201
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Krysiak JM, Kreuzer J, Macheroux P, Hermetter A, Sieber SA, Breinbauer R. Activity-based probes for studying the activity of flavin-dependent oxidases and for the protein target profiling of monoamine oxidase inhibitors. Angew Chem Int Ed Engl 2012; 51:7035-40. [PMID: 22689512 PMCID: PMC3470703 DOI: 10.1002/anie.201201955] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Indexed: 01/11/2023]
Abstract
High profile: new activity-based protein profiling (ABPP) probes have been designed that target exclusively monoamine oxidases A and B within living cells (see picture; FAD=flavin adenine dinucleotide, FMN=flavin monodinucleotide). With these probes it could be shown that the MAO inhibitor deprenyl, which is in clinical use against Parkinson's disease, shows unique protein specificity despite its covalent mechanism of action.
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Affiliation(s)
- Joanna M Krysiak
- Institute of Organic Chemistry, Graz University of TechnologyStremayrgasse 9, 8010 Graz (Austria)
| | - Johannes Kreuzer
- Center for Integrated Protein Science CIPSM, Department of Chemistry, Institute of Advanced Studies IAS, Technische Universität MünchenLichtenbergstraße 4, 85747 Garching (Germany)
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of TechnologyPetersgasse 12, 8010 Graz (Austria)
| | - Albin Hermetter
- Institute of Biochemistry, Graz University of TechnologyPetersgasse 12, 8010 Graz (Austria)
| | - Stephan A Sieber
- Center for Integrated Protein Science CIPSM, Department of Chemistry, Institute of Advanced Studies IAS, Technische Universität MünchenLichtenbergstraße 4, 85747 Garching (Germany)
| | - Rolf Breinbauer
- Institute of Organic Chemistry, Graz University of TechnologyStremayrgasse 9, 8010 Graz (Austria)
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202
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Krysiak JM, Kreuzer J, Macheroux P, Hermetter A, Sieber SA, Breinbauer R. Aktivitätsbasierte Sondenmoleküle zur Untersuchung der Aktivität Flavin-abhängiger Oxidasen und zum Zielprotein-Profiling von Monoaminooxidase-Inhibitoren. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201955] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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203
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An activity-based probe reveals dynamic protein-protein interactions mediating IGF-1R transactivation by the GABA(B) receptor. Biochem J 2012; 443:627-34. [PMID: 22394253 DOI: 10.1042/bj20120188] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Many GPCRs (G-protein-coupled receptors) can activate RTKs (receptor tyrosine kinases) in the absence of RTK ligands, a phenomenon called transactivation. However, the underlying molecular mechanisms remain undefined. In the present study we investigate the molecular basis of GABA(B) (γ-aminobutyric acid B) receptor-mediated transactivation of IGF-1R (insulin-like growth factor type I receptor) in primary neurons. We take a chemical biology approach by developing an activity-based probe targeting the GABA(B) receptor. This probe enables us first to lock the GABA(B) receptor in an inactive state and then activate it with a positive allosteric modulator, thereby permitting monitoring of the dynamic of the protein complex associated with IGF-1R transactivation. We find that activation of the GABA(B) receptor induces a dynamic assembly and disassembly of a protein complex, including both receptors and their downstream effectors. FAK (focal adhesion kinase), a non-RTK, plays a key role in co-ordinating this dynamic process. Importantly, this dynamic of the GABA(B) receptor-associated complex is critical for transactivation and transactivation-dependent neuronal survival. The present study has identified an important mechanism underlying GPCR transactivation of RTKs, which was enabled by a new chemical biology tool generally applicable for dissecting GPCR signalling.
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204
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Moellering RE, Cravatt BF. How chemoproteomics can enable drug discovery and development. ACTA ACUST UNITED AC 2012; 19:11-22. [PMID: 22284350 DOI: 10.1016/j.chembiol.2012.01.001] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 12/29/2011] [Accepted: 01/03/2012] [Indexed: 12/15/2022]
Abstract
Creating first-in-class medications to treat human disease is an extremely challenging endeavor. While genome sequencing and genetics are making direct connections between mutations and human disorders at an unprecedented rate, matching molecular targets with a suitable therapeutic indication must ultimately be achieved by pharmacology. Here, we discuss how the integration of chemical proteomic platforms (such as activity-based protein profiling) into the earliest stages of the drug discovery process has the potential to greatly expand the scope of proteins that can be pharmacologically evaluated in living systems, and, through doing so, promote the identification and prioritization of new therapeutic targets.
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Affiliation(s)
- Raymond E Moellering
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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205
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van der Hoorn RAL, Kaiser M. Probes for activity-based profiling of plant proteases. PHYSIOLOGIA PLANTARUM 2012; 145:18-27. [PMID: 21985675 DOI: 10.1111/j.1399-3054.2011.01528.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Proteases are key players in plant development and immunity. When and where these proteases act during these processes is difficult to predict from proteomic or transcriptomic data because proteases are tightly regulated by post-translational mechanisms such as processing, phosphorylation and the presence of cofactors or inhibitors. Protease activities can be displayed using activity-based probes that react with the catalytic site of proteases in a mechanism-dependent manner. Plant proteomes have been labeled with probes for caspases, vacuolar processing enzymes, papain-like cysteine proteases, the proteasome, subtilases, prolyloligopeptidases, serine carboxypeptidases and matrix metalloproteases. Here, we review these protease probes with a focus on the specificity determinants that reside in the probe and the detection methods dictated by the reporter tag.
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Affiliation(s)
- Renier A L van der Hoorn
- Plant Chemetics lab, Chemical Genomics Centre of the Max Planck Society, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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206
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Pucci M, Pasquariello N, Battista N, Di Tommaso M, Rapino C, Fezza F, Zuccolo M, Jourdain R, Finazzi Agrò A, Breton L, Maccarrone M. Endocannabinoids stimulate human melanogenesis via type-1 cannabinoid receptor. J Biol Chem 2012; 287:15466-78. [PMID: 22431736 DOI: 10.1074/jbc.m111.314880] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We show that a fully functional endocannabinoid system is present in primary human melanocytes (normal human epidermal melanocyte cells), including anandamide (AEA), 2-arachidonoylglycerol, the respective target receptors (CB(1), CB(2), and TRPV1), and their metabolic enzymes. We also show that at higher concentrations AEA induces normal human epidermal melanocyte apoptosis (∼3-fold over controls at 5 μM) through a TRPV1-mediated pathway that increases DNA fragmentation and p53 expression. However, at lower concentrations, AEA and other CB(1)-binding endocannabinoids dose-dependently stimulate melanin synthesis and enhance tyrosinase gene expression and activity (∼3- and ∼2-fold over controls at 1 μM). This CB(1)-dependent activity was fully abolished by the selective CB(1) antagonist SR141716 or by RNA interference of the receptor. CB(1) signaling engaged p38 and p42/44 mitogen-activated protein kinases, which in turn activated the cyclic AMP response element-binding protein and the microphthalmia-associated transcription factor. Silencing of tyrosinase or microphthalmia-associated transcription factor further demonstrated the involvement of these proteins in AEA-induced melanogenesis. In addition, CB(1) activation did not engage the key regulator of skin pigmentation, cyclic AMP, showing a major difference compared with the regulation of melanogenesis by α-melanocyte-stimulating hormone through melanocortin 1 receptor.
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Affiliation(s)
- Mariangela Pucci
- Department of Biomedical Sciences, University of Teramo, 64100 Teramo, Italy
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207
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Azad MA, Wright GD. Determining the mode of action of bioactive compounds. Bioorg Med Chem 2012; 20:1929-39. [DOI: 10.1016/j.bmc.2011.10.088] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 10/14/2011] [Accepted: 10/30/2011] [Indexed: 10/14/2022]
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208
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Yan X, Luo Y, Zhang Z, Li Z, Luo Q, Yang L, Zhang B, Chen H, Bai P, Wang Q. Europium-Labeled Activity-Based Probe through Click Chemistry: Absolute Serine Protease Quantification Using 153Eu Isotope Dilution ICP/MS. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108277] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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209
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Yan X, Luo Y, Zhang Z, Li Z, Luo Q, Yang L, Zhang B, Chen H, Bai P, Wang Q. Europium-Labeled Activity-Based Probe through Click Chemistry: Absolute Serine Protease Quantification Using 153Eu Isotope Dilution ICP/MS. Angew Chem Int Ed Engl 2012; 51:3358-63. [DOI: 10.1002/anie.201108277] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 01/08/2012] [Indexed: 11/11/2022]
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210
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Kaschani F, Nickel S, Pandey B, Cravatt BF, Kaiser M, van der Hoorn RAL. Selective inhibition of plant serine hydrolases by agrochemicals revealed by competitive ABPP. Bioorg Med Chem 2012; 20:597-600. [PMID: 21764588 PMCID: PMC3634566 DOI: 10.1016/j.bmc.2011.06.040] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2011] [Revised: 05/27/2011] [Accepted: 06/14/2011] [Indexed: 12/11/2022]
Abstract
Organophosphate and -phosphonates and their thio derivatives are often used in agroindustry as herbicides and insecticides, but their potential off-targets in the plant are poorly investigated. Here, we use competitive activity-based protein profiling (ABPP) of serine hydrolases (SHs) to detect targets of these agrochemicals and other compounds in Arabidopsis thaliana. Using broad-range and specific probes, and by overexpression of various SHs in planta, we are able to confirm eight SH-compound interactions, including selective inhibition of carboxylesterase CXE12, prolyloligopeptidase, methylesterase MES2 and tripeptidyl peptidase TPP2. These observations can be used for the design of novel probes and selective inhibitors and may help to assess physiological effects of agrochemicals on crop plants.
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Affiliation(s)
- Farnusch Kaschani
- The Plant Chemetics Laboratory, Chemical Genomics Centre of the Max Planck Society, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, D-50829 Cologne, Germany
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211
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Bachovchin DA, Cravatt BF. The pharmacological landscape and therapeutic potential of serine hydrolases. Nat Rev Drug Discov 2012; 11:52-68. [PMID: 22212679 PMCID: PMC3665514 DOI: 10.1038/nrd3620] [Citation(s) in RCA: 220] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Serine hydrolases perform crucial roles in many biological processes, and several of these enzymes are targets of approved drugs for indications such as type 2 diabetes, Alzheimer's disease and infectious diseases. Despite this, most of the human serine hydrolases (of which there are more than 200) remain poorly characterized with respect to their physiological substrates and functions, and the vast majority lack selective, in vivo-active inhibitors. Here, we review the current state of pharmacology for mammalian serine hydrolases, including marketed drugs, compounds that are under clinical investigation and selective inhibitors emerging from academic probe development efforts. We also highlight recent methodological advances that have accelerated the rate of inhibitor discovery and optimization for serine hydrolases, which we anticipate will aid in their biological characterization and, in some cases, therapeutic validation.
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Affiliation(s)
- Daniel A Bachovchin
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, USA
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212
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Alkyne derivatives of isocoumarins as clickable activity-based probes for serine proteases. Bioorg Med Chem 2012; 20:633-40. [DOI: 10.1016/j.bmc.2011.03.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 03/02/2011] [Accepted: 03/07/2011] [Indexed: 11/22/2022]
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213
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Nickel S, Kaschani F, Colby T, van der Hoorn RA, Kaiser M. A para-nitrophenol phosphonate probe labels distinct serine hydrolases of Arabidopsis. Bioorg Med Chem 2012; 20:601-6. [DOI: 10.1016/j.bmc.2011.06.041] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 04/21/2011] [Accepted: 06/14/2011] [Indexed: 01/26/2023]
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214
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Kaschani F, Gu C, van der Hoorn RAL. Activity-based protein profiling of infected plants. Methods Mol Biol 2012; 835:47-59. [PMID: 22183646 DOI: 10.1007/978-1-61779-501-5_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Activity-based protein profiling (ABPP) is a powerful analytical method to detect and compare the activity of proteins in proteomes. This is achieved using specific activity-based probes that are often derived from inhibitors and are linked to reporter groups like rhodamine or biotin for fluorescence detection and/or affinity purification, respectively. The probes react with the active site residue of proteins and become covalently and irreversibly attached, facilitating the separation, detection and identification of the labelled proteins. In this protocol we describe all the steps required for labelling, purification and identification of labelled proteins from gels and show how activities in two proteomes can be compared. The identification of serine hydrolases from Arabidopsis plants infected with Botrytis cinerea using the trifunctional probe TriFP is used as an example.
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Affiliation(s)
- Farnusch Kaschani
- The Plant Chemetics Laboratory, Chemical Genomics Centre, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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215
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Lin EC, Hu Y, Amantea CM, Pham LM, Cajica J, Okerberg E, Brown HE, Fraser A, Du L, Kohno Y, Ishiyama J, Kozarich JW, Shreder KR. Amides of xanthurenic acid as zinc-dependent inhibitors of Lp-PLA2. Bioorg Med Chem Lett 2012; 22:868-71. [DOI: 10.1016/j.bmcl.2011.12.045] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 12/05/2011] [Accepted: 12/08/2011] [Indexed: 10/14/2022]
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216
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Crow JA, Bittles V, Herring KL, Borazjani A, Potter PM, Ross MK. Inhibition of recombinant human carboxylesterase 1 and 2 and monoacylglycerol lipase by chlorpyrifos oxon, paraoxon and methyl paraoxon. Toxicol Appl Pharmacol 2011; 258:145-50. [PMID: 22100607 DOI: 10.1016/j.taap.2011.10.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 10/22/2011] [Accepted: 10/26/2011] [Indexed: 11/24/2022]
Abstract
Oxons are the bioactivated metabolites of organophosphorus insecticides formed via cytochrome P450 monooxygenase-catalyzed desulfuration of the parent compound. Oxons react covalently with the active site serine residue of serine hydrolases, thereby inactivating the enzyme. A number of serine hydrolases other than acetylcholinesterase, the canonical target of oxons, have been reported to react with and be inhibited by oxons. These off-target serine hydrolases include carboxylesterase 1 (CES1), CES2, and monoacylglycerol lipase. Carboxylesterases (CES, EC 3.1.1.1) metabolize a number of xenobiotic and endobiotic compounds containing ester, amide, and thioester bonds and are important in the metabolism of many pharmaceuticals. Monoglyceride lipase (MGL, EC 3.1.1.23) hydrolyzes monoglycerides including the endocannabinoid, 2-arachidonoylglycerol (2-AG). The physiological consequences and toxicity related to the inhibition of off-target serine hydrolases by oxons due to chronic, low level environmental exposures are poorly understood. Here, we determined the potency of inhibition (IC(50) values; 15 min preincubation, enzyme and inhibitor) of recombinant CES1, CES2, and MGL by chlorpyrifos oxon, paraoxon and methyl paraoxon. The order of potency for these three oxons with CES1, CES2, and MGL was chlorpyrifos oxon>paraoxon>methyl paraoxon, although the difference in potency for chlorpyrifos oxon with CES1 and CES2 did not reach statistical significance. We also determined the bimolecular rate constants (k(inact)/K(I)) for the covalent reaction of chlorpyrifos oxon, paraoxon and methyl paraoxon with CES1 and CES2. Consistent with the results for the IC(50) values, the order of reactivity for each of the three oxons with CES1 and CES2 was chlorpyrifos oxon>paraoxon>methyl paraoxon. The bimolecular rate constant for the reaction of chlorpyrifos oxon with MGL was also determined and was less than the values determined for chlorpyrifos oxon with CES1 and CES2 respectively. Together, the results define the kinetics of inhibition of three important hydrolytic enzymes by activated metabolites of widely used agrochemicals.
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Affiliation(s)
- J Allen Crow
- Center for Environmental Health Sciences, Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
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217
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Affiliation(s)
- Howard C. Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, 1230 York Avenue, New York, NY 10065 (USA)
| | - Maurine E. Linder
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853 (USA)
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218
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Schramm VL. Enzymatic transition states, transition-state analogs, dynamics, thermodynamics, and lifetimes. Annu Rev Biochem 2011; 80:703-32. [PMID: 21675920 DOI: 10.1146/annurev-biochem-061809-100742] [Citation(s) in RCA: 165] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Experimental analysis of enzymatic transition-state structures uses kinetic isotope effects (KIEs) to report on bonding and geometry differences between reactants and the transition state. Computational correlation of experimental values with chemical models permits three-dimensional geometric and electrostatic assignment of transition states formed at enzymatic catalytic sites. The combination of experimental and computational access to transition-state information permits (a) the design of transition-state analogs as powerful enzymatic inhibitors, (b) exploration of protein features linked to transition-state structure, (c) analysis of ensemble atomic motions involved in achieving the transition state, (d) transition-state lifetimes, and (e) separation of ground-state (Michaelis complexes) from transition-state effects. Transition-state analogs with picomolar dissociation constants have been achieved for several enzymatic targets. Transition states of closely related isozymes indicate that the protein's dynamic architecture is linked to transition-state structure. Fast dynamic motions in catalytic sites are linked to transition-state generation. Enzymatic transition states have lifetimes of femtoseconds, the lifetime of bond vibrations. Binding isotope effects (BIEs) reveal relative reactant and transition-state analog binding distortion for comparison with actual transition states.
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Affiliation(s)
- Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
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219
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Tarhoni MH, Vigneswara V, Smith M, Anderson S, Wigmore P, Lees JE, Ray DE, Carter WG. Detection, quantification, and microlocalisation of targets of pesticides using microchannel plate autoradiographic imagers. Molecules 2011; 16:8535-51. [PMID: 21989313 PMCID: PMC6264342 DOI: 10.3390/molecules16108535] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 09/30/2011] [Accepted: 09/30/2011] [Indexed: 12/12/2022] Open
Abstract
Organophosphorus (OP) compounds are a diverse chemical group that includes nerve agents and pesticides. They share a common chemical signature that facilitates their binding and adduction of acetylcholinesterase (AChE) within nerve synapses to induce cholinergic toxicity. However, this group diversity results in non-uniform binding and inactivation of other secondary protein targets, some of which may be adducted and protein activity influenced, even when only a relatively minor portion of tissue AChE is inhibited. The determination of individual OP protein binding targets has been hampered by the sensitivity of methods of detection and quantification of protein-pesticide adducts. We have overcome this limitation by the employment of a microchannel plate (MCP) autoradiographic detector to monitor a radiolabelled OP tracer compound. We preincubated rat thymus tissue in vitro with the OP pesticides, azamethiphos-oxon, chlorfenvinphos-oxon, chlorpyrifos-oxon, diazinon-oxon, and malaoxon, and then subsequently radiolabelled the free OP binding sites remaining with 3H-diisopropylfluorophosphate (3H-DFP). Proteins adducted by OP pesticides were detected as a reduction in 3H-DFP radiolabelling after protein separation by one dimensional polyacrylamide gel electrophoresis and quantitative digital autoradiography using the MCP imager. Thymus tissue proteins of molecular weights -28 kDa, 59 kDa, 66 kDa, and 82 kDa displayed responsiveness to adduction by this panel of pesticides. The 59 kDa protein target (previously putatively identified as carboxylesterase I) was only significantly adducted by chlorfenvinphos-oxon (p < 0.001), chlorpyrifos-oxon (p < 0.0001), and diazinon-oxon (p < 0.01), the 66 kDa protein target (previously identified as serum albumin) similarly only adducted by the same three pesticides (p < 0.0001), (p < 0.001), and (p < 0.01), and the 82 kDa protein target (previously identified as acyl peptide hydrolase) only adducted by chlorpyrifos-oxon (p < 0.0001) and diazinon-oxon (p < 0.001), when the average values of tissue AChE inhibition were 30%, 35%, and 32% respectively. The -28 kDa protein target was shown to be heterogeneous in nature and was resolved to reveal nineteen 3H-DFP radiolabelled protein spots by two dimensional polyacrylamide gel electrophoresis and MCP autoradiography. Some of these 3H-DFP proteins spots were responsive to adduction by preincubation with chlorfenvinphos-oxon. In addition, we exploited the useful spatial resolution of the MCP imager (-70 mm) to determine pesticide micolocalisation in vivo, after animal dosing and autoradiography of brain tissue sections. Collectively, MCP autoradiographic imaging provided a means to detect targets of OP pesticides, quantify their sensitivity of adduction relative to tissue AChE inhibition, and highlighted that these common pesticides exhibit specific binding character to protein targets, and therefore their toxicity will need to be evaluated on an individual compound basis. In addition, MCP autoradiography afforded a useful method of visualisation of the localisation of a small radiolabelled tracer within brain tissue.
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Affiliation(s)
- Mabruka H. Tarhoni
- School of Biomedical Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, Nottinghamshire NG7 2UH, UK; (M.H.T.); (V.V.); (P.W.); (D.E.R.)
| | - Vasanthy Vigneswara
- School of Biomedical Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, Nottinghamshire NG7 2UH, UK; (M.H.T.); (V.V.); (P.W.); (D.E.R.)
| | - Marie Smith
- School of Graduate Entry Medicine & Health, University of Nottingham Medical School, Royal Derby Hospital, Uttoxeter Road, Derby DE22 3DT, UK; (M.S.); (S.A.)
| | - Susan Anderson
- School of Graduate Entry Medicine & Health, University of Nottingham Medical School, Royal Derby Hospital, Uttoxeter Road, Derby DE22 3DT, UK; (M.S.); (S.A.)
| | - Peter Wigmore
- School of Biomedical Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, Nottinghamshire NG7 2UH, UK; (M.H.T.); (V.V.); (P.W.); (D.E.R.)
| | - John E. Lees
- BioImaging Unit, Space Research Centre, Department of Physics & Astronomy, University of Leicester, Leicester, LE1 7RH, UK;
| | - David E. Ray
- School of Biomedical Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, Nottinghamshire NG7 2UH, UK; (M.H.T.); (V.V.); (P.W.); (D.E.R.)
| | - Wayne G. Carter
- School of Biomedical Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, Nottinghamshire NG7 2UH, UK; (M.H.T.); (V.V.); (P.W.); (D.E.R.)
- School of Graduate Entry Medicine & Health, University of Nottingham Medical School, Royal Derby Hospital, Uttoxeter Road, Derby DE22 3DT, UK; (M.S.); (S.A.)
- Author to whom correspondence should be addressed; ; Tel: +44-0-1332-724738; Fax: +44-0-1332-724626
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220
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Long JZ, Cisar JS, Milliken D, Niessen S, Wang C, Trauger SA, Siuzdak G, Cravatt BF. Metabolomics annotates ABHD3 as a physiologic regulator of medium-chain phospholipids. Nat Chem Biol 2011; 7:763-5. [PMID: 21926997 PMCID: PMC3201731 DOI: 10.1038/nchembio.659] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 07/08/2011] [Indexed: 01/08/2023]
Abstract
All organisms, including humans, possess a huge number of uncharacterized enzymes. Here, we describe a general cell-based screen for enzyme substrate discovery by untargeted metabolomics and its application to identify α/β-hydrolase domain-containing 3 (ABHD3) as a lipase that selectively cleaves medium-chain and oxidatively-truncated phospholipids. Abhd3−/− mice possess elevated myristoyl (C14)-phospholipids, including the bioactive lipid C14-lysophosphatidylcholine, confirming the physiological relevance of our substrate assignments.
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221
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Chang JW, Nomura DK, Cravatt BF. A potent and selective inhibitor of KIAA1363/AADACL1 that impairs prostate cancer pathogenesis. ACTA ACUST UNITED AC 2011; 18:476-84. [PMID: 21513884 DOI: 10.1016/j.chembiol.2011.02.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 02/07/2011] [Accepted: 02/08/2011] [Indexed: 01/17/2023]
Abstract
Cancer cells show alterations in metabolism that support malignancy and disease progression. Prominent among these metabolic changes is elevations in neutral ether lipids (NELs). We have previously shown that the hydrolytic enzyme KIAA1363 (or AADACL1) is highly elevated in aggressive cancer cells, where it plays a key role in generating the monoalkylglycerol ether (MAGE) class of NELs. Here, we use activity-based protein profiling-guided medicinal chemistry to discover a highly potent and selective inhibitor of KIAA1363, the carbamate JW480. We show that JW480, and an shRNA probe that targets KIAA1363, reduce MAGEs and impair the migration, invasion, survival, and in vivo tumor growth of human prostate cancer cell lines. These findings indicate that the KIAA1363-MAGE pathway is important for prostate cancer pathogenesis and designate JW480 as a versatile pharmacological probe for disrupting this pro-tumorigenic metabolic pathway.
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Affiliation(s)
- Jae Won Chang
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Abstract
Activity-based protein profiling (ABPP) is emerging as a game-changing tool for drug discovery, target validation, and basic biology. In this issue, Chang et al. (2011) report the ABPP-facilitated discovery of JW480, a highly selective potent and orally bioavailable inhibitor of monoalkylglycerol ether hydrolase KIAA1363 that dramatically impairs in vivo growth of human prostate cancer cell lines.
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Affiliation(s)
- Remigiusz Serwa
- Institute of Chemical Biology, Department of Chemistry, Imperial College London, South Kensington Campus, London SW72AZ, UK
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223
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The Role of Proteomics in the Diagnosis and Treatment of Women's Cancers: Current Trends in Technology and Future Opportunities. INTERNATIONAL JOURNAL OF PROTEOMICS 2011; 2011. [PMID: 21886869 PMCID: PMC3163496 DOI: 10.1155/2011/373584] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Technological and scientific innovations over the last decade have greatly contributed to improved diagnostics, predictive models, and prognosis among cancers affecting women. In fact, an explosion of information in these areas has almost assured future generations that outcomes in cancer will continue to improve. Herein we discuss the current status of breast, cervical, and ovarian cancers as it relates to screening, disease diagnosis, and treatment options. Among the differences in these cancers, it is striking that breast cancer has multiple predictive tests based upon tumor biomarkers and sophisticated, individualized options for prescription therapeutics while ovarian cancer lacks these tools. In addition, cervical cancer leads the way in innovative, cancer-preventative vaccines and multiple screening options to prevent disease progression. For each of these malignancies, emerging proteomic technologies based upon mass spectrometry, stable isotope labeling with amino acids, high-throughput ELISA, tissue or protein microarray techniques, and click chemistry in the pursuit of activity-based profiling can pioneer the next generation of discovery. We will discuss six of the latest techniques to understand proteomics in cancer and highlight research utilizing these techniques with the goal of improvement in the management of women's cancers.
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224
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Johnson CM, Monzingo AF, Ke Z, Yoon DW, Linsky TW, Guo H, Robertus JD, Fast W. On the mechanism of dimethylarginine dimethylaminohydrolase inactivation by 4-halopyridines. J Am Chem Soc 2011; 133:10951-9. [PMID: 21630706 PMCID: PMC3135753 DOI: 10.1021/ja2033684] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small molecules capable of selective covalent protein modification are of significant interest for the development of biological probes and therapeutics. We recently reported that 2-methyl-4-bromopyridine is a quiescent affinity label for the nitric oxide controlling enzyme dimethylarginine dimethylaminohydrolase (DDAH) (Johnson, C. M.; Linsky, T. W.; Yoon, D. W.; Person, M. D.; Fast, W. J. Am. Chem. Soc. 2011, 133, 1553-1562). Discovery of this novel protein modifier raised the possibility that the 4-halopyridine motif may be suitable for wider application. Therefore, the inactivation mechanism of the related compound 2-hydroxymethyl-4-chloropyridine is probed here in more detail. Solution studies support an inactivation mechanism in which the active site Asp66 residue stabilizes the pyridinium form of the inactivator, which has enhanced reactivity toward the active site Cys, resulting in covalent bond formation, loss of the halide, and irreversible inactivation. A 2.18 Å resolution X-ray crystal structure of the inactivated complex elucidates the orientation of the inactivator and its covalent attachment to the active site Cys, but the structural model does not show an interaction between the inactivator and Asp66. Molecular modeling is used to investigate inactivator binding, reaction, and also a final pyridinium deprotonation step that accounts for the apparent differences between the solution-based and structural studies with respect to the role of Asp66. This work integrates multiple approaches to elucidate the inactivation mechanism of a novel 4-halopyridine "warhead," emphasizing the strategy of using pyridinium formation as a "switch" to enhance reactivity when bound to the target protein.
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Affiliation(s)
| | | | | | | | | | - Hua Guo
- To whom correspondence should be addressed. W.F.: College of Pharmacy, PHAR-MED CHEM, 1 University Station; C0850, Austin, Texas 78712; Phone: (512) 232-4000; Fax: (512) 232-2606; ; J.D.R.: Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712. Phone: (512) 471-3175. Fax: (512) 471-6135. , and H.G.: Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131;
| | - Jon D. Robertus
- To whom correspondence should be addressed. W.F.: College of Pharmacy, PHAR-MED CHEM, 1 University Station; C0850, Austin, Texas 78712; Phone: (512) 232-4000; Fax: (512) 232-2606; ; J.D.R.: Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712. Phone: (512) 471-3175. Fax: (512) 471-6135. , and H.G.: Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131;
| | - Walter Fast
- To whom correspondence should be addressed. W.F.: College of Pharmacy, PHAR-MED CHEM, 1 University Station; C0850, Austin, Texas 78712; Phone: (512) 232-4000; Fax: (512) 232-2606; ; J.D.R.: Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712. Phone: (512) 471-3175. Fax: (512) 471-6135. , and H.G.: Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131;
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225
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Martín-Couce L, Martín-Fontecha M, Capolicchio S, López-Rodríguez ML, Ortega-Gutiérrez S. Development of endocannabinoid-based chemical probes for the study of cannabinoid receptors. J Med Chem 2011; 54:5265-9. [PMID: 21675776 DOI: 10.1021/jm2004392] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We report the synthesis of new chemical probes (1a,b, 2a-c, 3a-c) based on the structure of the main endocannabinoids for their use in biological systems directly or via click chemistry. As proof of concept, 2-arachidonyl glyceryl ether based biotinylated 3b enables direct visualization of CB(1) receptor in cells. These results represent the starting point for the development of advanced small molecule chemical probes able to generate valuable information about the cannabinoid receptors.
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Affiliation(s)
- Lidia Martín-Couce
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
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226
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Long JZ, Cravatt BF. The metabolic serine hydrolases and their functions in mammalian physiology and disease. Chem Rev 2011; 111:6022-63. [PMID: 21696217 DOI: 10.1021/cr200075y] [Citation(s) in RCA: 299] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jonathan Z Long
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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227
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Two-step bioorthogonal activity-based proteasome profiling using copper-free click reagents: a comparative study. Bioorg Med Chem 2011; 20:662-6. [PMID: 21757357 DOI: 10.1016/j.bmc.2011.06.037] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Revised: 06/01/2011] [Accepted: 06/13/2011] [Indexed: 11/20/2022]
Abstract
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 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.
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228
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Watson DS, Feng X, Askew DS, Jambunathan K, Kodukula K, Galande AK. Substrate specifity profiling of the Aspergillus fumigatus proteolytic secretome reveals consensus motifs with predominance of Ile/Leu and Phe/Tyr. PLoS One 2011; 6:e21001. [PMID: 21695046 PMCID: PMC3117871 DOI: 10.1371/journal.pone.0021001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 05/16/2011] [Indexed: 01/12/2023] Open
Abstract
Background The filamentous fungus Aspergillus fumigatus (AF) can cause devastating infections in immunocompromised individuals. Early diagnosis improves patient outcomes but remains challenging because of the limitations of current methods. To augment the clinician's toolkit for rapid diagnosis of AF infections, we are investigating AF secreted proteases as novel diagnostic targets. The AF genome encodes up to 100 secreted proteases, but fewer than 15 of these enzymes have been characterized thus far. Given the large number of proteases in the genome, studies focused on individual enzymes may overlook potential diagnostic biomarkers. Methodology and Principal Findings As an alternative, we employed a combinatorial library of internally quenched fluorogenic probes (IQFPs) to profile the global proteolytic secretome of an AF clinical isolate in vitro. Comparative protease activity profiling revealed 212 substrate sequences that were cleaved by AF secreted proteases but not by normal human serum. A central finding was that isoleucine, leucine, phenylalanine, and tyrosine predominated at each of the three variable positions of the library (44.1%, 59.1%, and 57.0%, respectively) among substrate sequences cleaved by AF secreted proteases. In contrast, fewer than 10% of the residues at each position of cleaved sequences were cationic or anionic. Consensus substrate motifs were cleaved by thermostable serine proteases that retained activity up to 50°C. Precise proteolytic cleavage sites were reliably determined by a simple, rapid mass spectrometry-based method, revealing predominantly non-prime side specificity. A comparison of the secreted protease activities of three AF clinical isolates revealed consistent protease substrate specificity fingerprints. However, secreted proteases of A. flavus, A. nidulans, and A. terreus strains exhibited striking differences in their proteolytic signatures. Conclusions This report provides proof-of-principle for the use of protease substrate specificity profiling to define the proteolytic secretome of Aspergillus fumigatus. Expansion of this technique to protease secretion during infection could lead to development of novel approaches to fungal diagnosis.
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Affiliation(s)
- Douglas S. Watson
- Center for Advanced Drug Research, Biosciences Division, SRI International, Harrisonburg, Virginia, United States of America
| | - Xizhi Feng
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - David S. Askew
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Kalyani Jambunathan
- Center for Advanced Drug Research, Biosciences Division, SRI International, Harrisonburg, Virginia, United States of America
| | - Krishna Kodukula
- Center for Advanced Drug Research, Biosciences Division, SRI International, Harrisonburg, Virginia, United States of America
| | - Amit K. Galande
- Center for Advanced Drug Research, Biosciences Division, SRI International, Harrisonburg, Virginia, United States of America
- * E-mail:
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229
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Adibekian A, Martin BR, Wang C, Hsu KL, Bachovchin DA, Niessen S, Hoover H, Cravatt BF. Click-generated triazole ureas as ultrapotent in vivo-active serine hydrolase inhibitors. Nat Chem Biol 2011; 7:469-78. [PMID: 21572424 PMCID: PMC3118922 DOI: 10.1038/nchembio.579] [Citation(s) in RCA: 182] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 03/30/2011] [Indexed: 01/07/2023]
Abstract
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 (<1 mg kg(-1)). We show that APEH inhibition leads to accumulation of N-acetylated proteins and promotes proliferation in T cells. These data indicate 1,2,3-triazole ureas are a pharmacologically privileged chemotype for serine hydrolase inhibition, combining broad activity across the serine hydrolase class with tunable selectivity for individual enzymes.
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Affiliation(s)
- Alexander Adibekian
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Brent R. Martin
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Chu Wang
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Ku-Lung Hsu
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Daniel A. Bachovchin
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Sherry Niessen
- Center for Physiological Proteomics, and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Heather Hoover
- Center for Physiological Proteomics, and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Benjamin F. Cravatt
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
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230
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Affiliation(s)
- Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, USA.
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231
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Liang J, Luo Y, Zhao H. Synthetic biology: putting synthesis into biology. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 3:7-20. [PMID: 21064036 PMCID: PMC3057768 DOI: 10.1002/wsbm.104] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The ability to manipulate living organisms is at the heart of a range of emerging technologies that serve to address important and current problems in environment, energy, and health. However, with all its complexity and interconnectivity, biology has for many years been recalcitrant to engineering manipulations. The recent advances in synthesis, analysis, and modeling methods have finally provided the tools necessary to manipulate living systems in meaningful ways and have led to the coining of a field named synthetic biology. The scope of synthetic biology is as complicated as life itself—encompassing many branches of science and across many scales of application. New DNA synthesis and assembly techniques have made routine customization of very large DNA molecules. This in turn has allowed the incorporation of multiple genes and pathways. By coupling these with techniques that allow for the modeling and design of protein functions, scientists have now gained the tools to create completely novel biological machineries. Even the ultimate biological machinery—a self‐replicating organism—is being pursued at this moment. The aim of this article is to dissect and organize these various components of synthetic biology into a coherent picture. WIREs Syst Biol Med 2011 3 7–20 DOI: 10.1002/wsbm.104 This article is categorized under:
Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Genetic/Genomic Methods Laboratory Methods and Technologies > Metabolomics
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Affiliation(s)
- Jing Liang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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232
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Comparative analysis of cleavable azobenzene-based affinity tags for bioorthogonal chemical proteomics. ACTA ACUST UNITED AC 2011; 17:1212-22. [PMID: 21095571 DOI: 10.1016/j.chembiol.2010.09.012] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 09/05/2010] [Accepted: 09/14/2010] [Indexed: 01/17/2023]
Abstract
The advances in bioorthogonal ligation methods have provided new opportunities for proteomic analysis of newly synthesized proteins, posttranslational modifications, and specific enzyme families using azide/alkyne-functionalized chemical reporters and activity-based probes. Efficient enrichment and elution of azide/alkyne-labeled proteins with selectively cleavable affinity tags are essential for protein identification and quantification applications. Here, we report the synthesis and comparative analysis of Na₂S₂O₄-cleavable azobenzene-based affinity tags for bioorthogonal chemical proteomics. We demonstrated that ortho-hydroxyl substituent is required for efficient azobenzene-bond cleavage and show that these cleavable affinity tags can be used to identify newly synthesized proteins in bacteria targeted by amino acid chemical reporters as well as their sites of modification on endogenously expressed proteins. The azobenzene-based affinity tags are compatible with in-gel, in-solution, and on-bead enrichment strategies and should afford useful tools for diverse bioorthogonal proteomic applications.
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233
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van der Hoorn RAL, Colby T, Nickel S, Richau KH, Schmidt J, Kaiser M. Mining the Active Proteome of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2011; 2:89. [PMID: 22639616 PMCID: PMC3355598 DOI: 10.3389/fpls.2011.00089] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 11/08/2011] [Indexed: 05/20/2023]
Abstract
Assigning functions to the >30,000 proteins encoded by the Arabidopsis genome is a challenging task of the Arabidopsis Functional Genomics Network. Although genome-wide technologies like proteomics and transcriptomics have generated a wealth of information that significantly accelerated gene annotation, protein activities are poorly predicted by transcript or protein levels as protein activities are post-translationally regulated. To directly display protein activities in Arabidopsis proteomes, we developed and applied activity-based protein profiling (ABPP). ABPP is based on the use of small molecule probes that react with the catalytic residues of distinct protein classes in an activity-dependent manner. Labeled proteins are separated and detected from proteins gels and purified and identified by mass spectrometry. Using probes of six different chemotypes we have displayed activities of 76 Arabidopsis proteins. These proteins represent over 10 different protein classes that contain over 250 Arabidopsis proteins, including cysteine, serine, and metalloproteases, lipases, acyltransferases, and the proteasome. We have developed methods for identification of in vivo labeled proteins using click chemistry and for in vivo imaging with fluorescent probes. In vivo labeling has revealed additional protein activities and unexpected subcellular activities of the proteasome. Labeling of extracts displayed several differential activities, e.g., of the proteasome during immune response and methylesterases during infection. These studies illustrate the power of ABPP to display the functional proteome and testify to a successful interdisciplinary collaboration involving chemical biology, organic chemistry, and proteomics.
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Affiliation(s)
- Renier A. L. van der Hoorn
- Plant Chemetics Lab, Chemical Genomics Centre of the Max Planck Society, Max Planck Institute for Plant Breeding ResearchCologne, Germany
- *Correspondence: Renier A. L. van der Hoorn, Plant Chemetics Lab, Chemical Genomics Centre of the Max Planck Society, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany. e-mail:
| | - Tom Colby
- Proteomics Service Unit, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Sabrina Nickel
- Fakultät für Biologie, Chemische Biologie, Zentrum für Medizinische Biotechnologie, University of Duisburg-EssenEssen, Germany
| | - Kerstin H. Richau
- Plant Chemetics Lab, Chemical Genomics Centre of the Max Planck Society, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Jürgen Schmidt
- Proteomics Service Unit, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Markus Kaiser
- Fakultät für Biologie, Chemische Biologie, Zentrum für Medizinische Biotechnologie, University of Duisburg-EssenEssen, Germany
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234
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Long JZ, LaCava M, Jin X, Cravatt BF. An anatomical and temporal portrait of physiological substrates for fatty acid amide hydrolase. J Lipid Res 2010; 52:337-44. [PMID: 21097653 DOI: 10.1194/jlr.m012153] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fatty acid amide hydrolase (FAAH) regulates amidated lipid transmitters, including the endocannabinoid anandamide and its N-acyl ethanolamine (NAE) congeners and transient receptor potential channel agonists N-acyl taurines (NATs). Using both the FAAH inhibitor PF-3845 and FAAH(-/-) mice, we present a global analysis of changes in NAE and NAT metabolism caused by FAAH disruption in central and peripheral tissues. Elevations in anandamide (and other NAEs) were tissue dependent, with the most dramatic changes occurring in brain, testis, and liver of PF-3845-treated or FAAH(-/-) mice. Polyunsaturated NATs accumulated to very high amounts in the liver, kidney, and plasma of these animals. The NAT profile in brain tissue was markedly different and punctuated by significant increases in long-chain NATs found exclusively in FAAH(-/-), but not in PF-3845-treated animals. Suspecting that this difference might reflect a slow pathway for NAT biosynthesis, we treated mice chronically with PF-3845 for 6 days and observed robust elevations in brain NATs. These studies, taken together, define the anatomical and temporal features of FAAH-mediated NAE and NAT metabolism, which are complemented and probably influenced by kinetically distinguishable biosynthetic pathways that produce these lipids in vivo.
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Affiliation(s)
- Jonathan Z Long
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA
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235
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Superfamily-wide portrait of serine hydrolase inhibition achieved by library-versus-library screening. Proc Natl Acad Sci U S A 2010; 107:20941-6. [PMID: 21084632 DOI: 10.1073/pnas.1011663107] [Citation(s) in RCA: 201] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
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.
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236
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Heal WP, Dang THT, Tate EW. Activity-based probes: discovering new biology and new drug targets. Chem Soc Rev 2010; 40:246-57. [PMID: 20886146 DOI: 10.1039/c0cs00004c] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The development and application of chemical technologies enabling direct analysis of enzyme activity in living systems has undergone explosive growth in recent years. Activity-based protein profiling (ABPP) is a key constituent of this broad field, and is among the most powerful and mature chemical proteomic technologies. This tutorial review introduces the essential features of ABPP and the design and application of activity-based probes (ABPs) from drug target elucidation and in vivo visualisation of enzyme activity to comprehensive profiling of the catalytic content of living systems, and the discovery of new biological pathways.
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Affiliation(s)
- William P Heal
- Department of Chemistry, South Kensington Campus, Imperial College, London, SW7 2AZ, UK
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237
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Abstract
Large-scale profiling methods have uncovered numerous gene and protein expression changes that correlate with tumorigenesis. However, determining the relevance of these expression changes and which biochemical pathways they affect has been hindered by our incomplete understanding of the proteome and its myriad functions and modes of regulation. Activity-based profiling platforms enable both the discovery of cancer-relevant enzymes and selective pharmacological probes to perturb and characterize these proteins in tumour cells. When integrated with other large-scale profiling methods, activity-based proteomics can provide insight into the metabolic and signalling pathways that support cancer pathogenesis and illuminate new strategies for disease diagnosis and treatment.
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Affiliation(s)
- Daniel K. Nomura
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Melissa M. Dix
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Benjamin F. Cravatt
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
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238
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Chemical Proteomic Technologies for Drug Target Identification. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2010. [DOI: 10.1016/s0065-7743(10)45021-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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