101
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Yamaura K, Kuwata K, Tamura T, Kioi Y, Takaoka Y, Kiyonaka S, Hamachi I. Live cell off-target identification of lapatinib using ligand-directed tosyl chemistry. Chem Commun (Camb) 2015; 50:14097-100. [PMID: 25275302 DOI: 10.1039/c4cc05885b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate that ligand-directed tosyl (LDT) chemistry is applicable to off-target identification in live cells. Lapatinib (Lap)-based LDT reagents not only labeled a receptor tyrosine kinase, HER2, target protein, but also the protein disulfide isomerase (PDI) that should be an off-target protein for Lap.
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Affiliation(s)
- Kei Yamaura
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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102
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Nickel S, Serwa RA, Kaschani F, Ninck S, Zweerink S, Tate EW, Kaiser M. Chemoproteomic Evaluation of the Polyacetylene Callyspongynic Acid. Chemistry 2015; 21:10721-8. [PMID: 26079733 DOI: 10.1002/chem.201500934] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Indexed: 01/17/2023]
Abstract
Polyacetylenes are a class of alkyne-containing natural products. Although potent bioactivities and thus possible applications as chemical probes have already been reported for some polyacetylenes, insights into the biological activities or molecular mode of action are still rather limited in most cases. To overcome this limitation, we describe the application of the polyacetylene callyspongynic acid in the development of an experimental roadmap for characterizing potential protein targets of alkyne-containing natural products. To this end, we undertook the first chemical synthesis of callyspongynic acid. We then used in situ chemical proteomics methods to demonstrate extensive callyspongynic acid-mediated chemical tagging of endoplasmic reticulum-associated lipid-metabolizing and modifying enzymes. We anticipate that an elucidation of protein targets of natural products may serve as an effective guide to the development of subsequent biological assays that aim to identify chemical phenotypes and bioactivities.
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Affiliation(s)
- Sabrina Nickel
- Chemische Biologie, ZMB, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen (Germany)
| | - Remigiusz A Serwa
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ (UK)
| | - Farnusch Kaschani
- Chemische Biologie, ZMB, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen (Germany)
| | - Sabrina Ninck
- Chemische Biologie, ZMB, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen (Germany)
| | - Susanne Zweerink
- Chemische Biologie, ZMB, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen (Germany)
| | - Edward W Tate
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ (UK)
| | - Markus Kaiser
- Chemische Biologie, ZMB, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen (Germany).
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103
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Zhu B, Ge J, Yao SQ. Developing new chemical tools for DNA methyltransferase 1 (DNMT 1): A small-molecule activity-based probe and novel tetrazole-containing inhibitors. Bioorg Med Chem 2015; 23:2917-27. [DOI: 10.1016/j.bmc.2015.03.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 02/25/2015] [Accepted: 03/02/2015] [Indexed: 12/31/2022]
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104
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105
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106
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Yang P, Liu K. Activity-based protein profiling: recent advances in probe development and applications. Chembiochem 2015; 16:712-24. [PMID: 25652106 DOI: 10.1002/cbic.201402582] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Indexed: 11/08/2022]
Abstract
The completion of the human genome sequencing project has provided a wealth of new information regarding the genomic blueprint of the cell. Although, to date, there are roughly 20,000 genes in the human genome, the functions of only a handful of proteins are clear. The major challenge lies in translating genomic information into an understanding of their cellular functions. The recently developed activity-based protein profiling (ABPP) is an unconventional approach that is complementary for gene expression analysis and an ideal utensil in decoding this overflow of genomic information. This approach makes use of synthetic small molecules that covalently modify a set of related proteins and subsequently facilitates identification of the target protein, enabling rapid biochemical analysis and inhibitor discovery. This tutorial review introduces recent advances in the field of ABPP and its applications.
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Affiliation(s)
- Pengyu Yang
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037 (USA)
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107
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Abstract
Eukaryotic and prokaryotic organisms possess huge numbers of uncharacterized enzymes. Selective inhibitors offer powerful probes for assigning functions to enzymes in native biological systems. Here, we discuss how the chemical proteomic platform activity-based protein profiling (ABPP) can be implemented to discover selective and in vivo-active inhibitors for enzymes. We further describe how these inhibitors have been used to delineate the biochemical and cellular functions of enzymes, leading to the discovery of metabolic and signaling pathways that make important contributions to human physiology and disease. These studies demonstrate the value of selective chemical probes as drivers of biological inquiry.
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Affiliation(s)
- Micah J Niphakis
- The Skaggs Institute for Chemical Biology and the Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037;
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108
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Su Y, Pan S, Li Z, Li L, Wu X, Hao P, Sze SK, Yao SQ. Multiplex imaging and cellular target identification of kinase inhibitors via an affinity-based proteome profiling approach. Sci Rep 2015; 5:7724. [PMID: 25579846 PMCID: PMC4290084 DOI: 10.1038/srep07724] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 12/09/2014] [Indexed: 12/14/2022] Open
Abstract
MLN8237 is a highly potent and presumably selective inhibitor of Aurora kinase A (AKA) and has shown promising antitumor activities. Like other kinase inhibitors which target the ATP-binding site of kinases, MLN8237 might be expected to have potential cellular off-targets. Herein, we report the first photoaffinity-based, small molecule AKA probe capable of both live-cell imaging of AKA activities and in situ proteome profiling of potential off-targets of MLN8237 (including AKA-associating proteins). By using two mutually compatible, bioorthogonal reactions (copper-catalyzed azide-alkyne cycloaddition chemistry and TCO-tetrazine ligation), we demostrate small molecule-based multiplex bioimaging for simultaneous in situ monitoring of two important cell-cycle regulating kinases (AKA and CDK1). A broad range of proteins, as potential off-targets of MLN8237 and AKA's-interacting partners, is subsequently identified by affinity-based proteome profiling coupled with large-scale LC-MS/MS analysis. From these studies, we discover novel AKA interactions which were further validated by cell-based immunoprecipitation (IP) experiments.
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Affiliation(s)
- Ying Su
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Sijun Pan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Zhengqiu Li
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Lin Li
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Xiaoyuan Wu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Piliang Hao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
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109
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Kalesh KA, Clulow JA, Tate EW. Target profiling of zerumbone using a novel cell-permeable clickable probe and quantitative chemical proteomics. Chem Commun (Camb) 2015; 51:5497-500. [DOI: 10.1039/c4cc09527h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first target profile for zerumbone in live cancer cells determined through quantitative competitive chemical proteomics with a cell-permeable probe.
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Affiliation(s)
| | - James A. Clulow
- Department of Chemistry
- Imperial College London
- London SW7 2AZ
- UK
| | - Edward W. Tate
- Department of Chemistry
- Imperial College London
- London SW7 2AZ
- UK
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110
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Durgampudi C, Noel P, Patel K, Cline R, Trivedi RN, DeLany JP, Yadav D, Papachristou GI, Lee K, Acharya C, Jaligama D, Navina S, Murad F, Singh VP. Acute lipotoxicity regulates severity of biliary acute pancreatitis without affecting its initiation. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 184:1773-84. [PMID: 24854864 DOI: 10.1016/j.ajpath.2014.02.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 02/07/2014] [Accepted: 02/27/2014] [Indexed: 02/07/2023]
Abstract
Obese patients have worse outcomes during acute pancreatitis (AP). Previous animal models of AP have found worse outcomes in obese rodents who may have a baseline proinflammatory state. Our aim was to study the role of acute lipolytic generation of fatty acids on local severity and systemic complications of AP. Human postpancreatitis necrotic collections were analyzed for unsaturated fatty acids (UFAs) and saturated fatty acids. A model of biliary AP was designed to replicate the human variables by intraductal injection of the triglyceride glyceryl trilinoleate alone or with the chemically distinct lipase inhibitors orlistat or cetilistat. Parameters of AP etiology and outcomes of local and systemic severity were measured. Patients with postpancreatitis necrotic collections were obese, and 13 of 15 had biliary AP. Postpancreatitis necrotic collections were enriched in UFAs. Intraductal glyceryl trilinoleate with or without the lipase inhibitors resulted in oil red O-positive areas, resembling intrapancreatic fat. Both lipase inhibitors reduced the glyceryl trilinoleate-induced increase in serum lipase, UFAs, pancreatic necrosis, serum inflammatory markers, systemic injury, and mortality but not serum alanine aminotransferase, bilirubin, or amylase. We conclude that UFAs are enriched in human necrotic collections and acute UFA generation via lipolysis worsens pancreatic necrosis, systemic inflammation, and injury associated with severe AP. Inhibition of lipolysis reduces UFA generation and improves these outcomes of AP without interfering with its induction.
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Affiliation(s)
- Chandra Durgampudi
- Department of Medicine, University of Pittsburgh Medical Center Pasavant, Pittsburgh, Pennsylvania
| | - Pawan Noel
- Department of Medicine, Mayo Clinic, Scottsdale, Arizona
| | - Krutika Patel
- Department of Medicine, Mayo Clinic, Scottsdale, Arizona
| | - Rachel Cline
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ram N Trivedi
- Department of Medicine, Mayo Clinic, Scottsdale, Arizona
| | - James P DeLany
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Dhiraj Yadav
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Kenneth Lee
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Chathur Acharya
- Department of Medicine, University of Pittsburgh Medical Center Pasavant, Pittsburgh, Pennsylvania
| | - Deepthi Jaligama
- Department of Medicine, University of Pittsburgh Medical Center Pasavant, Pittsburgh, Pennsylvania
| | - Sarah Navina
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Faris Murad
- Department of Medicine, Washington University, St. Louis, Missouri
| | - Vijay P Singh
- Department of Medicine, Mayo Clinic, Scottsdale, Arizona.
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111
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Hanson PR, Jayasinghe S, Maitra S, Markley JL. Phosphate tethers in natural product synthesis. Top Curr Chem (Cham) 2014; 361:253-71. [PMID: 25518970 DOI: 10.1007/128_2014_572] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Recent advances in phosphate tether-mediated natural product synthesis are reviewed. Synthetic approaches toward dolabelide C, (-)-salicylihalimide A, (-)-tetrahydrolipstatin, and (+)-strictifolione are included. In addition, current efforts in method development are briefly reviewed, including a detailed study on the effect of stereochemical complexity on the phosphate-mediated, diastereoselective ring-closing metathesis reaction and recent advances in multi-reaction, one-pot sequential processes mediated by the phosphate tether. Overall, this review seeks to highlight the utility of phosphate triesters to serve as multifunctional tethers with protecting group and latent leaving group characteristics and the ability to orchestrate multiple, orthogonal reaction pathways to allow for the facile synthesis of complex, bioactive small molecules and their analogs.
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Affiliation(s)
- Paul R Hanson
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Dr., 2010 Malott Hall, Lawrence, KS, 66045-7572, USA,
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112
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Barman S, Desper J, Levy CJ. Synthesis and characterization of TiL 2 complexes with tridentate (ONO) ( S )-NOBIN Schiff-base ligands. Polyhedron 2014. [DOI: 10.1016/j.poly.2014.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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113
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Nasheri N, McKay CS, Fulton K, Twine S, Powdrill MH, Sherratt AR, Pezacki JP. Hydrophobic triaryl-substituted β-lactams as activity-based probes for profiling eukaryotic enzymes and host-pathogen interactions. Chembiochem 2014; 15:2195-200. [PMID: 25179744 DOI: 10.1002/cbic.201402097] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Indexed: 02/06/2023]
Affiliation(s)
- Neda Nasheri
- Life Sciences Division, National Research Council of Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6 (Canada); Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5 (Canada)
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114
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Lanning BR, Whitby LR, Dix MM, Douhan J, Gilbert AM, Hett EC, Johnson TO, Joslyn C, Kath JC, Niessen S, Roberts LR, Schnute ME, Wang C, Hulce JJ, Wei B, Whiteley LO, Hayward MM, Cravatt BF. A road map to evaluate the proteome-wide selectivity of covalent kinase inhibitors. Nat Chem Biol 2014; 10:760-767. [PMID: 25038787 PMCID: PMC4138289 DOI: 10.1038/nchembio.1582] [Citation(s) in RCA: 254] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/03/2014] [Indexed: 01/05/2023]
Abstract
Kinases are principal components of signal transduction pathways and the focus of intense basic and drug discovery research. Irreversible inhibitors that covalently modify non-catalytic cysteines in kinase active sites have emerged as valuable probes and approved drugs. Many protein classes, however, have functional cysteines, and therefore understanding the proteome-wide selectivity of covalent kinase inhibitors is imperative. Here, we accomplish this objective using activity-based protein profiling coupled with quantitative MS to globally map the targets, both specific and nonspecific, of covalent kinase inhibitors in human cells. Many of the specific off-targets represent nonkinase proteins that, notably, have conserved active site cysteines. We define windows of selectivity for covalent kinase inhibitors and show that, when these windows are exceeded, rampant proteome-wide reactivity and kinase target-independent cell death conjointly occur. Our findings, taken together, provide an experimental road map to illuminate opportunities and surmount challenges for the development of covalent kinase inhibitors.
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Affiliation(s)
- Bryan R. Lanning
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. La Jolla, CA, 92307
| | - Landon R. Whitby
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. La Jolla, CA, 92307
| | - Melissa M. Dix
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. La Jolla, CA, 92307
| | - John Douhan
- Pfizer Worldwide Research and Development, 200 Cambridge Park Drive, Cambridge, MA 02140
| | - Adam M. Gilbert
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340
| | - Erik C. Hett
- Pfizer Worldwide Research and Development, 200 Cambridge Park Drive, Cambridge, MA 02140
| | - Theodore O. Johnson
- Pfizer Worldwide Research and Development, 10770 Science Park Drive, San Diego, CA 92121
| | - Chris Joslyn
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. La Jolla, CA, 92307
| | - John C. Kath
- Pfizer Worldwide Research and Development, 10770 Science Park Drive, San Diego, CA 92121
| | - Sherry Niessen
- Pfizer Worldwide Research and Development, 10770 Science Park Drive, San Diego, CA 92121
| | - Lee R. Roberts
- Pfizer Worldwide Research and Development, 200 Cambridge Park Drive, Cambridge, MA 02140
| | - Mark E. Schnute
- Pfizer Worldwide Research and Development, 200 Cambridge Park Drive, Cambridge, MA 02140
| | - Chu Wang
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. La Jolla, CA, 92307
| | - Jonathan J. Hulce
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. La Jolla, CA, 92307
| | - Baoxian Wei
- Pfizer Worldwide Research and Development, 1 Burtt Rd, Andover, MA 01810
| | | | - Matthew M. Hayward
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340
| | - Benjamin F. Cravatt
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. La Jolla, CA, 92307
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115
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Eey STC, Lear MJ. Total Synthesis of (−)-Platensimycin by Advancing Oxocarbenium- and Iminium-Mediated Catalytic Methods. Chemistry 2014; 20:11556-73. [DOI: 10.1002/chem.201400131] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Indexed: 11/10/2022]
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116
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Mulzer M, Lamb JR, Nelson Z, Coates GW. Carbonylative enantioselective meso-desymmetrization of cis-epoxides to trans-β-lactones: effect of salen-ligand electronic variation on enantioselectivity. Chem Commun (Camb) 2014; 50:9842-5. [DOI: 10.1039/c4cc04397a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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117
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Li Z, Wang D, Li L, Pan S, Na Z, Tan CYJ, Yao SQ. "Minimalist" cyclopropene-containing photo-cross-linkers suitable for live-cell imaging and affinity-based protein labeling. J Am Chem Soc 2014; 136:9990-8. [PMID: 24972113 DOI: 10.1021/ja502780z] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Target identification of bioactive compounds within the native cellular environment is important in biomedical research and drug discovery, but it has traditionally been carried out in vitro. Information about how such molecules interact with their endogenous targets (on and off) is currently highly limited. An ideal strategy would be one that recapitulates protein-small molecule interactions in situ (e.g., in living cells) and at the same time enables enrichment of these complexes for subsequent proteome-wide target identification. Similarly, small molecule-based imaging approaches are becoming increasingly available for in situ monitoring of a variety of proteins including enzymes. Chemical proteomic strategies for simultaneous bioimaging and target identification of noncovalent bioactive compounds in live mammalian cells, however, are currently not available. This is due to a lack of photoaffinity labels that are minimally modified from their parental compounds, yet chemically tractable using copper-free bioorthogonal chemistry. We have herein developed novel minimalist linkers containing both an alkyl diazirine and a cyclopropene. We have shown chemical probes (e.g., BD-2) made from such linkers could be used for simultaneous in situ imaging and covalent labeling of endogenous BRD-4 (an important epigenetic protein) via a rapid, copper-free, tetrazine-cyclopropene ligation reaction (k2 > 5 M(-1) s(-1)). The key features of our cyclopropenes, with their unique C-1 linkage to BRD-4-targeting moiety, are their tunable reactivity and solubility, relative stability, and synthetic accessibility. BD-2, which is a linker-modified analogue of (+)-JQ1 (a recently discovered nanomolar protein-protein-interaction inhibitor of BRD-4), was subsequently used in a cell-based proteome profiling experiment for large-scale identification of potential off-targets of (+)-JQ1. Several newly identified targets were subsequently confirmed by preliminary validation experiments.
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Affiliation(s)
- Zhengqiu Li
- Department of Chemistry, National University of Singapore , 3 Science Drive 3, Singapore 117543
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118
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Noel A, Delpech B, Crich D. Chemistry of the β-thiolactones: substituent and solvent effects on thermal decomposition and comparison with the β-lactones. J Org Chem 2014; 79:4068-77. [PMID: 24716459 DOI: 10.1021/jo500577c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The synthesis of a series of di-, tri-, and tetraalkyl β-thiolactones and β-lactones is described as well as their thermal decomposition with extrusion of carbon oxysulfide and carbon dioxide in two solvents of opposite polarities. The β-thiolactones are considerably more thermally stable than the β-lactones and require higher temperatures for efficient decomposition in both solvents, whatever the degree of substitution. The results are interpreted in terms of a zwitterionic mechanism for fragmentation with a change in the rate-determining step between the two series.
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Affiliation(s)
- Amandine Noel
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, CNRS , Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
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119
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Konnert L, Lamaty F, Martinez J, Colacino E. Solventless mechanosynthesis of N-protected amino esters. J Org Chem 2014; 79:4008-17. [PMID: 24738762 DOI: 10.1021/jo500463y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Mechanochemical derivatizations of N- or C-protected amino acids were performed in a ball mill under solvent-free conditions. A vibrational ball mill was used for the preparation of N-protected α- and β-amino esters starting from the corresponding N-unmasked precursors via a carbamoylation reaction in the presence of di-tert-butyl dicarbonate (Boc2O), benzyl chloroformate (Z-Cl) or 9-fluorenylmethoxycarbonyl chloroformate (Fmoc-Cl). A planetary ball mill proved to be more suitable for the synthesis of amino esters from N-protected amino acids via a one-pot activation/esterification reaction in the presence of various dialkyl dicarbonates or chloroformates. The spot-to-spot reactions were straightforward, leading to the final products in reduced reaction times with improved yields and simplified work-up procedures.
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Affiliation(s)
- Laure Konnert
- Institut des Biomolécules Max Mousseron , UMR 5247 CNRS-UM I-UM II, Place E. Bataillon, cc 1703, 34095 Montpellier, France
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120
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Liu Y, Guo M. Chemical proteomic strategies for the discovery and development of anticancer drugs. Proteomics 2014; 14:399-411. [DOI: 10.1002/pmic.201300261] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 09/26/2013] [Accepted: 10/11/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Yuanzhen Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture; Wuhan Botanical Garden; Chinese Academy of Sciences; Wuhan P. R. China
| | - Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture; Wuhan Botanical Garden; Chinese Academy of Sciences; Wuhan P. R. China
- The Keck School of Medicine; University of Southern California; Los Angeles CA USA
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121
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Cheng X, Li L, Uttamchandani M, Yao SQ. In Situ Proteome Profiling of C75, a Covalent Bioactive Compound with Potential Anticancer Activities. Org Lett 2014; 16:1414-7. [DOI: 10.1021/ol500206w] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Xiamin Cheng
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543
| | - Lin Li
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543
| | - Mahesh Uttamchandani
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543
- Defence Medical and Environmental Research Institute, DSO National Laboratories, 27 Medical Drive, Singapore 117510, Singapore
| | - Shao Q. Yao
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543
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122
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Lajkiewicz NJ, Cognetta A, Niphakis MJ, Cravatt BF, Porco JA. Remodeling natural products: chemistry and serine hydrolase activity of a rocaglate-derived β-lactone. J Am Chem Soc 2014; 136:2659-64. [PMID: 24447064 PMCID: PMC3978386 DOI: 10.1021/ja412431g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Indexed: 12/22/2022]
Abstract
Flavaglines are a class of natural products with potent insecticidal and anticancer activities. β-Lactones are a privileged structural motif found in both therapeutic agents and chemical probes. Herein, we report the synthesis, unexpected light-driven di-epimerization, and activity-based protein profiling of a novel rocaglate-derived β-lactone. In addition to in vitro inhibition of the serine hydrolases ABHD10 and ACOT1/2, the most potent β-lactone enantiomer was also found to inhibit these enzymes, as well as the serine peptidases CTSA and SCPEP1, in PC3 cells.
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Affiliation(s)
- Neil J. Lajkiewicz
- Department
of Chemistry, Center for Chemical Methodology and Library Development
(CMLD-BU), Boston University, 590 Commonwealth Avenue Boston, Massachusetts 02215, United States
| | - Armand
B. Cognetta
- Department
of Chemical Physiology, The Scripps Research
Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - Micah J. Niphakis
- Department
of Chemical Physiology, The Scripps Research
Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - Benjamin F. Cravatt
- Department
of Chemical Physiology, The Scripps Research
Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - John A. Porco
- Department
of Chemistry, Center for Chemical Methodology and Library Development
(CMLD-BU), Boston University, 590 Commonwealth Avenue Boston, Massachusetts 02215, United States
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123
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Wang J, Tan XF, Nguyen VS, Yang P, Zhou J, Gao M, Li Z, Lim TK, He Y, Ong CS, Lay Y, Zhang J, Zhu G, Lai SL, Ghosh D, Mok YK, Shen HM, Lin Q. A quantitative chemical proteomics approach to profile the specific cellular targets of andrographolide, a promising anticancer agent that suppresses tumor metastasis. Mol Cell Proteomics 2014; 13:876-86. [PMID: 24445406 DOI: 10.1074/mcp.m113.029793] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Drug target identification is a critical step toward understanding the mechanism of action of a drug, which can help one improve the drug's current therapeutic regime and expand the drug's therapeutic potential. However, current in vitro affinity-chromatography-based and in vivo activity-based protein profiling approaches generally face difficulties in discriminating specific drug targets from nonspecific ones. Here we describe a novel approach combining isobaric tags for relative and absolute quantitation with clickable activity-based protein profiling to specifically and comprehensively identify the protein targets of andrographolide (Andro), a natural product with known anti-inflammation and anti-cancer effects, in live cancer cells. We identified a spectrum of specific targets of Andro, which furthered our understanding of the mechanism of action of the drug. Our findings, validated through cell migration and invasion assays, showed that Andro has a potential novel application as a tumor metastasis inhibitor. Moreover, we have unveiled the target binding mechanism of Andro with a combination of drug analog synthesis, protein engineering, and mass-spectrometry-based approaches and determined the drug-binding sites of two protein targets, NF-κB and actin.
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Affiliation(s)
- Jigang Wang
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543
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124
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Jayakumar S, Muthusamy S, Prakash M, Kesavan V. Enantioselective Synthesis of Spirooxindole α-exo-Methylene-γ-butyrolactones from 3-OBoc-Oxindoles. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301684] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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125
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Mulzer M, Ellis WC, Lobkovsky EB, Coates GW. Enantioenriched β-lactone and aldol-type products from regiodivergent carbonylation of racemic cis-epoxides. Chem Sci 2014. [DOI: 10.1039/c4sc00075g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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126
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Ghosh B, Jones LH. Target validation using in-cell small molecule clickable imaging probes. MEDCHEMCOMM 2014. [DOI: 10.1039/c3md00277b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The application of click chemistry to the visualization of chemical probes in in-cell chemical biology experiments is reviewed and the influence this research has had on target validation and molecular mode of action studies is also highlighted.
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Affiliation(s)
| | - Lyn H. Jones
- Pfizer
- Chemical Biology Group
- BioTherapeutics Chemistry
- WorldWide Medicinal Chemistry
- Cambridge
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127
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Ravindran MS, Rao SPS, Cheng X, Shukla A, Cazenave-Gassiot A, Yao SQ, Wenk MR. Targeting lipid esterases in mycobacteria grown under different physiological conditions using activity-based profiling with tetrahydrolipstatin (THL). Mol Cell Proteomics 2013; 13:435-48. [PMID: 24345785 DOI: 10.1074/mcp.m113.029942] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tetrahydrolipstatin (THL) is bactericidal but its precise target spectrum is poorly characterized. Here, we used a THL analog and activity-based protein profiling to identify target proteins after enrichment from whole cell lysates of Mycobacterium bovis Bacillus Calmette-Guérin cultured under replicating and non-replicating conditions. THL targets α/β-hydrolases, including many lipid esterases (LipD, G, H, I, M, N, O, V, W, and TesA). Target protein concentrations and total esterase activity correlated inversely with cellular triacylglycerol upon entry into and exit from non-replicating conditions. Cellular overexpression of lipH and tesA led to decreased THL susceptibility thus providing functional validation. Our results define the target spectrum of THL in a biological species with particularly diverse lipid metabolic pathways. We furthermore derive a conceptual approach that demonstrates the use of such THL probes for the characterization of substrate recognition by lipases and related enzymes.
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Affiliation(s)
- Madhu Sudhan Ravindran
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456
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128
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Reversible lipid accumulation and associated division arrest of Mycobacterium avium in lipoprotein-induced foamy macrophages may resemble key events during latency and reactivation of tuberculosis. Infect Immun 2013; 82:476-90. [PMID: 24478064 DOI: 10.1128/iai.01196-13] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During the dormant phase of tuberculosis, Mycobacterium tuberculosis persists in lung granulomas by residing in foamy macrophages (FM) that contain abundant lipid bodies (LB) in their cytoplasm, allowing bacilli to accumulate lipids as intracytoplasmic lipid inclusions (ILI). An experimental model of FM is presented where bone marrow-derived mouse macrophages are infected with M. avium and exposed to very-low-density lipoprotein (VLDL) as a lipid source. Quantitative analysis of detailed electron microscope observations showed the following results. (i) Macrophages became foamy, and mycobacteria formed ILI, for which host triacylglycerides, rather than cholesterol, was essential. (ii) Lipid transfer occurred via mycobacterium-induced fusion between LB and phagosomes. (iii) Mycobacteria showed a thinned cell wall and became elongated but did not divide. (iv) Upon removal of VLDL, LB and ILI declined within hours, and simultaneous resumption of mycobacterial division restored the number of mycobacteria to the same level as that found in untreated control macrophages. This showed that the presence of ILI resulted in a reversible block of division without causing a change in the mycobacterial replication rate. Fluctuation between ILI either partially or fully extending throughout the mycobacterial cytoplasm was suggestive of bacterial cell cycle events. We propose that VLDL-driven FM constitute a well-defined cellular system in which to study changed metabolic states of intracellular mycobacteria that may relate to persistence and reactivation of tuberculosis.
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129
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Characterization of an acid inducible lipase Rv3203 from Mycobacterium tuberculosis H37Rv. Mol Biol Rep 2013; 41:285-96. [DOI: 10.1007/s11033-013-2861-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 11/05/2013] [Indexed: 10/26/2022]
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130
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Ge J, Zhang CJ, Li L, Chong LM, Wu X, Hao P, Sze SK, Yao SQ. Small molecule probe suitable for in situ profiling and inhibition of protein disulfide isomerase. ACS Chem Biol 2013; 8:2577-85. [PMID: 24070012 DOI: 10.1021/cb4002602] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Proper folding of cellular proteins is assisted by protein disulfide isomerases (PDIs) in the endoplasmic reticulum of mammalian cells. Of the at least 21 PDI family members known in humans, the 57-kDa PDI has been found to be a potential therapeutic target for a variety of human diseases including cancer and neurodegenerative diseases. Consequently, small molecule PDI-targeting inhibitors have been actively pursued in recent years, and thus far, compounds possessing moderate inhibitory activities (IC50 between 0.1 and 100 μM against recombinant PDI) have been discovered. In this article, by using in situ proteome profiling experiments in combination with in vitro PDI enzymatic inhibition assays, we have discovered a phenyl vinyl sulfonate-containing small molecule (P1; shown) as a relatively potent and specific inhibitor of endogenous human PDI in several mammalian cancer cells (e.g., GI50 ∼ 4 μM). It also possesses an IC50 value of 1.7 ± 0.4 μM in an in vitro insulin aggregation assay. Our results indicate P1 is indeed a novel, cell-permeable small molecule PDI inhibitor, and the electrophilic vinyl sulfonate scaffold might serve as a starting point for future development of next-generation PDI inhibitors and probes.
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Affiliation(s)
- Jingyan Ge
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Chong-Jing Zhang
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Lin Li
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Li Min Chong
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Xiaoyuan Wu
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Piliang Hao
- School of Biological
Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Siu Kwan Sze
- School of Biological
Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Shao Q. Yao
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
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131
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Baggelaar MP, Janssen FJ, van Esbroeck ACM, den Dulk H, Allarà M, Hoogendoorn S, McGuire R, Florea BI, Meeuwenoord N, van den Elst H, van der Marel GA, Brouwer J, Di Marzo V, Overkleeft HS, van der Stelt M. Development of an Activity-Based Probe and In Silico Design Reveal Highly Selective Inhibitors for Diacylglycerol Lipase-α in Brain. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306295] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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132
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Baggelaar MP, Janssen FJ, van Esbroeck ACM, den Dulk H, Allarà M, Hoogendoorn S, McGuire R, Florea BI, Meeuwenoord N, van den Elst H, van der Marel GA, Brouwer J, Di Marzo V, Overkleeft HS, van der Stelt M. Development of an activity-based probe and in silico design reveal highly selective inhibitors for diacylglycerol lipase-α in brain. Angew Chem Int Ed Engl 2013; 52:12081-5. [PMID: 24173880 DOI: 10.1002/anie.201306295] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/11/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Marc P Baggelaar
- Dept. of Bio-organic Synthesis, Leiden University, Einsteinweg 55, 2333 CC Leiden (The Netherlands)
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133
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Nasheri N, Joyce M, Rouleau Y, Yang P, Yao S, Tyrrell DL, Pezacki JP. Modulation of fatty acid synthase enzyme activity and expression during hepatitis C virus replication. ACTA ACUST UNITED AC 2013; 20:570-82. [PMID: 23601646 DOI: 10.1016/j.chembiol.2013.03.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 02/22/2013] [Accepted: 03/19/2013] [Indexed: 02/07/2023]
Abstract
The hepatitis C virus (HCV) induces alterations of host cells to facilitate its life cycle. Fatty acid synthase (FASN) is a multidomain enzyme that plays a key role in the biosynthesis of fatty acids and is upregulated during HCV infection. Herein, we applied activity-based protein profiling (ABPP) that allows for the identification of differentially active enzymes in complex proteomic samples, to study the changes in activity of FASN during HCV replication. For this purpose, we used an activity-based probe based on the FASN inhibitor Orlistat, and observed an increase in the activity of FASN in the presence of a subgenomic and a genomic HCV replicon as well as in chimeric SCID/Alb-uPA mice infected with HCV genotype 1a. To study the molecular basis for this increase in FASN activity, we overexpressed individual HCV proteins in Huh7 cells and observed increased expression and activity of FASN in the presence of core and NS4B, as measured by western blots and ABPP, respectively. Triglyceride levels were also elevated in accordance with FASN expression and activity. Lastly, immunofluorescence and ABPP imaging analyses demonstrated that while the abundance and activity of FASN increases significantly in the presence of HCV, its localization does not change. Together these data suggest that the HCV-induced production of fatty acids and neutral lipids is provided by an increase in FASN abundance and activity that is sufficient to allow HCV propagation without transporting FASN to the replication complexes.
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Affiliation(s)
- Neda Nasheri
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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134
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Su Y, Ge J, Zhu B, Zheng YG, Zhu Q, Yao SQ. Target identification of biologically active small molecules via in situ methods. Curr Opin Chem Biol 2013; 17:768-75. [DOI: 10.1016/j.cbpa.2013.06.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 05/27/2013] [Accepted: 06/02/2013] [Indexed: 12/25/2022]
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135
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Yang KS, Budin G, Tassa C, Kister O, Weissleder R. Bioorthogonal Approach to Identify Unsuspected Drug Targets in Live Cells. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201304096] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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136
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Yang KS, Budin G, Tassa C, Kister O, Weissleder R. Bioorthogonal approach to identify unsuspected drug targets in live cells. Angew Chem Int Ed Engl 2013; 52:10593-7. [PMID: 23960025 DOI: 10.1002/anie.201304096] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 06/24/2013] [Indexed: 11/12/2022]
Abstract
A proteomics method to pull down secondary drug targets from live cells is described. The drug of interest is modified with trans-cyclooctene (TCO) and incubated with live cells. Upon cell lysis, the modified drug bound to the protein is pulled down using magnetic beads decorated with a cleavable tetrazine-modified linker. Samples are then run on an SDS-PAGE gel and isolated bands are submitted for mass spectrometry analysis to identify drug targets.
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Affiliation(s)
- Katherine S Yang
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114 (USA)
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137
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Li Z, Hao P, Li L, Tan CYJ, Cheng X, Chen GYJ, Sze SK, Shen HM, Yao SQ. Design and Synthesis of Minimalist Terminal Alkyne-Containing Diazirine Photo-Crosslinkers and Their Incorporation into Kinase Inhibitors for Cell- and Tissue-Based Proteome Profiling. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300683] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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138
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Li Z, Hao P, Li L, Tan CYJ, Cheng X, Chen GYJ, Sze SK, Shen HM, Yao SQ. Design and synthesis of minimalist terminal alkyne-containing diazirine photo-crosslinkers and their incorporation into kinase inhibitors for cell- and tissue-based proteome profiling. Angew Chem Int Ed Engl 2013; 52:8551-6. [PMID: 23754342 DOI: 10.1002/anie.201300683] [Citation(s) in RCA: 255] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 04/26/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Zhengqiu Li
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
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139
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Tam EKW, Li Z, Goh YL, Cheng X, Wong SY, Santhanakrishnan S, Chai CLL, Yao SQ. Cell-Based Proteome Profiling Using an Affinity-Based Probe (AfBP) Derived from 3-Deazaneplanocin A (). Chem Asian J 2013; 8:1818-28. [DOI: 10.1002/asia.201300303] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/11/2013] [Indexed: 12/23/2022]
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140
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Ziegler S, Pries V, Hedberg C, Waldmann H. Identifizierung der Zielproteine bioaktiver Verbindungen: Die Suche nach der Nadel im Heuhaufen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208749] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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141
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Ziegler S, Pries V, Hedberg C, Waldmann H. Target identification for small bioactive molecules: finding the needle in the haystack. Angew Chem Int Ed Engl 2013; 52:2744-92. [PMID: 23418026 DOI: 10.1002/anie.201208749] [Citation(s) in RCA: 359] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Indexed: 01/10/2023]
Abstract
Identification and confirmation of bioactive small-molecule targets is a crucial, often decisive step both in academic and pharmaceutical research. Through the development and availability of several new experimental techniques, target identification is, in principle, feasible, and the number of successful examples steadily grows. However, a generic methodology that can successfully be applied in the majority of the cases has not yet been established. Herein we summarize current methods for target identification of small molecules, primarily for a chemistry audience but also the biological community, for example, the chemist or biologist attempting to identify the target of a given bioactive compound. We describe the most frequently employed experimental approaches for target identification and provide several representative examples illustrating the state-of-the-art. Among the techniques currently available, protein affinity isolation using suitable small-molecule probes (pulldown) and subsequent mass spectrometric analysis of the isolated proteins appears to be most powerful and most frequently applied. To provide guidance for rapid entry into the field and based on our own experience we propose a typical workflow for target identification, which centers on the application of chemical proteomics as the key step to generate hypotheses for potential target proteins.
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Affiliation(s)
- Slava Ziegler
- Max-Planck-Institut für molekulare Physiologie, Abt. Chemische Biologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
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142
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Gersch M, Gut F, Korotkov VS, Lehmann J, Böttcher T, Rusch M, Hedberg C, Waldmann H, Klebe G, Sieber SA. The mechanism of caseinolytic protease (ClpP) inhibition. Angew Chem Int Ed Engl 2013; 52:3009-14. [PMID: 23361916 DOI: 10.1002/anie.201204690] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 10/29/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Malte Gersch
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Institute of Advanced Studies, Lichtenbergstrasse 4, 85747 Garching, Germany
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143
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Gersch M, Gut F, Korotkov VS, Lehmann J, Böttcher T, Rusch M, Hedberg C, Waldmann H, Klebe G, Sieber SA. Der Inhibitionsmechanismus der caseinolytischen Protease (ClpP). Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201204690] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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144
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Wang K, Yang T, Wu Q, Zhao X, Nice EC, Huang C. Chemistry-based functional proteomics for drug target deconvolution. Expert Rev Proteomics 2013; 9:293-310. [PMID: 22809208 DOI: 10.1586/epr.12.19] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Drug target deconvolution, a process that identifies targets to small molecules in complex biological samples, which underlie the biological responses that are observed when a drug is administered, plays an important role in current drug discovery. Despite the fact that genomics and proteomics have provided a flood of information that contributes to the progress of drug target identification and validation, the current approach to drug target deconvolution still poses dilemmas. Chemistry-based functional proteomics, a multidisciplinary strategy, has become the preferred method of choice to deconvolute drug target pools, based on direct interactions between small molecules and their protein targets. This approach has already identified a broad panel of previously undefined enzymes with potential as drug targets and defined targets that can rationalize side effects and toxicity for new drug candidates and existing therapeutics. Herein, the authors discuss both activity-based protein profiling and compound-centric chemical proteomics approaches used in chemistry-based functional proteomics and their applications for the identification and characterization of small molecular targets.
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Affiliation(s)
- Kui Wang
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, PR China
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145
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Miao Q, Zhang CC, Kast J. Chemical proteomics and its impact on the drug discovery process. Expert Rev Proteomics 2013; 9:281-91. [PMID: 22809207 DOI: 10.1586/epr.12.22] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Despite the rapid growth of postgenomic data and fast-paced technology advancement, drug discovery is still a lengthy and difficult process. More effective drug design requires a better understanding of the interaction between drug candidates and their targets/off-targets in various situations. The ability of chemical proteomics to integrate a multiplicity of disciplines enables the direct analysis of protein activities on a proteome-wide scale, which has enormous potential to facilitate drug target elucidation and lead drug verification. Over recent years, chemical proteomics has experienced rapid growth and provided a valuable method for drug target identification and inhibitor discovery. This review introduces basic concepts and technologies of different popular chemical proteomic approaches. It also covers the essential features and recent advances of each approach while underscoring their potentials in drug discovery and development.
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Affiliation(s)
- Qing Miao
- The Biomedical Research Centre, University of British Columbia, Room #401, 2222 Health Sciences Mall, Vancouver, BC, V6T1Z3 Canada
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146
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Park J, Koh M, Park SB. From noncovalent to covalent bonds: a paradigm shift in target protein identification. MOLECULAR BIOSYSTEMS 2013; 9:544-50. [DOI: 10.1039/c2mb25502b] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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147
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Point V, Malla RK, Diomande S, Martin BP, Delorme V, Carriere F, Canaan S, Rath NP, Spilling CD, Cavalier JF. Synthesis and kinetic evaluation of cyclophostin and cyclipostins phosphonate analogs as selective and potent inhibitors of microbial lipases. J Med Chem 2012; 55:10204-19. [PMID: 23095026 DOI: 10.1021/jm301216x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new series of customizable diastereomeric cis- and trans-monocyclic enol-phosphonate analogs to Cyclophostin and Cyclipostins were synthesized. Their potencies and mechanisms of inhibition toward six representative lipolytic enzymes belonging to distinct lipase families were examined. With mammalian gastric and pancreatic lipases no inhibition occurred with any of the compounds tested. Conversely, Fusarium solani Cutinase and lipases from Mycobacterium tuberculosis (Rv0183 and LipY) were all fully inactivated. The best inhibitors displayed a cis conformation (H and OMe) and exhibited higher inhibitory activities than the lipase inhibitor Orlistat toward the same enzymes. Our results have revealed that chemical group at the γ-carbon of the phosphonate ring strongly impacts the inhibitory efficiency, leading to a significant improvement in selectivity toward a target lipase over another. The powerful and selective inhibition of microbial (fungal and mycobacterial) lipases suggests that these seven-membered monocyclic enol-phosphonates should provide useful leads for the development of novel and highly selective antimicrobial agents.
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Affiliation(s)
- Vanessa Point
- CNRS - Aix-Marseille Université , Enzymologie Interfaciale et Physiologie de la Lipolyse, UMR 7282, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France
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148
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Point V, Pavan Kumar KVP, Marc S, Delorme V, Parsiegla G, Amara S, Carrière F, Buono G, Fotiadu F, Canaan S, Leclaire J, Cavalier JF. Analysis of the discriminative inhibition of mammalian digestive lipases by 3-phenyl substituted 1,3,4-oxadiazol-2(3H)-ones. Eur J Med Chem 2012; 58:452-63. [PMID: 23153815 DOI: 10.1016/j.ejmech.2012.10.040] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 09/05/2012] [Accepted: 10/21/2012] [Indexed: 01/13/2023]
Abstract
We report here the reactivity and selectivity of three 5-Methoxy-N-3-Phenyl substituted-1,3,4-Oxadiazol-2(3H)-ones (MPOX, as well as meta and para-PhenoxyPhenyl derivatives, i.e.MmPPOX and MpPPOX) with respect to the inhibition of mammalian digestive lipases: dog gastric lipase (DGL), human (HPL) and porcine (PPL) pancreatic lipases, human (HPLRP2) and guinea pig (GPLRP2) pancreatic lipase-related proteins 2, human pancreatic carboxyl ester hydrolase (hCEH), and porcine pancreatic extracts (PPE). All three oxadiazolones displayed similar inhibitory activities on DGL, PLRP2s and hCEH than the FDA-approved anti-obesity drug Orlistat towards the same enzymes. These compounds appeared however to be discriminative of HPL (poorly inhibited) and PPL (fully inhibited). The inhibitory activities obtained experimentally in vitro were further rationalized using in silico molecular docking. In the case of DGL, we demonstrated that the phenoxy group plays a key role in specific molecular interactions within the lipase's active site. The absence of this group in the case of MPOX, as well as its connectivity to the neighbouring aromatic ring in the case of MmPPOX and MpPPOX, strongly impacts the inhibitory efficiency of these oxadiazolones and leads to a significant gain in selectivity towards the lipases tested. The powerful inhibition of PPL, DGL, PLRP2s, hCEH and to a lesser extend HPL, suggests that oxadiazolone derivatives could also provide useful leads for the development of novel and more discriminative inhibitors of digestive lipases. These inhibitors could be used for a better understanding of individual lipase function as well as for drug development aiming at the regulation of the whole gastrointestinal lipolysis process.
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Affiliation(s)
- Vanessa Point
- CNRS - Aix-Marseille Université - Enzymologie Interfaciale et Physiologie de Lipolyse - UMR 7282, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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Inhibitors of fatty acid synthesis in prokaryotes and eukaryotes as anti-infective, anticancer and anti-obesity drugs. Future Med Chem 2012; 4:1113-51. [PMID: 22709254 DOI: 10.4155/fmc.12.62] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
There is a large range of diseases, such diabetes and cancer, which are connected to abnormal fatty acid metabolism in human cells. Therefore, inhibitors of human fatty acid synthase have great potential to manage or treat these diseases. In prokaryotes, fatty acid synthesis is important for signaling, as well as providing starting materials for the synthesis of phospholipids, which are required for the formation of the cell membrane. Recently, there has been renewed interest in the development of new molecules that target bacterial fatty acid synthases for the treatment of bacterial diseases. In this review, we look at the differences and similarities between fatty acid synthesis in humans and bacteria and highlight various small molecules that have been shown to inhibit either the mammalian or bacterial fatty acid synthase or both.
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150
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MmPPOX inhibits Mycobacterium tuberculosis lipolytic enzymes belonging to the hormone-sensitive lipase family and alters mycobacterial growth. PLoS One 2012; 7:e46493. [PMID: 23029536 PMCID: PMC3460867 DOI: 10.1371/journal.pone.0046493] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 09/05/2012] [Indexed: 11/19/2022] Open
Abstract
Lipid metabolism plays an important role during the lifetime of Mycobacterium tuberculosis, the causative agent of tuberculosis. Although M. tuberculosis possesses numerous lipolytic enzymes, very few have been characterized yet at a biochemical/pharmacological level. This study was devoted to the M. tuberculosis lipolytic enzymes belonging to the Hormone-Sensitive Lipase (HSL) family, which encompasses twelve serine hydrolases closely related to the human HSL. Among them, nine were expressed, purified and biochemically characterized using a broad range of substrates. In vitro enzymatic inhibition studies using the recombinant HSL proteins, combined with mass spectrometry analyses, revealed the potent inhibitory activity of an oxadiazolone compound, named MmPPOX. In addition, we provide evidence that MmPPOX alters mycobacterial growth. Overall, these findings suggest that the M. tuberculosis HSL family displays important metabolic functions, thus opening the way to further investigations linking the involvement of these enzymes in mycobacterial growth.
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