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Shrimp JH, Garlick JM, Tezil T, Sorum AW, Worth AJ, Blair IA, Verdin E, Snyder NW, Meier JL. Defining Metabolic and Nonmetabolic Regulation of Histone Acetylation by NSAID Chemotypes. Mol Pharm 2017; 15:729-736. [PMID: 29240439 DOI: 10.1021/acs.molpharmaceut.7b00943] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nonsteroidal anti-inflammatory drugs (NSAIDs) are well-known for their effects on inflammatory gene expression. Although NSAIDs are known to impact multiple cellular signaling mechanisms, a recent finding is that the NSAID salicylate can disrupt histone acetylation, in part through direct inhibition of the lysine acetyltransferase (KAT) p300/CBP. While salicylate is a relatively weak KAT inhibitor, its CoA-linked metabolite is more potent; however, the ability of NSAID metabolites to inhibit KAT enzymes biochemically and in cells remains relatively unexplored. Here we define the role of metabolic and nonmetabolic mechanisms in inhibition of KAT activity by NSAID chemotypes. First, we screen a small panel of NSAIDs for biochemical inhibition of the prototypical KAT p300, leading to the finding that many carboxylate-containing NSAIDs, including ibuprofen, are able to function as weak inhibitors. Assessing the inhibition of p300 by ibuprofen-CoA, a known NSAID metabolite, reveals that linkage of ibuprofen to CoA increases its biochemical potency toward p300 and other KAT enzymes. In cellular studies, we find that carboxylate-containing NSAIDs inhibit histone acetylation. Finally, we exploit the stereoselective metabolism of ibuprofen to assess the role of its acyl-CoA metabolite in regulation of histone acetylation. This unique strategy reveals that formation of ibuprofen-CoA and histone acetylation are poorly correlated, suggesting metabolism may not be required for ibuprofen to inhibit histone acetylation. Overall, these studies provide new insights into the ability of NSAIDs to alter histone acetylation, and illustrate how selective metabolism may be leveraged as a tool to explore the influence of metabolic acyl-CoAs on cellular enzyme activity.
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Affiliation(s)
- Jonathan H Shrimp
- Chemical Biology Laboratory , National Cancer Institute , Frederick , Maryland 21702 , United States
| | - Julie M Garlick
- Chemical Biology Laboratory , National Cancer Institute , Frederick , Maryland 21702 , United States
| | - Tugsan Tezil
- Buck Institute for Research on Aging, Novato , California 94945 , United States
| | - Alexander W Sorum
- Chemical Biology Laboratory , National Cancer Institute , Frederick , Maryland 21702 , United States
| | - Andrew J Worth
- Penn SRP Center, Center of Excellence in Environmental Toxicology , University of Pennsylvania , Philadelphia Pennsylvania 19104 , United States
| | - Ian A Blair
- Penn SRP Center, Center of Excellence in Environmental Toxicology , University of Pennsylvania , Philadelphia Pennsylvania 19104 , United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato , California 94945 , United States
| | - Nathaniel W Snyder
- Drexel University, A.J. Drexel Autism Institute , 3020 Market Street , Philadelphia Pennsylvania 19104 , United States
| | - Jordan L Meier
- Chemical Biology Laboratory , National Cancer Institute , Frederick , Maryland 21702 , United States
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2
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Kulkarni RA, Worth AJ, Zengeya TT, Shrimp JH, Garlick JM, Roberts AM, Montgomery DC, Sourbier C, Gibbs BK, Mesaros C, Tsai YC, Das S, Chan KC, Zhou M, Andresson T, Weissman AM, Linehan WM, Blair IA, Snyder NW, Meier JL. Discovering Targets of Non-enzymatic Acylation by Thioester Reactivity Profiling. Cell Chem Biol 2017; 24:231-242. [PMID: 28163016 DOI: 10.1016/j.chembiol.2017.01.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 10/14/2016] [Accepted: 01/10/2017] [Indexed: 01/15/2023]
Abstract
Non-enzymatic protein modification driven by thioester reactivity is thought to play a major role in the establishment of cellular lysine acylation. However, the specific protein targets of this process are largely unknown. Here we report an experimental strategy to investigate non-enzymatic acylation in cells. Specifically, we develop a chemoproteomic method that separates thioester reactivity from enzymatic utilization, allowing selective enrichment of non-enzymatic acylation targets. Applying this method to cancer cell lines identifies numerous candidate targets of non-enzymatic acylation, including several enzymes in lower glycolysis. Functional studies highlight malonyl-CoA as a reactive thioester metabolite that can modify and inhibit glycolytic enzyme activity. Finally, we show that synthetic thioesters can be used as novel reagents to probe non-enzymatic acylation in living cells. Our studies provide new insights into the targets and drivers of non-enzymatic acylation, and demonstrate the utility of reactivity-based methods to experimentally investigate this phenomenon in biology and disease.
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Affiliation(s)
- Rhushikesh A Kulkarni
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Andrew J Worth
- Penn SRP Center, Center for Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Thomas T Zengeya
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Jonathan H Shrimp
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Julie M Garlick
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Allison M Roberts
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - David C Montgomery
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Carole Sourbier
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20817, USA
| | - Benjamin K Gibbs
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20817, USA
| | - Clementina Mesaros
- Penn SRP Center, Center for Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yien Che Tsai
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Sudipto Das
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - King C Chan
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Ming Zhou
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Allan M Weissman
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20817, USA
| | - Ian A Blair
- Penn SRP Center, Center for Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathaniel W Snyder
- Drexel University, A.J. Drexel Autism Institute, 3020 Market Street, Philadelphia, PA 19104, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
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3
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Shirakawa K, Wang L, Man N, Maksimoska J, Sorum AW, Lim HW, Lee IS, Shimazu T, Newman JC, Schröder S, Ott M, Marmorstein R, Meier J, Nimer S, Verdin E. Salicylate, diflunisal and their metabolites inhibit CBP/p300 and exhibit anticancer activity. eLife 2016; 5. [PMID: 27244239 PMCID: PMC4931907 DOI: 10.7554/elife.11156] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 05/26/2016] [Indexed: 12/19/2022] Open
Abstract
Salicylate and acetylsalicylic acid are potent and widely used anti-inflammatory drugs. They are thought to exert their therapeutic effects through multiple mechanisms, including the inhibition of cyclo-oxygenases, modulation of NF-κB activity, and direct activation of AMPK. However, the full spectrum of their activities is incompletely understood. Here we show that salicylate specifically inhibits CBP and p300 lysine acetyltransferase activity in vitro by direct competition with acetyl-Coenzyme A at the catalytic site. We used a chemical structure-similarity search to identify another anti-inflammatory drug, diflunisal, that inhibits p300 more potently than salicylate. At concentrations attainable in human plasma after oral administration, both salicylate and diflunisal blocked the acetylation of lysine residues on histone and non-histone proteins in cells. Finally, we found that diflunisal suppressed the growth of p300-dependent leukemia cell lines expressing AML1-ETO fusion protein in vitro and in vivo. These results highlight a novel epigenetic regulatory mechanism of action for salicylate and derivative drugs. DOI:http://dx.doi.org/10.7554/eLife.11156.001 People have been using a chemical called salicylate, which was once extracted from willow tree bark, as medicine for pain, fever and inflammation since ancient Greece. Aspirin is derived from salicylate but is a more potent drug. Aspirin exerts its anti-inflammatory effect by shutting down the activity of proteins that would otherwise boost inflammation. Aspirin achieves this by releasing a chemical marker, called an acetyl group, to be added to these proteins via a process known as protein acetylation. However, salicylate cannot trigger protein acetylation and so it was not clear how it reduces inflammation. An anti-diabetes drug that is converted into salicylate in the body reduces inflammation by inhibiting a protein called NF-κB. In 2001, a group of researchers reported that NF-κB becomes active when an enzyme called p300 adds an acetyl group to it. This raised the question: does salicylate reduce inflammation by blocking, instead of triggering, protein acetylation. Now, Shirakawa et al. – who include a researcher involved in the 2001 study – show that salicylate does indeed block the activity of the p300 enzyme. Shirakawa et al. then searched a database looking for drugs that have salicylate as part of their molecular structure. The search led to a drug called diflunisal, which was even more effective at blocking p300 in laboratory tests. Some cancers, including a blood cancer, rely on p300 to grow; diflunisal was shown to stop this kind of cancer cell from growing, both in the laboratory and in mice. Together, the experiments suggest that salicylate and drugs that share some of its structure might represent useful treatments for certain cancers, as well as other diseases that involve the p300 enzyme. DOI:http://dx.doi.org/10.7554/eLife.11156.002
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Affiliation(s)
- Kotaro Shirakawa
- Gladstone Institutes, University of California, San Francisco, United States.,Department of Medicine, University of California, San Francisco, United States.,Department of Hematology and Oncology, Kyoto University, Kyoto, Japan.,Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Lan Wang
- University of Miami, Gables, United States.,Sylvester Comprehensive Cancer Center, Miami, United States
| | - Na Man
- University of Miami, Gables, United States.,Sylvester Comprehensive Cancer Center, Miami, United States
| | - Jasna Maksimoska
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Philadelphia, United States
| | - Alexander W Sorum
- Chemical Biology Laboratory, National Cancer Institute, Frederick, United States
| | - Hyung W Lim
- Gladstone Institutes, University of California, San Francisco, United States.,Department of Medicine, University of California, San Francisco, United States
| | - Intelly S Lee
- Gladstone Institutes, University of California, San Francisco, United States.,Department of Medicine, University of California, San Francisco, United States
| | - Tadahiro Shimazu
- Gladstone Institutes, University of California, San Francisco, United States.,Department of Medicine, University of California, San Francisco, United States
| | - John C Newman
- Gladstone Institutes, University of California, San Francisco, United States.,Department of Medicine, University of California, San Francisco, United States
| | - Sebastian Schröder
- Gladstone Institutes, University of California, San Francisco, United States.,Department of Medicine, University of California, San Francisco, United States
| | - Melanie Ott
- Gladstone Institutes, University of California, San Francisco, United States.,Department of Medicine, University of California, San Francisco, United States
| | - Ronen Marmorstein
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Philadelphia, United States
| | - Jordan Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick, United States
| | - Stephen Nimer
- University of Miami, Gables, United States.,Sylvester Comprehensive Cancer Center, Miami, United States
| | - Eric Verdin
- Gladstone Institutes, University of California, San Francisco, United States.,Department of Medicine, University of California, San Francisco, United States
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4
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Montgomery DC, Sorum AW, Guasch L, Nicklaus MC, Meier JL. Metabolic Regulation of Histone Acetyltransferases by Endogenous Acyl-CoA Cofactors. ACTA ACUST UNITED AC 2015; 22:1030-1039. [PMID: 26190825 DOI: 10.1016/j.chembiol.2015.06.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/04/2015] [Accepted: 06/05/2015] [Indexed: 10/23/2022]
Abstract
The finding that chromatin modifications are sensitive to changes in cellular cofactor levels potentially links altered tumor cell metabolism and gene expression. However, the specific enzymes and metabolites that connect these two processes remain obscure. Characterizing these metabolic-epigenetic axes is critical to understanding how metabolism supports signaling in cancer, and developing therapeutic strategies to disrupt this process. Here, we describe a chemical approach to define the metabolic regulation of lysine acetyltransferase (KAT) enzymes. Using a novel chemoproteomic probe, we identify a previously unreported interaction between palmitoyl coenzyme A (palmitoyl-CoA) and KAT enzymes. Further analysis reveals that palmitoyl-CoA is a potent inhibitor of KAT activity and that fatty acyl-CoA precursors reduce cellular histone acetylation levels. These studies implicate fatty acyl-CoAs as endogenous regulators of histone acetylation, and suggest novel strategies for the investigation and metabolic modulation of epigenetic signaling.
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Affiliation(s)
- David C Montgomery
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick MD, 21702, USA
| | - Alexander W Sorum
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick MD, 21702, USA
| | - Laura Guasch
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick MD, 21702, USA
| | - Marc C Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick MD, 21702, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick MD, 21702, USA
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5
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Chowdhury S, Thomas MG, Escalante-Semerena JC, Banerjee R. The coenzyme b12 analog 5'-deoxyadenosylcobinamide-gdp supports catalysis by methylmalonyl-coa mutase in the absence of trans-ligand coordination. J Biol Chem 2001; 276:1015-9. [PMID: 11031263 DOI: 10.1074/jbc.m006842200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Methylmalonyl-CoA mutase is an 5'-adenosylcobalamin (AdoCbl)-dependent enzyme that catalyzes the rearrangement of methylmalonyl-CoA to succinyl-CoA. The crystal structure of this protein revealed that binding of the cofactor is accompanied by a significant conformational change in which dimethylbenzimidazole, the lower axial ligand to cobalt in solution, is replaced by His(610) donated by the active site. The role of the lower axial ligand in the trillion-fold labilization of the upper axial cobalt-carbon bond has been the subject of enduring debate in the model inorganic literature. In this study, we have used a cofactor analog, 5'deoxyadenosylcobinamide GDP (AdoCbi-GDP), which reconstitutes the enzyme in a "histidine-off" form and which allows us to evaluate the contribution of the lower axial ligand to catalysis. The k(cat) for the enzyme in the presence of AdoCbi-GDP is reduced by a factor of 4 compared with the native cofactor AdoCbl. The overall deuterium isotope effect in the presence of AdoCbi-GDP ((D)V = 7.2 +/- 0.8) is comparable with that observed in the presence of AdoCbl (5.0 +/- 0.6) and indicates that the hydrogen transfer steps in this reaction are not significantly affected by the change in coordination state of the bound cofactor. These surprising results are in marked contrast to the effects ascribed to the corresponding lower axial histidine ligands in the cobalamin-dependent enzymes glutamate mutase and methionine synthase.
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Affiliation(s)
- S Chowdhury
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664 , USA
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6
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Taoka S, Padmakumar R, Grissom CB, Banerjee R. Magnetic field effects on coenzyme B12-dependent enzymes: validation of ethanolamine ammonia lyase results and extension to human methylmalonyl CoA mutase. Bioelectromagnetics 2000; 18:506-13. [PMID: 9338632 DOI: 10.1002/(sici)1521-186x(1997)18:7<506::aid-bem6>3.0.co;2-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Enzymes with radical-pair intermediates have been considered as a likely target for purported magnetic field effects in humans. The bacterial enzyme ethanolamine ammonia lyase and the human enzyme methylmalonyl-CoA mutase catalyze coenzyme B12-dependent rearrangement reactions. A common step in the mechanism of these two enzymes is postulated to be homolysis of the cobalt-carbon bond of the cofactor to generate a spin-correlated radical pair consisting of the 5'-deoxyadenosyl radical and cob(II)alamin [Ado. Cbl(II)]. Thus, the reactions catalyzed by these enzymes are expected to be sensitive to an applied magnetic field according to the same principles that control radical pair chemical reactions. The magnetic field effect on ethanolamine ammonia lyase reported previously has been corroborated independently in one of the authors' laboratory. However, neither the human nor the bacterial mutase from Propionibacterium shermanii exhibits a magnetic field effect that could be greater than about 15%, considering the error limit imposed by the uncertainty of the coupled assay. Our studies suggest that putative magnetic field effects on physiological processes are not likely to be mediated by methylmalonyl-CoA mutase.
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Affiliation(s)
- S Taoka
- Biochemistry Department, University of Nebraska, Lincoln 68588-0664, USA
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