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Critical to the function of mast cells in immune responses including allergy is their production of lipid mediators, among which only omega-6 (ω-6) arachidonate-derived eicosanoids have been well characterized. Here, by employing comprehensive lipidomics, we identify omega-3 (ω-3) fatty acid epoxides as new mast cell-derived lipid mediators and show that they are produced by PAF-AH2, an oxidized-phospholipid-selective phospholipase A2. Genetic or pharmacological deletion of PAF-AH2 reduced the steady-state production of ω-3 epoxides, leading to attenuated mast cell activation and anaphylaxis following FcɛRI cross-linking. Mechanistically, the ω-3 epoxides promote IgE-mediated activation of mast cells by downregulating Srcin1, a Src-inhibitory protein that counteracts FcɛRI signaling, through a pathway involving PPARg. Thus, the PAF-AH2-ω-3 epoxide-Srcin1 axis presents new potential drug targets for allergic diseases.

In this study, we demonstrate that appendage of a single asparagusic acid residue (AspA tag) is sufficient to ensure efficient cellular uptake and intracellular distribution of fully unprotected peptides. We apply this new delivery method to induce apoptotic response in cancer cells using long (up to 20mer) BH3 domain peptides. Moreover, to understand the molecular mechanism of the cellular uptake, we perform chemical proteomics experiments and identify the direct molecular targets of the asparagusic acid tag. Our findings document covalent bond formation between the asparagusic acid moiety and the cysteines 556 and 558 on the surface of the transferrin receptor resulting in subsequent endocytic uptake of the payload. We believe that the small size, low cellular toxicity and the efficient transferrin receptor-mediated uptake render the AspA tag highly attractive for various life science applications.

Severe forms of pneumococcal meningitis, bacteraemia and pneumonia result in more than 1 million deaths each year despite the widespread introduction of carbohydrate-protein conjugate vaccines against Streptococcus pneumoniae. Here we describe a new and highly efficient antipneumococcal vaccine design based on synthetic conjugation of S. pneumoniae capsule polysaccharides to the potent lipid antigen α-galactosylceramide, which stimulates invariant natural killer T (iNKT) cells when presented by the nonpolymorphic antigen-presenting molecule CD1d. Mice injected with the new lipid-carbohydrate conjugate vaccine produced high-affinity IgG antibodies specific for pneumococcal polysaccharides. Vaccination stimulated germinal center formation; accumulation of iNKT cells with a T follicular helper cell phenotype; and increased frequency of carbohydrate-specific, long-lived memory B cells and plasmablasts. This new lipid-carbohydrate vaccination strategy induced potent antipolysaccharide immunity that protected against pneumococcal disease in mice and may also prove effective for the design of carbohydrate-based vaccines against other major bacterial pathogens.

The 2016 International Symposium on Chemical Biology was organized by the Swiss National Centre of Competence in Research (NCCR) Chemical Biology. The NCCR Chemical Biology is located at the University of Geneva (UniGE; Director: Prof. Howard Riezman) and the Ecole Polytechnique Fedé rale de Lausanne (EPFL; Co-director: Prof. ́ Kai Johnsson). The symposium was held on January 13−15, 2016 at the Campus Biotech, a new center for biotechnology and life science research that was formed through a unique partnership between the University of Geneva and EPFL and is located within walking distance from the city center of Geneva. This exciting scientific venue attracted more than 240 attendees from around the world. With the aim of providing a sound overview of key challenges in cutting edge chemical biology, as well as fostering an open dialogue with networking opportunities, the organizing committee selected 15 plenary lectures with diverse scope under the broad subject of chemical biology. The scientific program was rounded up by four poster sessions with over 60 posters.

The endocannabinoid 2-arachidonoylglycerol (2-AG) is biosynthesized by diacylglycerol lipases DAGLα and DAGLβ. Chemical probes to perturb DAGLs are needed to characterize endocannabinoid function in biological processes. Here, we report a series of in vivo-active 1,2,3-triazole urea inhibitors, along with paired negative-control and activity-based probes, for the functional analysis of DAGLβ in living systems. Optimized inhibitors showed excellent selectivity for DAGLβ over other serine hydrolases, including DAGLα (~60-fold selectivity), and the limited off-targets, such as ABHD6, were also inhibited by the negative-control probe. Using these agents and Daglb−/− mice, we show that DAGLβ inactivation lowers 2-AG, as well as arachidonic acid and eicosanoids, in mouse peritoneal macrophages in a manner that is distinct and complementary to disruption of cytosolic phospholipase-A2 (PLA2G4A). We observed a corresponding reduction in lipopolysaccharide-induced tumor necrosis factor-α release. These findings indicate that DAGLβ is a key metabolic hub within a lipid network that regulates proinflammatory responses in macrophages.

The reversible thioester linkage of palmitic acid on cysteines, known as protein S-palmitoylation, facilitates the membrane association and proper subcellular localization of proteins. Here we report the metabolic incorporation of the palmitic acid analog 17-octadecynoic acid (17-ODYA) in combination with stable-isotope labeling with amino acids in cell culture (SILAC) and pulse-chase methods to generate a global quantitative map of dynamic protein palmitoylation events in cells. We distinguished stably palmitoylated proteins from those that turn over rapidly. Treatment with a serine lipase-selective inhibitor identified a pool of dynamically palmitoylated proteins regulated by palmitoyl-protein thioesterases. This subset was enriched in oncoproteins and other proteins linked to aberrant cell growth, migration and cancer. Our method provides a straightforward way to characterize global palmitoylation dynamics in cells and confirms enzyme-mediated depalmitoylation as a critical regulatory mechanism for a specific subset of rapidly cycling palmitoylated proteins.

Serine hydrolases are a diverse enzyme class representing ∼1% of all human proteins. The biological functions of most serine hydrolases remain poorly characterized owing to a lack of selective inhibitors to probe their activity in living systems. Here we show that a substantial number of serine hydrolases can be irreversibly inactivated by 1,2,3-triazole ureas, which show negligible cross-reactivity with other protein classes. Rapid lead optimization by click chemistry-enabled synthesis and competitive activity-based profiling identified 1,2,3-triazole ureas that selectively inhibit enzymes from diverse branches of the serine hydrolase class, including peptidases (acyl-peptide hydrolase, or APEH), lipases (platelet-activating factor acetylhydrolase-2, or PAFAH2) and uncharacterized hydrolases (α,β-hydrolase-11, or ABHD11), with exceptional potency in cells (sub-nanomolar) and mice (

SummaryNosocomial infections with the Gram-positive pathogen Clostridium difficile pose a major risk for hospitalized patients and result in significant costs to health care systems. Here, we present the chemical synthesis of a PS-II hapten of a cell wall polysaccharide of hypervirulent ribotype 027 of C. difficile. Mice were immunized with a conjugate consisting of the synthetic hexasaccharide and the diphtheria toxoid variant CRM197. The immunogenicity of the glycan repeating unit was demonstrated by the presence of specific IgG antibodies in the serum of immunized mice. Murine monoclonal antibodies interact with the synthetic hexasaccharide, as determined by microarray analysis. Finally, we found that specific IgA antibodies in the stool of hospital patients infected with C. difficile recognize the synthetic PS-II hexasaccharide hapten.

3-Deoxysugars are important constituents of complex carbohydrates. For example, 2-keto-3-deoxy-D-manno-octulosonic acid (KDO) is an essential component of lipopolysaccharides in Gram-negative bacteria, 2-keto-3-deoxy-D-glycero-D-galacto-nonulosonic acid (KDN) is widely found in carbohydrates of the bacterial cell wall and in lower vertebrates, and sialic acid is a common cap of mammalian glycoproteins. Although ready access to such sugars would benefit the creation of vaccine candidates, antibiotics and small-molecule drugs, their chemical synthesis is difficult. Here we present a simple chemoenzymatic method for preparing differentially protected 3-deoxysugar derivatives from readily available starting materials. It exploits the promiscuous aldolase activity of the enzyme macrophomate synthase (MPS) to add pyruvate enolate diastereoselectively to a wide range of structurally complex aldehydes. A short synthesis of KDN illustrates the utility of this approach. Enzyme promiscuity, which putatively fosters large functional leaps in natural evolution, has great promise as a source of synthetically useful catalytic transformations.

An efficient de novo synthesis of uronic acid building blocks is described. The synthetic strategy relies on the stereoselective elongation of thioacetal protected dialdehydes 12 a and 17. The dialdehydes are prepared from D-xylose, a cheap and commercially available source. A highly stereoselective MgBr 2 .OEt 2 -mediated Mukaiyama aldol addition to C4-aldehyde 12a is performed to obtain D-glucuronic acid building block 16, whereas L-iduronic acid building block 22 is prepared by MgBr 2 .OEt 2 -mediated cyanation of C5-aldehyde 17. Synthesis of a heparin disaccharide demonstrates the utility of the de novo strategy for the assembly of glycosaminoglycan oligosaccharides.

An analogue 2 of the pentasaccharide 1 found on the spore surface protein BclA of Bacillus anthracis was synthesized by a (3+2) glycosylation approach. A robust building block for 3-linked α-rhamnose is presented. Benzoate groups were used to ensure α-selectivity for the rhamnose units. A radical-initiated reduction with tributyltin hydride was shown to be able to convert the NHTCA group into an acetylated amine as well as an azido group into a free amine on one strike. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)

In this study, we present a highly efficient method for proteomic profiling of cysteine residues in complex proteomes and in living cells. Our method is based on alkynylation of cysteines in complex proteomes using a "clickable" alkynyl benziodoxolone bearing an azide group. This reaction proceeds fast, under mild physiological conditions, and with a very high degree of chemoselectivity. The formed azide-capped alkynyl-cysteine adducts are readily detectable by LC-MS/MS, and can be further functionalized with TAMRA or biotin alkyne via CuAAC. We demonstrate the utility of alkynyl benziodoxolones for chemical proteomics applications by identifying the proteomic targets of curcumin, a diarylheptanoid natural product that was and still is part of multiple human clinical trials as anticancer agent. Our results demonstrate that curcumin covalently modifies several key players of cellular signaling and metabolism, most notably the enzyme casein kinase I gamma. We anticipate that this new method for cysteine profiling will find broad application in chemical proteomics and drug discovery.

Hypochlorite and chlorite exchange resins are evaluated as co-oxidants or oxidants, respectively, for the oxidation of alcohols to the corresponding aldehydes, ketones or carboxylic acids. Polymer-bound hypochlorite can act as a co-oxidant in TEMPO-mediated oxidations of alcohols. The formation of aldehydes only works under weakly acidic conditions. However, the cheap hypochlorite exchange resin is less efficient as co-oxidant compared to the use of ionically immobilised bisacetoxybromate(I) anions. In contrast, the chlorite exchange resin is a highly potent co-oxidant for the preparation of carboxylic acids from the corresponding primary alcohols in the presence of TEMPO. It is demonstrated that in this case also the resin acts as a polymer-bound co-oxidant for both oxidation steps. Yields are commonly excellent as is also demonstrated for examples taken from natural product synthesis which include acid labile glycosides. In most cases, work-up of this heavy metal-free oxidation is kept to a minimum. It often includes filtration followed by removal of the solvent.

The process for selecting potent and effective carbohydrate antigens is not well-established. A combination of synthetic glycan microarray screening, surface plasmon resonance analysis, and saturation transfer difference NMR spectroscopy was used to dissect the antibody-binding surface of a carbohydrate antigen, revealing crucial binding elements with atomic-level detail. This analysis takes the first step toward uncovering the rules for structure-based design of carbohydrate antigens.

PEGylated quantum dots (QDs) capped with d-mannose, d-galactose, and d-galactosamine have been synthesized. The stable, high quantum yield fluorescence of QDs was exploited to study specific carbohydrate-protein interactions in vitro and in vivo.

S-palmitoylation involves the attachment of a 16-carbon long fatty acid chain to the cysteine residues of proteins. The process is enzymatic and dynamic with DHHC enzymes mediating palmitoylation and acyl-protein thioesterases reverting the reaction. Proteins that undergo this modification span almost all cellular functions. While the increase in hydrophobicity generated by palmitoylation has the obvious consequence of triggering membrane association, the effects on transmembrane proteins are less intuitive and span a vast range. We review here the current knowledge on palmitoylating and depalmitoylating enzymes, the methods that allow the study of this lipid modification and which drugs can affect it, and finally we focus on four cellular processes for which recent studies reveal an involvement of palmitoylation: endocytosis, reproduction and cell growth, fat and sugar homeostasis and signal transduction at the synapse. (C) 2014 Elsevier Ireland Ltd. All rights reserved.

We have established the diced electrophoresis gel (DEG) assay as a proteome-wide screening tool to identify enzymes with activities of interest using turnover-based fluorescent substrates. The method utilizes the combination of native polyacrylamide gel electrophoresis (PAGE) with a multiwell-plate-based fluorometric assay to find protein spots with the specified activity. By developing fluorescent substrates that mimic the structure of neutrophil chemoattractants, we could identify enzymes involved in metabolic inactivation of the chemoattractants.

The MPS-catalyzed pyruvate addition is characterized by high diastereoselectivity and mild reaction conditions.

In eukaryotic organisms, cysteine palmitoylation is an important reversible modification that impacts protein targeting, folding, stability, and interactions with partners. Evidence suggests that protein palmitoylation contributes to key biological processes in Apicomplexa with the recent palmitome of the malaria parasite Plasmodium falciparum reporting over 400 substrates that are modified with palmitate by a broad range of protein S-acyl transferases. Dynamic palmitoylation cycles require the action of an acyl-protein thioesterase (APT) that cleaves palmitate from substrates and conveys reversibility to this posttranslational modification. In this work, we identified candidates for APT activity in Toxoplasma gondii. Treatment of parasites with low micromolar concentrations of β-lactone- or triazole urea-based inhibitors that target human APT1 showed varied detrimental effects at multiple steps of the parasite lytic cycle. The use of an activity-based probe in combination with these inhibitors revealed the existence of several serine hydrolases that are targeted by APT1 inhibitors. The active serine hydrolase, TgASH1, identified as the homologue closest to human APT1 and APT2, was characterized further. Biochemical analysis of TgASH1 indicated that this enzyme cleaves substrates with a specificity similar to APTs, and homology modeling points toward an APT-like enzyme. TgASH1 is dispensable for parasite survival, which indicates that the severe effects observed with the β-lactone inhibitors are caused by the inhibition of non-TgASH1 targets. Other ASH candidates for APT activity were functionally characterized, and one of them was found to be resistant to gene disruption due to the potential essential nature of the protein.

A chemoenzymatic synthesis of sialic acid from inexpensive N-acetyl-D-glucosamine is described. In a three-step Wittig–protection–ozonolysis strategy manno-configured aldehydes are obtained. Treatment with oxaloacetate in the presence of macrophomate synthase affords the signature α-keto-γ-hydroxy acid moiety with high diastereoselectivity.

The development of small-molecule inhibitors for perturbing enzyme function requires assays to confirm that the inhibitors interact with their enzymatic targets in vivo. Determining target engagement in vivo can be particularly challenging for poorly characterized enzymes that lack known biomarkers (e.g., endogenous substrates and products) to report on their inhibition. Here, we describe a competitive activity-based protein profiling (ABPP) method for measuring the binding of reversible inhibitors to enzymes in animal models. Key to the success of this approach is the use of activity-based probes that show tempered rates of reactivity with enzymes, such that competition for target engagement with reversible inhibitors can be measured in vivo. We apply the competitive ABPP strategy to evaluate a newly described class of piperazine amide reversible inhibitors for the serine hydrolases LYPAL1 and LYPLA2, two enzymes for which selective, in vivo-active inhibitors are lacking. Competitive ABPP identified individual piperazine amides that selectively inhibit LYPLA1 or LYPLA2 in mice. In summary, competitive ABPP adapted to operate with moderately reactive probes can assess the target engagement of reversible inhibitors in animal models to facilitate the discovery of small-molecule probes for characterizing enzyme function in vivo.

A comparative analysis of bacterial and mammalian glycomes based on the statistical analysis of two major carbohydrate databases, Bacterial Carbohydrate Structure Data Base (BCSDB) and GLYCOSCIENCES.de (GS), is presented. An in-depth comparison of these two glycomes reveals both striking differences and unexpected similarities. Within the prokaryotic kingdom, we focus on the glycomes of seven classes of pathogenic bacteria with respect to (i) their most abundant monosaccharide units; (ii) disaccharide pairs; (iii) carbohydrate modifications; (iv) occurrence and use of sialic acids; and (v) class-specific monosaccharides. The aim of this work is to gain insights into unique carbohydrate patterns in bacteria. Data interpretation reveals significant trends in the composition of specific carbohydrate classes as result of evolution-driven structural adaptations of bacterial pathogens and symbionts to their mammalian hosts. The differences are discussed in light of their value for biomedical applications, such as the targeting of unique glycosyl transferases, vaccine development, and devising novel diagnostic tools. peerReviewed

Serine hydrolases (SHs) are one of the largest and most diverse enzyme classes in mammals. They play fundamental roles in virtually all physiological processes and are targeted by drugs to treat diseases such as diabetes, obesity, and neurodegenerative disorders. Despite this, we lack biological understanding for most of the 110+ predicted mammalian metabolic SHs, in large part because of a dearth of assays to assess their biochemical activities and a lack of selective inhibitors to probe their function in living systems. We show here that the vast majority (> 80%) of mammalian metabolic SHs can be labeled in proteomes by a single, active site-directed fluorophosphonate probe. We exploit this universal activity-based assay in a library-versus-library format to screen 70+ SHs against 140+ structurally diverse carbamates. Lead inhibitors were discovered for ∼40% of the screened enzymes, including many poorly characterized SHs. Global profiles identified carbamate inhibitors that discriminate among highly sequence-related SHs and, conversely, enzymes that share inhibitor sensitivity profiles despite lacking sequence homology. These findings indicate that sequence relatedness is not a strong predictor of shared pharmacology within the SH superfamily. Finally, we show that lead carbamate inhibitors can be optimized into pharmacological probes that inactivate individual SHs with high specificity in vivo.

A short and enantioselective de novo synthesis of an L-glycero-D-manno-heptose building block for the total synthesis of a Yersinia pestis cell wall polysaccharide is described.

A short and enantioselective de novo synthesis of an L-glycero-D-manno-heptose building block for the total synthesis of a Yersinia pestis cell wall polysaccharide is described.

A facile and flexible approach for the preparation of Ru(II) complexes containing different carbohydrates based on the Cu(II)-catalyzed Huisgen-[3+2] cycloaddition is described.

A divergent de novo synthesis of six differentially protected l -iduronic acid thioglycosides from a common advanced precursor is described. The key step of this synthetic sequence is the stereoselective elongation of dithioacetal protected C5-dialdehyde 11 via a highly diastereoselective MgBr 2 ·OEt 2 -mediated cyanation. Orthogonally protected l -iduronic acid building blocks obtained by this synthesis are expected to facilitate access to differentially sulfated heparins for microarray-based structure–activity relationship studies.

Vaccinations provide an efficient and cost-effective way to combat devastating human diseases. Besides pathogenic protein markers, cell surface carbohydrates from biological sources are widely used as vaccines. Recently, synthetic immunogenic carbohydrate-protein conjugates have been advanced to vaccine candidates. Progress in the chemical synthesis of oligosaccharides and conjugation methods stimulated the development of novel carbohydrate-based vaccine candidates.

A diastereoselective domino nitro-Michael/Henry reaction involving a β-hydroxyaldehyde and a nitroalkene provides direct access to fully functionalized D-glucosamine monosaccharides.

A diastereoselective domino nitro-Michael/Henry reaction involving a beta-hydroxyaldehyde and a nitroalkene provides direct access to fully functionalized D-glucosamine monosaccharides.

A concise synthesis of a differentially protected d-galacturonic acid (d-GalA) thioglycoside and the construction of a potent immunomodulating glycosphingolipid are described. The key steps of the synthesis are an Evans aldol reaction between a C4 aldehyde and a PMB-protected glycolyloxazolidinone as well as a tandem-PMB-deprotection/cyclization to thioglycosides. The key glycosylation step is optimized by varying the anomeric leaving group, the activating agent, and the solvent system.

The diversity of three major classes of mammalian carbohydrates, mainly glycolipids and O- and N-linked glycans, deposited in the databank GLYCOSCIENCES.de was subjected to statistical analyses. Size, chain length, and branching complexity were accessed and revealed that the average oligosaccharide is composed of about eight monosaccharide units. About a quarter of all oligosaccharides are strictly linear, and the remainder are branched at least once. Glucosamine, galactose, and mannose are dominating and comprise ~75% of the monosaccharides within mammalian oligosaccharide frameworks. alpha-Linked sialic acid, alpha-linked fucose, and beta-linked galactose decorate the majority of reducing termini. Glucose as the most abundant carbohydrate in mammals plays only a very minor role within these structures. Particular emphasis was placed on analyzing the way the monosaccharide units are linked within the oligomeric framework. Just 11 monosaccharide connections account for >75% of all linkages. Thus, the number of structural combinations found in nature, the part of the occupied mammalian glycospace, is much smaller than expected. As a result, a potential set of building blocks for oligosaccharide assembly is presented. This potential building block set was correlated with the accessible 3299 mammalian carbohydrate structures in the GLYCOSCIENCES.de databank. Only 36 building blocks are required to construct 75% of the 3299 mammalian oligosaccharides.

The total synthesis of the cyclic diterpene ent-tonantzitlolone (ent-1) is presented. Key steps for assembling the macrocyclic core structure of 1 are a highly selective aldol reaction and an E selective ring-closing metathesis reaction. A detailed investigation of these two steps and the final transformations towards the completion of the synthesis is disclosed.

The regulation of transcriptional programs by epigenetic readers (bromodomains) has been linked to the development of several pathologies. Notably, it has been implicated in the regulation of cellular growth and evasion of apoptosis, in cancer as well as in inflammation. The discovery of small-molecule probes to dissect the role of bromodomains is thus important. We demonstrate that specific cysteine residues conserved across the bromodomains can be harnessed for covalent trapping. We report the discovery of two small molecules that form a covalent bond with cysteine residues conserved across the bromodomain family, analyze the subset of bromodomains that can be addressed through covalent binding, and show proteomic analyses enabled by the enrichment of bromodomains from native lysates.

Nat. Chem. Biol. 7, 469–478 (2011); published online 15 May 2011; corrected after print 15 February 2012 In the version of this article initially published, the authors concluded, on the basis of the substantial (approximately five-fold) N1 regioselectivity observed for reactions that form the unsubstituted triazole ureas shown in Figures 1–3, that the major regioisomeric product for the 4-substituted triazole ureas shown in Figures 1 and 3 was also the N1 regioisomer.

Efficient methods to introduce bioorthogonal groups, such as terminal alkynes, into biomolecules are important tools for chemical biology. State-of-the-art approaches are based on the introduction of a linker between the targeted amino acid and the alkyne, and still present limitations of either reactivity, selectivity or adduct stability. Herein, we present an ethynylation method of cysteine residues based on the use of ethynylbenziodoxolone (EBX) reagents. In contrast to other approaches, the acetylene group is directly introduced onto the thiol group of cysteine and can be used in one-pot in a copper-catalyzed alkyne-azide cycloaddition (CuAAC) for further functionalization. Labeling proceeded with reaction rates comparable or higher than the most often used iodoacetamide on peptides or maleimide on the antibody trastuzumab. Under optimized conditions, high cysteine selectivity was observed. The reagents were also used in living cells for cysteine proteomic profiling and displayed an improved coverage of the cysteinome compared to previously reported iodoacetamide or hypervalent iodine-reagent based probes. Fine-tuning of the EBX reagents allowed optimization of their reactivity and physical properties for the desired application.