with a mechanism that requires the sugar to maintain a degree of flexibility within the active site.

Animals↗
PubMed2006

Structural basis of the inhibition of Golgi alpha-mannosidase II by mannostatin A and the role of the thiomethyl moiety in ligand-protein interactions.

The X-ray crystal structures of mannose trimming enzyme drosophila Golgi alpha-mannosidase II (dGMII) complexed with the inhibitors mannostatin A (1) and an N-benzyl analogue (2) have been determined. Molecular dynamics simulations and NMR studies have shown that the five-membered ring of mannostatin A is rather flexible occupying pseudorotational itineraries between 2T3 and 5E, and 2T3 and 4E. In the bound state, mannostatin A adopts a 2T1 twist envelope conformation, which is not significantly populated in solution. Possible conformations of the mannosyl oxacarbenium ion and an enzyme-linked intermediate have been compared to the conformation of mannostatin A in the cocrystal structure with dGMII. It has been found that mannostatin A best mimics the covalent linked mannosyl intermediate, which adopts a 1S5 skew boat conformation. The thiomethyl group, which is critical for high affinity, superimposes with the C-6 hydroxyl of the covalent linked intermediate. This functionality is able to make a number of additional polar and nonpolar interactions increasing the affinity for dGMII. Furthermore, the X-ray structures show that the environment surrounding the thiomethyl group of 1 is remarkably similar to the arrangements around the methionine residues in the protein. Collectively, our studies contradict the long held view that potent inhibitors of glycosidases must mimic an oxacarbenium ion like transition state.

Binding Sites↗
PubMed2006

Glycopeptides as versatile tools for glycobiology.

This review describes the recent advances in the field of glycopeptide and small glycoprotein synthesis. The strategies covered include chemical and chemoenzymatic synthesis, native chemical ligation (NCL), and expressed chemical ligation. The importance of glycopeptide synthesis is exemplified by giving the reader an overview of how versatile and important these well-defined glycopeptides are as tools in glycobiology.

Biology↗
PubMed2006

Trisaccharide mimetics of the aminoglycoside antibiotic neomycin.

A highly convergent approach for the chemical synthesis of eight structurally related trisaccharides that contain 3 to 5 amino groups has been described. Fourier-transformation ion cyclotron resonance mass spectrometry (FT-ICR MS) has been employed to determine the dissociation constants (Kd) for the binding of the trisaccharides to a prototypical fragment of 16S ribosomal RNA. A compound that contained a 4,6-dideoxy-4-amino-beta-D-glucopyranoside moiety at C-3 displayed binding in the low micromolar range. It was found that small structural changes of the saccharides resulted in large differences in affinity. The described structure-activity relationship is expected to be valuable for the development of novel antibiotics that target rRNA.

Carbohydrate Conformation↗
PubMed2006

Dual strategies for peptidoglycan discrimination by peptidoglycan recognition proteins (PGRPs).

The innate immune system constitutes the first line of defense against microorganisms in both vertebrates and invertebrates. Although much progress has been made toward identifying key receptors and understanding their role in host defense, far less is known about how these receptors recognize microbial ligands. Such studies have been severely hampered by the need to purify ligands from microbial sources and a reliance on biological assays, rather than direct binding, to monitor recognition. We used synthetic peptidoglycan (PGN) derivatives, combined with microcalorimetry, to define the binding specificities of human and insect peptidoglycan recognition proteins (PGRPs). We demonstrate that these innate immune receptors use dual strategies to distinguish between PGNs from different bacteria: one based on the composition of the PGN peptide stem and another that senses the peptide bridge crosslinking the stems. To pinpoint the site of PGRPs that mediates discrimination, we engineered structure-based variants having altered PGN-binding properties. The plasticity of the PGRP-binding site revealed by these mutants suggests an intrinsic capacity of the innate immune system to rapidly evolve specificities to meet new microbial challenges.

Animals↗
PubMed2006

The 2-aminogluconate isomer of rhizobium sin-1 lipid A can antagonize TNF-alpha production induced by enteric LPS.

The naturally occurring lipopolysaccharide (LPS) from Rhizobium sin-1, a nitrogen-fixing bacterial species, can prevent the induction of the tumor necrosis factor TNF-alpha induced by enteric LPS. The proximal saccharide moiety of R. sin-1 lipid A can exist in two forms, namely as a 2-aminogluconolactone or 2-aminogluconate. As it is unknown which of these forms is responsible for the antagonistic properties of R. sin-1 lipid A, compound 4 was prepared, and its inflammatory properties were studied. This compound contains a methyl ether at the C-5 hydroxyl, which prevents lactonization and therefore is ideally suited to determine whether the 2-aminogluconate possesses antagonistic properties. Compound 4 was synthesized by a highly convergent approach with a key disaccharide building block functionalized with a set of orthogonal protecting groups. The novel synthetic compound lacks proinflammatory properties, as indicated by an absence of TNF-alpha protein production. This compound was, however, able to antagonize the production of TNF-alpha induced by enteric LPS; this indicates that the 2-aminogluconate form of R. sin-1 lipid A is responsible for its biological properties.

Carbohydrate Conformation↗
PubMed2006

Crystal structure of human peptidoglycan recognition protein I alpha bound to a muramyl pentapeptide from Gram-positive bacteria.

Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors of the innate immune system that bind bacterial peptidoglycans (PGNs). We determined the crystal structure, to 2.1 A resolution, of the C-terminal PGN-binding domain of human PGRP-I alpha in complex with a muramyl pentapeptide (MPP) from Gram-positive bacteria containing a complete peptide stem (L-Ala-D-isoGln-L-Lys-D-Ala-D-Ala). The structure reveals important features not observed previously in the complex between PGRP-I alpha and a muramyl tripeptide lacking D-Ala at stem positions 4 and 5. Most notable are ligand-induced structural rearrangements in the PGN-binding site that are essential for entry of the C-terminal portion of the peptide stem and for locking MPP in the binding groove. We propose that similar structural rearrangements to accommodate the PGN stem likely characterize many PGRPs, both mammalian and insect.

Carrier Proteins↗
PubMed2006

Structural basis for the recognition of complex-type biantennary oligosaccharides by Pterocarpus angolensis lectin.

The crystal structure of Pterocarpus angolensis lectin is determined in its ligand-free state, in complex with the fucosylated biantennary complex type decasaccharide NA2F, and in complex with a series of smaller oligosaccharide constituents of NA2F. These results together with thermodynamic binding data indicate that the complete oligosaccharide binding site of the lectin consists of five subsites allowing the specific recognition of the pentasaccharide GlcNAc beta(1-2)Man alpha(1-3)[GlcNAc beta(1-2)Man alpha(1-6)]Man. The mannose on the 1-6 arm occupies the monosaccharide binding site while the GlcNAc residue on this arm occupies a subsite that is almost identical to that of concanavalin A (con A). The core mannose and the GlcNAc beta(1-2)Man moiety on the 1-3 arm on the other hand occupy a series of subsites distinct from those of con A.

Binding Sites↗
PubMed2005

Synthesis of a dimeric Lewis antigen and the evaluation of the epitope specificity of antibodies elicited in mice.

The Lewis(y)-Lewis(x) heptasaccharide, modified by an artificial aminopropyl spacer, was synthesized by an approach that employed two orthogonally protected lactosamine building blocks. A p-(benzoyl)-benzyl glycoside was used as a novel anomeric protecting group, which could be selectively removed at a late stage in the synthesis, thus offering the benefit of enhanced flexibility. The artificial aminopropyl moiety was modified by a thioacetyl group, which allowed an efficient conjugation to keyhole limpet hemocyanin (KLH) that had been activated with electrophilic 3-(bromoacetamido)-propionyl groups. Mice were immunized with the Le(y)Le(x)-BrAc-KLH antigen. Analysis of the sera by ELISA established that a strong helper T-cell immune response was raised against the Le(y)Le(x) saccharide. Further ELISA analysis showed that the titer for monomeric Le(y) tetrasaccharide was tenfold lower whereas recognition of the Le(x) trisaccharide was negligible.

Animals↗
PubMed2005

A general strategy for stereoselective glycosylations.

The principal challenge that the synthesis of oligosaccharides of biological importance presents is the development of a general approach for the stereoselective introduction of a glycosidic linkage. It is shown here that a (1S)-phenyl-2-(phenylsulfanyl)ethyl moiety at C-2 of a glycosyl donor can perform neighboring group participation to give a quasi-stable anomeric sulfonium ion. Due to steric and electronic factors, the sulfonium ion is formed as a trans-decalin ring system. Displacement of the sulfonium ion by a hydroxyl leads to the stereoselective formation of alpha-glycosides. NMR experiments were employed to show convincingly the presence of the beta-linked sulfonium ion intermediate. The (1S)-phenyl-2-(phenylsulfanyl)ethyl moiety could be introduced by reaction of a sugar alcohol with acetic acid (1S)-phenyl-2-(phenylsulfanyl)ethyl ester in the presence of BF(3)-OEt(2). Furthermore, it could be removed by conversion into acetate by treatment with BF(3)-OEt(2) in acetic anhydride. The introduction as well as the cleavage reaction proceeds through the formation of an intermediate episulfonium ion. The use of the new methodology in combination with traditional neighboring group participation by esters to introduce beta-glycosides makes it possible, for the first time, to synthesize a wide variety of oligosaccharides by routine procedures. The latter was demonstrated by the synthesis of the Galili trisaccharide, which has been identified as an epitope that can trigger acute rejections in xeno-transplantations, by the one-pot two-step glycosylation sequence.

Carbohydrate Conformation↗
PubMed2005

Selective recognition of synthetic lysine and meso-diaminopimelic acid-type peptidoglycan fragments by human peptidoglycan recognition proteins I{alpha} and S.

The interactions of a range of synthetic peptidoglycan derivatives with PGRP-Ialpha and PGRP-S have been studied in real-time using surface plasmon resonance. A dissociation constant of K(D) = 62 mum was obtained for the interaction of peptidoglycan recognition protein (PGRP)-Ialpha with the lysine-containing muramyl pentapeptide (compound 6). The normalized data for the lysine-containing muramyl tetra- (compound 5) and pentapeptide (compound 6) showed that these compounds have similar affinities, whereas a much lower affinity for muramyl tripeptide (compound 3) was measured. Similar affinities were obtained when the lysine moiety of the muramyl peptides was replaced by meso-diaminopimelic acid (DAP). Furthermore, the compounds that contained only a stem peptide (pentapeptide, compound 1) and (DAP-PP, compound 2) as well as muramyldipeptide (compound 3) exhibited no binding indicating that the muramyltripeptide (compound 4) is the smallest peptidoglycan fragment that can be recognized by PGRP-Ialpha. Surprisingly, PGRP-S derived significantly higher affinities for the DAP-containing fragments to similar lysine-containing derivatives, and the following dissociation constants were measured: muramylpentapeptide-DAP, K(D) = 104 nm; muramyltetrapeptide-DAP, 92.4 nm; and muramyltripeptide-DAP, 326 nm. The binding profiles were rationalized by using a recently reported x-ray crystal structure of PGRP-Ialpha with the lysine-containing muramyltripeptide (4).

Acetylmuramyl-Alanyl-Isoglutamine↗
PubMed2005

Synthesis of proteophosphoglycans of Leishmania major and Leishmania mexicana.

A novel approach for the synthesis of various fragments of proteophosphoglycans from Leishmania major and Leishmania mexicana proteophosphoglycans has been developed. These compounds have been obtained by coupling alpha-mannosyl and alpha-N-acetyl-glucosamine phosphoramidite derivatives with the serine hydroxyl of various amino acids and peptides to give, after oxidation with tert-BuOOH, phosphotriesters exclusively as alpha-anomers in good yield. The resulting compounds could be deblocked using conventional methods. Glycophosphorylation of preassembled and properly protected peptides was found to be more efficient for the preparation of proteophosphoglycan fragments than a building block approach strategy using a phosphoglycosylserine derivative.

Animals↗