Gijsbert A van der Marel

Publications of Gijsbert A van der Marel

• Protection Against Staphylococcus aureus by Antibody to the Polyglycerolphosphate Backbone of Heterologous Lipoteichoic Acid.

  Authors: Christian Theilacker, Andrea Kropec, Felix Hammer, Irina Sava, Dominique Wobser, Tuerkan Sakinc, Jeroen D C Codée, Wouter F J Hogendorf, Gijsbert A van der Marel, Johannes Huebner

  The Journal of infectious diseases. 04/2012; 205(7):1076-85.

  Type 1 lipoteichoic acid (LTA) is present in many clinically important gram-positive bacteria, including enterococci, streptococci, and staphylococci, and antibodies against LTA have been shown toType 1 lipoteichoic acid (LTA) is present in many clinically important gram-positive bacteria, including enterococci, streptococci, and staphylococci, and antibodies against LTA have been shown to opsonize nonencapsulated Enterococcus faecalis strains. In the present study, we show that antibodies against E. faecalis LTA also bind to type 1 LTA from other gram-positive species and opsonized Staphylocccus epidermidis and Staphylcoccus aureus strains as well as group B streptococci. Inhibition studies using teichoic acid oligomers indicated that cross-reactive opsonic antibodies bind to the teichoic acid backbone. Passive immunization with rabbit antibodies against E. faecalis LTA promoted the clearance of bacteremia by E. faecalis and S. epidermidis in mice. Furthermore, passive protection also reduced mortality in a murine S. aureus peritonitis model. The effectiveness of rabbit antibody against LTA suggests that this conserved bacterial structure could function as a single vaccine antigen that targets multiple gram-positive pathogens.

• Triple Bioorthogonal Ligation Strategy for Simultaneous Labeling of Multiple Enzymatic Activities.

  Authors: Lianne I Willems, Nan Li, Bogdan I Florea, Mark Ruben, Gijsbert A van der Marel, Herman S Overkleeft

  Angewandte Chemie (International ed. in English). 03/2012;

  Three at the same time: A ligation strategy combining tetrazine-norbornene cycloaddition, Staudinger-Bertozzi ligation, and copper(I)-catalyzed click reaction was used to label the three catalyticThree at the same time: A ligation strategy combining tetrazine-norbornene cycloaddition, Staudinger-Bertozzi ligation, and copper(I)-catalyzed click reaction was used to label the three catalytic activities of the proteasome simultaneously in a single experiment. The orthogonality of the three ligation reactions enables selective monitoring of multiple targets at the same time in complex biological samples.

• Automated Solid-Phase Synthesis of β-Mannuronic Acid Alginates.

  Authors: Marthe T C Walvoort, Hans van den Elst, Obadiah J Plante, Lenz Kröck, Peter H Seeberger, Herman S Overkleeft, Gijsbert A van der Marel, Jeroen D C Codée

  Angewandte Chemie (International ed. in English). 02/2012;

  A big step towards routine: The title synthesis provides of mannuronic acid alginate fragments featuring up to 12 cis-mannosidic linkages, in multi-milligram quantities (see scheme; Bn=benzyl,A big step towards routine: The title synthesis provides of mannuronic acid alginate fragments featuring up to 12 cis-mannosidic linkages, in multi-milligram quantities (see scheme; Bn=benzyl, Lev=levulinoyl). Mannuronic acid building blocks were used in a second-generation carbohydrate synthesizer to secure the stereoselective introduction of the β-mannosidic bonds in a fully automated fashion.

• β-Rhamnosides from 6-thio mannosides.

  Authors: Alphert E Christina, Daan van der Es, Jasper Dinkelaar, Hermen S Overkleeft, Gijsbert A van der Marel, Jeroen D C Codée

  Chemical communications (Cambridge, England). 02/2012; 48(21):2686-8.

  Upon condensation of 6-thio-6-deoxy-mannosyl donors 1,2-cis products are obtained with a high degree of stereoselectivity. Subsequent reductive removal of the 6-thio functionality gives 1,2-cisUpon condensation of 6-thio-6-deoxy-mannosyl donors 1,2-cis products are obtained with a high degree of stereoselectivity. Subsequent reductive removal of the 6-thio functionality gives 1,2-cis rhamnosides. The 1,2-cis-selectivity can be rationalized with a product forming (3)H(4)-oxocarbenium, which is in equilibrium with a bridged sulfonium intermediate.

• Fluorous linker facilitated synthesis of teichoic acid fragments.

  Authors: Wouter F J Hogendorf, Lucien N Lameijer, Thomas J M Beenakker, Herman S Overkleeft, Dmitri V Filippov, Jeroen D C Codée, Gijsbert A Van der Marel

  Organic letters. 02/2012; 14(3):848-51.

  The use of perfluorooctylpropylsulfonylethanol as a new phosphate protecting group and fluorous linker is evaluated in the stepwise solution phase synthesis of a number of biologically relevantThe use of perfluorooctylpropylsulfonylethanol as a new phosphate protecting group and fluorous linker is evaluated in the stepwise solution phase synthesis of a number of biologically relevant (carbohydrate substituted) glycerol teichoic acid fragments. Teichoic acid fragments, up to the dodecamer level, were assembled by means of phosphoramidite chemistry, using a relatively small excess of the building blocks and a repetitive efficient purification procedure of the protected intermediates by fluorous solid phase extraction (F-SPE).

• Exploring and exploiting the reactivity of glucuronic acid donors.

  Authors: Ana-Rae de Jong, Bas Hagen, Vincent van der Ark, Herman S Overkleeft, Jeroen D C Codée, Gijsbert A Van der Marel

  The Journal of organic chemistry. 11/2011; 77(1):108-25.

  The relative reactivity of glucuronic acid esters was established in a series of competition experiments, in which two thioglucoside and/or thioglucuronic acid ester donors competed for a limitedThe relative reactivity of glucuronic acid esters was established in a series of competition experiments, in which two thioglucoside and/or thioglucuronic acid ester donors competed for a limited amount of activator (NIS-TfOH). Although glucuronic acid esters are often considered to be of very low reactivity, the series of competition reactions revealed that the reactivity of the glucuronic acid esters studied is sufficient to provide productive glycosylation reactions. The latter is illustrated in the synthesis of two Streptococcus pneumoniae trisaccharides, in which the applicability of the two similarly protected frame-shifted thiodisaccharide donors, Glc-GlcA and GlcA-Glc, were compared. The Glc-GlcA disaccharide, featuring the glucuronic acid donor moiety, proved to be the most productive in the assembly of a protected S. pneumoniae trisaccharide.

• Synthesis of pH-activatable red fluorescent BODIPY dyes with distinct functionalities.

  Authors: Sascha Hoogendoorn, Annet E M Blom, Lianne I Willems, Gijsbert A van der Marel, Herman S Overkleeft

  Organic letters. 09/2011; 13(20):5656-9.

  A series of tunable pH-dependent BODIPY dyes were synthesized and further functionalized in a Knoevenagel condensation reaction with various aldehydes. In this fashion, monofunctional dyes containingA series of tunable pH-dependent BODIPY dyes were synthesized and further functionalized in a Knoevenagel condensation reaction with various aldehydes. In this fashion, monofunctional dyes containing an alkyne, azide, or carboxylic acid (masked as its methyl ester) as ligation sites as well as asymmetrical bifunctional dyes were obtained, without compromising their pH-dependency. In addition, fluorescence excitation and emission maxima for these dyes were shown to be significantly red-shifted in comparison to their tetramethyl precursors.

• Irreversible inhibitors and activity-based probes as research tools in chemical glycobiology.

  Authors: Martin D Witte, Gijsbert A van der Marel, Johannes M F G Aerts, Herman S Overkleeft

  Organic & biomolecular chemistry. 09/2011; 9(17):5908-26.

  In this review, we will discuss the enzymes that are involved in the synthesis and degradation of glycoconjugates and we will give an overview of the inhibitors and activity-based probes (ABPs) thatIn this review, we will discuss the enzymes that are involved in the synthesis and degradation of glycoconjugates and we will give an overview of the inhibitors and activity-based probes (ABPs) that have been used to study these. Following discussion of some general aspects of the biosynthesis and degradation of N-linked glycoproteins, attention is focused on the enzymes that hydrolyze the protein-carbohydrate linkage, peptide N-glycanase and glycosylasparaginase and their mechanism. We then focus on the biosynthesis of O-linked glycoproteins and glycolipids and in particular on the enzymes that hydrolyze the interglycosidic linkages in these, the glycosidases. Some important mechanism-based glycosidase inhibitors that form a covalent bond with the targeted enzyme(s), their corresponding ABPs and their application to study this class of enzymes are highlighted. Finally, alternative pathways for degradation of glycoconjugates and an ABP-based strategy to study these will be discussed.

• Targeted pH-dependent fluorescent activity-based cathepsin probes.

  Authors: Sascha Hoogendoorn, Kim L Habets, Solène Passemard, Johan Kuiper, Gijsbert A van der Marel, Bogdan I Florea, Herman S Overkleeft

  Chemical communications (Cambridge, England). 09/2011; 47(33):9363-5.

  Bifunctional, pH-activatable BODIPY dyes were developed and incorporated in mannose cluster-containing activity-based probes for cysteine proteases. Mannose receptor-dependent uptake of the probes inBifunctional, pH-activatable BODIPY dyes were developed and incorporated in mannose cluster-containing activity-based probes for cysteine proteases. Mannose receptor-dependent uptake of the probes in dendritic cells, followed by trafficking to acidic cellular compartments resulted in fluorescence as seen by live-cell imaging, and subsequent cathepsin inhibition.

• Automated solid phase synthesis of teichoic acids.

  Authors: Wouter F J Hogendorf, Nico Meeuwenoord, Herman S Overkleeft, Dmitri V Filippov, Diana Laverde, Andrea Kropec, Johannes Huebner, Gijsbert A Van der Marel, Jeroen D C Codée

  Chemical communications (Cambridge, England). 08/2011; 47(31):8961-3.

  This communication describes the first automated solid phase synthesis of teichoic acids (TAs) and the preparation by this method of a number of well-defined TA structures, which were probed forThis communication describes the first automated solid phase synthesis of teichoic acids (TAs) and the preparation by this method of a number of well-defined TA structures, which were probed for their antigenicity. An opsonophagocytic killing assay revealed a clear TA-length-activity relationship and indicated a promising candidate for future vaccine development.

• Mannopyranosyl uronic acid donor reactivity.

  Authors: Marthe T C Walvoort, Wilbert de Witte, Jesse van Dijk, Jasper Dinkelaar, Gerrit Lodder, Herman S Overkleeft, Jeroen D C Codée, Gijsbert A van der Marel

  Organic letters. 08/2011; 13(16):4360-3.

  The reactivity of a variety of mannopyranosyl uronic acid donors was assessed in a set of competition experiments, in which two (S)-tolyl mannosyl donors were made to compete for a limited amount ofThe reactivity of a variety of mannopyranosyl uronic acid donors was assessed in a set of competition experiments, in which two (S)-tolyl mannosyl donors were made to compete for a limited amount of promoter (NIS/TfOH). These experiments revealed that the reactivity of mannuronic acid donors is significantly higher than expected based on the electron-withdrawing capacity of the C-5 carboxylic acid ester function. A 4-O-acetyl-β-(S)-tolyl mannuronic acid donor was found to have similar reactivity as per-O-benzyl-α-(S)-tolyl mannose.

• Stereoselective synthesis of 2,3-diamino-2,3-dideoxy-β-D-mannopyranosyl uronates.

  Authors: Marthe T C Walvoort, Gert-Jan Moggré, Gerrit Lodder, Herman S Overkleeft, Jeroen D C Codée, Gijsbert A van der Marel

  The Journal of organic chemistry. 08/2011; 76(18):7301-15.

  With the aim to find an efficient synthetic procedure for the construction of 2,3-diamino-2,3-dideoxy-β-D-mannuronic acids, we evaluated three mannosyl donors: (S)-phenyl 4,6-di-O-acetyl-2,3-diazidoWith the aim to find an efficient synthetic procedure for the construction of 2,3-diamino-2,3-dideoxy-β-D-mannuronic acids, we evaluated three mannosyl donors: (S)-phenyl 4,6-di-O-acetyl-2,3-diazido mannopyranoside, (S)-phenyl 2,3-diazido-4,6-O-benzylidene mannopyranoside, and (S)-phenyl 2,3-diazido mannopyranosyl methyl uronate. The first two mannosylating agents are rather unselective or slightly α-selective in their condensation with three different acceptors. The mannuronic acid donor on the other hand reliably provides the desired β-mannosidic linkage. A mechanistic rationale is put forward to account for the different behavior of the three donor types. Suitably protected 2,3-diazido mannuronic acids were employed to construct the all-cis-linked tetrasaccharide repeating unit of the capsular polysaccharide of Bacillus stearothermophilus , featuring two 2,3-diacetamido-2,3-dideoxy-β-D-mannuronic acids.

• Two-step bioorthogonal activity-based proteasome profiling using copper-free click reagents: a comparative study.

  Authors: Wouter A van der Linden, Nan Li, Sascha Hoogendoorn, Mark Ruben, Martijn Verdoes, Jun Guo, Geert-Jan Boons, Gijsbert A van der Marel, Bogdan I Florea, Herman S Overkleeft

  Bioorganic & medicinal chemistry. 06/2011; 20(2):662-6.

  The development and application of bioorthogonal two-step labeling techniques receives much attention. Employing bifunctional proteasome probe 2 the efficiency of two-step labeling of recentlyThe development and application of bioorthogonal two-step labeling techniques receives much attention. Employing bifunctional proteasome probe 2 the efficiency of two-step labeling of recently published biotinylated cyclooctynes 3-5 is compared to Staudinger-Bertozzi ligation in cell extracts and living cells. While cyclooctynes 3-5 react faster and at a much lower concentration then the Staudinger-Bertozzi benchmark, background labeling is considerable with these reagents.

• Ribosylation of adenosine: an orthogonally protected building block for the synthesis of ADP-ribosyl oligomers.

  Authors: Gerbrand J van der Heden van Noort, Herman S Overkleeft, Gijsbert A van der Marel, Dmitri V Filippov

  Organic letters. 06/2011; 13(11):2920-3.

  A method to ribosylate adenosine on the 2' hydroxyl function in an α-selective fashion and in good yield is presented. Protective groups chosen for the acceptor and donor used in this glycosylationA method to ribosylate adenosine on the 2' hydroxyl function in an α-selective fashion and in good yield is presented. Protective groups chosen for the acceptor and donor used in this glycosylation not only direct α-selectivity but also allow the construction of a fully orthogonally protected building block for the future assembly of oligo-ADP-ribosylated peptides and proteins.

• Activity-based profiling of retaining β-glucosidases: a comparative study.

  Authors: Martin D Witte, Marthe T C Walvoort, Kah-Yee Li, Wouter W Kallemeijn, Wilma E Donker-Koopman, Rolf G Boot, Johannes M F G Aerts, Jeroen D C Codée, Gijsbert A van der Marel, Herman S Overkleeft

  Chembiochem : a European journal of chemical biology. 05/2011; 12(8):1263-9.

  Activity-based protein profiling (ABPP) is a versatile strategy to report on enzyme activity in vitro, in situ, and in vivo. The development and use of ABPP tools and techniques has met withActivity-based protein profiling (ABPP) is a versatile strategy to report on enzyme activity in vitro, in situ, and in vivo. The development and use of ABPP tools and techniques has met with considerable success in monitoring physiological processes involving esterases and proteases. Activity-based profiling of glycosidases, on the other hand, has proven more difficult, and to date no broad-spectrum glycosidase activity-based probes (ABPs) have been reported. In a comparative study, we investigated both 2-deoxy-2-fluoroglycosides and cyclitol epoxides for their utility as a starting point towards retaining β-glucosidase ABP. We also investigated the merits of direct labeling and two-step bio-orthogonal labeling in reporting on glucosidase activity under various conditions. Our results demonstrate that 1) in general cyclitol epoxides are the superior glucosidase ABPs, 2) that direct labeling is the more efficient approach but it hinges on the ability of the glucosidase to be accommodated in the active site of the reporter (BODIPY) entity, and 3) that two-step bio-orthogonal labeling can be achieved on isolated enzymes but translating this protocol to cell extracts requires more investigation.

• Evaluation of readily accessible azoles as mimics of the aromatic ring of D-phenylalanine in the turn region of gramicidin S.

  Authors: Matthijs van der Knaap, Lianne T Lageveen, Henk J Busscher, Roos Mars-Groenendijk, Daan Noort, José M Otero, Antonio L Llamas-Saiz, Mark J van Raaij, Gijsbert A van der Marel, Herman S Overkleeft, Mark Overhand

  ChemMedChem. 03/2011; 6(5):840-7.

  The influence of replacing the d-phenylalanine residue with substituted and unsubstituted azoles on the structure and biological activity of the antibiotic gramicidin S was investigated against aThe influence of replacing the d-phenylalanine residue with substituted and unsubstituted azoles on the structure and biological activity of the antibiotic gramicidin S was investigated against a representative panel of Gram-positive and Gram-negative bacteria strains. Substituted triazole derivatives, obtained using a convergent synthetic strategy, are as active as gramicidin S, provided that any substituent on the triazole moiety is not too large. The unsubstituted triazole derivative was biologically less active than the parent natural product, gramicidin S. In general for the triazole series, the hemolytic activity could be correlated with the antibacterial activity, that is, the higher the antibacterial activity, the higher the toxicity towards blood cells. Interestingly, its imidazole counterpart showed high antibacterial activity, combined with significantly diminished hemolytic activity.

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• Galacturonic acid lactones in the synthesis of all trisaccharide repeating units of the zwitterionic polysaccharide Sp1.

  Authors: Alphert E Christina, Leendert J van den Bos, Herman S Overkleeft, Gijsbert A van der Marel, Jeroen D C Codée

  The Journal of organic chemistry. 02/2011; 76(6):1692-706.

  A modular approach toward the synthesis of all possible trimer repeating units of the type 1 capsular polysaccharide of Streptococcus pneumonia, Sp1, is described. This zwitterionic polysaccharide isA modular approach toward the synthesis of all possible trimer repeating units of the type 1 capsular polysaccharide of Streptococcus pneumonia, Sp1, is described. This zwitterionic polysaccharide is built up from trisaccharide repeats, which in turn are composed of two galacturonic acid monomers and a 2,4,6-trideoxy-4-amino-2-acetamido-D-galactose moiety. All monomeric constituents are linked through cis-glycosidic bonds. To overcome the difficulty associated with the efficient stereoselective introduction of the α-galacturonic acid bonds, we have employed galacturonic acid-[3,6]-lactone building blocks. Not only did these building blocks perform well when used as donor galactosides, they were also shown to be reactive acceptor glycosides when equipped with a free hydroxyl function. All three frame-shifted trimer repeats were constructed via highly stereoselective glycosylation reactions, with one exception. The epimeric mixture of trisaccharides, formed in the nonselective glycosylation event, could be readily separated after global deprotection using high performance anion exchange chromatography (HPEAC).

• Uronic acids in oligosaccharide and glycoconjugate synthesis.

  Authors: Jeroen D C Codée, Alphert E Christina, Marthe T C Walvoort, Herman S Overkleeft, Gijsbert A van der Marel

  Topics in current chemistry. 01/2011; 301:253-89.

  This chapter describes the assembly of uronic acid containing oligosaccharides and glycoconjugates. Two strategies are available to access these target molecules, namely a pre-glycosylation oxidationThis chapter describes the assembly of uronic acid containing oligosaccharides and glycoconjugates. Two strategies are available to access these target molecules, namely a pre-glycosylation oxidation approach, in which uronic acid building blocks are used, and a post-glycosylation oxidation strategy, which employs an oxidation step after the assembly of the oligosaccharide chain. Because uronic acid building blocks are generally considered to be less reactive than their non-oxidized counterparts, the latter approach has found most application in carbohydrate synthesis. With the aid of selected examples of recent syntheses of biologically relevant oligosaccharides and glycoconjugates, the reactivity of different uronic acid building blocks is evaluated. From these examples it is apparent that the generally assumed low reactivity of uronic acids does not a priori rule out an efficient assembly of these target compounds. Besides influencing the reactivity of a given pyranoside, the C-5 carboxylic acid function can also have a profound effect on the stereochemical course of a glycosylation reaction, which can be exploited in the stereoselective formation of glycosidic bonds.

• Ultrasensitive in situ visualization of active glucocerebrosidase molecules.

  Authors: Martin D Witte, Wouter W Kallemeijn, Jan Aten, Kah-Yee Li, Anneke Strijland, Wilma E Donker-Koopman, Adrianus M C H van den Nieuwendijk, Boris Bleijlevens, Gertjan Kramer, Bogdan I Florea, Berend Hooibrink, Carla E M Hollak, Roelof Ottenhoff, Rolf G Boot, Gijsbert A van der Marel, Herman S Overkleeft, Johannes M F G Aerts

  Nature chemical biology. 12/2010; 6(12):907-13.

  Deficiency of glucocerebrosidase (GBA) underlies Gaucher disease, a common lysosomal storage disorder. Carriership for Gaucher disease has recently been identified as major risk for parkinsonism.Deficiency of glucocerebrosidase (GBA) underlies Gaucher disease, a common lysosomal storage disorder. Carriership for Gaucher disease has recently been identified as major risk for parkinsonism. Presently, no method exists to visualize active GBA molecules in situ. We here report the design, synthesis and application of two fluorescent activity-based probes allowing highly specific labeling of active GBA molecules in vitro and in cultured cells and mice in vivo. Detection of in vitro labeled recombinant GBA on slab gels after electrophoresis is in the low attomolar range. Using cell or tissue lysates, we obtained exclusive labeling of GBA molecules. We present evidence from fluorescence-activated cell sorting analysis, fluorescence microscopy and pulse-chase experiments of highly efficient labeling of GBA molecules in intact cells as well as tissues of mice. In addition, we illustrate the use of the fluorescent probes to study inhibitors and tentative chaperones in living cells.

• Synthesis of oligoribonucleic acid conjugates using a cyclooctyne phosphoramidite.

  Authors: Pieter van Delft, Nico J Meeuwenoord, Sascha Hoogendoorn, Jasper Dinkelaar, Herman S Overkleeft, Gijsbert A van der Marel, Dmitri V Filippov

  Organic letters. 11/2010; 12(23):5486-9.

  The conjugation of a ribonucleic acid 16-mer with the cationic amphiphilic peptide penetratin and an anionic hyaluronan tetrasaccharide by means of Cu-free "click" chemistry is reported. TheThe conjugation of a ribonucleic acid 16-mer with the cationic amphiphilic peptide penetratin and an anionic hyaluronan tetrasaccharide by means of Cu-free "click" chemistry is reported. The alkyne-functionalized 16-mer was prepared by automated solid-phase synthesis, using a newly developed strained cyclooctyne phosphoramidite in the final coupling. Cycloaddition of the alkyne functionalized RNA to the azide containing biomolecules led to a clean conversion into the corresponding nucleic acid conjugates.