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 is known as protein S-palmitoylation, which facilitates the membrane association and proper subcellular localization of proteins. Here we report the metabolic incorporation of the palmitic acid analogue 17-octadecynoic acid (17-ODYA) in combination with stable-isotope labeling of cells (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 show rapid turnover. Treatment with a serine lipase-selective inhibitor identified a special pool of dynamically palmitoylated proteins regulated by palmitoyl-protein thioesterases. This subset was enriched in oncogenes 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 (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 110þ 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 activitybased assay in a library-versus-library format to screen 70þ SHs against 140þ 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.enzymology | mass spectrometry | profiling | proteomics A major challenge facing biological researchers in the 21st century is the functional characterization of the large number of unannotated gene products identified by genome sequencing efforts (1). Many proteins partly or completely uncharacterized with respect to their biochemical activities belong to expansive, sequence-related families (2). Although such membership can inform on the general mechanistic class to which a protein belongs (e.g., enzyme, receptor, or channel), it is insufficient to predict specific biochemical and physiological functions, which require knowledge of substrates, ligands, and interacting biomolecules. On the contrary, membership within a large protein family can even present a barrier to achieving these goals by frustrating the implementation of standard genetic and pharmacological methods to probe protein function. For example, targeted gene disruption of one member of a protein superfamily may result in cellular compensation from other family members.Problems are also encountered when attempting to develop specific inhibitors and/or ligands for uncharacterized members of large protein families, where at least two major experimental issues must be addressed. First, there is an intrinsic difficulty facing ligand discovery for uncharacterized proteins, which often lack the functional information required to develop high-quality assays for compound screening. Creative solutions to this problem have emerged for specific protein classes, such as G-protein coupled receptors (GPCRs) (3) and kinases (4, 5), where generic assays have been develop...

Serine hydrolases (SHs) are a diverse enzyme class representing > 1% of all human proteins. The biological functions for most SHs remain poorly characterized due to a lack of selective inhibitors to probe their activity in living systems. Here, we show that a substantial number of SHs can be irreversibly inactivated by 1,2,3-triazole ureas, which exhibit 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 SH superfamily, including peptidases (acyl-peptide hydrolase or APEH), lipases (platelet-activating factor acetylhyrolase-2 or PAFAH2), and uncharacterized hydrolases (α, β-hydrolase 11 or ABHD11), with exceptional potency in cells (sub-nM) and mice (< 1 mg/kg). We show that APEH inhibition leads to accumulation of N-acetylated proteins and promotes proliferation in T-cells. These data designate 1,2,3-triazole ureas as a pharmacologically privileged chemotype for SH inhibition that shows broad activity across the SH class coupled with tunable selectivity for individual enzymes.

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.

As the area of small molecules interacting with RNA advances, general routes to provide bioactive compounds are needed as ligands can bind RNA avidly to sites that will not affect function. Small-molecule targeted RNA degradation will thus provide a general route to affect RNA biology. A non–oligonucleotide-containing compound was designed from sequence to target the precursor to oncogenic microRNA-21 (pre–miR-21) for enzymatic destruction with selectivity that can exceed that for protein-targeted medicines. The compound specifically binds the target and contains a heterocycle that recruits and activates a ribonuclease to pre–miR-21 to substoichiometrically effect its cleavage and subsequently impede metastasis of breast cancer to lung in a mouse model. Transcriptomic and proteomic analyses demonstrate that the compound is potent and selective, specifically modulating oncogenic pathways. Thus, small molecules can be designed from sequence to have all of the functional repertoire of oligonucleotides, including inducing enzymatic degradation, and to selectively and potently modulate RNA function in vivo.

The disulfide dihedral angle in epidithiodiketopiperazines (ETPs) is near 0°. Application of this highest possible ring tension to strain-promoted thiol-mediated uptake results in efficient delivery to the cytosol and nucleus. Compared to the previous best asparagusic acid (AspA), ring-opening disulfide exchange with ETPs occurs more efficiently even with nonactivated thiols, and the resulting thiols exchange rapidly with nonactivated disulfides. ETP-mediated cellular uptake is more than 20 times more efficient compared to AspA, occurs without endosomal capture, depends on temperature, and is “unstoppable” by inhibitors of endocytosis and conventional thiol-mediated uptake, including siRNA against the transferrin receptor. These results suggest that ETP-mediated uptake not only maximizes delivery to the cytosol and nucleus but also opens the door to a new multitarget hopping mode of action.

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.