1
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Paniri A, Hosseini MM, Akhavan-Niaki H. Alzheimer's Disease-Related Epigenetic Changes: Novel Therapeutic Targets. Mol Neurobiol 2024; 61:1282-1317. [PMID: 37700216 DOI: 10.1007/s12035-023-03626-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
Aging is a significant risk factor for Alzheimer's disease (AD), although the precise mechanism and molecular basis of AD are not yet fully understood. Epigenetic mechanisms, such as DNA methylation and hydroxymethylation, mitochondrial DNA methylation, histone modifications, and non-coding RNAs (ncRNAs), play a role in regulating gene expression related to neuron plasticity and integrity, which are closely associated with learning and memory development. This review describes the impact of dynamic and reversible epigenetic modifications and factors on memory and plasticity throughout life, emphasizing their potential as target for therapeutic intervention in AD. Additionally, we present insight from postmortem and animal studies on abnormal epigenetics regulation in AD, as well as current strategies aiming at targeting these factors in the context of AD therapy.
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Affiliation(s)
- Alireza Paniri
- Genetics Department, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
- Zoonoses Research Center, Pasteur Institute of Iran, Amol, Iran
| | | | - Haleh Akhavan-Niaki
- Genetics Department, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran.
- Zoonoses Research Center, Pasteur Institute of Iran, Amol, Iran.
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2
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Gou P, Zhang W. Protein lysine acetyltransferase CBP/p300: A promising target for small molecules in cancer treatment. Biomed Pharmacother 2024; 171:116130. [PMID: 38215693 DOI: 10.1016/j.biopha.2024.116130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 01/14/2024] Open
Abstract
CBP and p300 are homologous proteins exhibiting remarkable structural and functional similarity. Both proteins function as acetyltransferase and coactivator, underscoring their significant roles in cellular processes. The function of histone acetyltransferases is to facilitate the release of DNA from nucleosomes and act as transcriptional co-activators to promote gene transcription. Transcription factors recruit CBP/p300 by co-condensation and induce transcriptional bursting. Disruption of CBP or p300 functions is associated with different diseases, especially cancer, which can result from either loss of function or gain of function. CBP and p300 are multidomain proteins containing HAT (histone acetyltransferase) and BRD (bromodomain) domains, which perform acetyltransferase activity and maintenance of HAT signaling, respectively. Inhibitors targeting HAT and BRD have been explored for decades, and some BRD inhibitors have been evaluated in clinical trials for treating hematologic malignancies or advanced solid tumors. Here, we review the development and application of CBP/p300 inhibitors. Several inhibitors have been evaluated in vivo, exhibiting notable potency but limited selectivity. Exploring these inhibitors emphasizes the promise of targeting CBP and p300 with small molecules in cancer therapy.
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Affiliation(s)
- Panhong Gou
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wenchao Zhang
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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3
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Bishop TR, Subramanian C, Bilotta EM, Garnar-Wortzel L, Ramos AR, Zhang Y, Asiaban JN, Ott CJ, Rock CO, Erb MA. Acetyl-CoA biosynthesis drives resistance to histone acetyltransferase inhibition. Nat Chem Biol 2023; 19:1215-1222. [PMID: 37127754 PMCID: PMC10538425 DOI: 10.1038/s41589-023-01320-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 03/23/2023] [Indexed: 05/03/2023]
Abstract
Histone acetyltransferases (HATs) are implicated as both oncogene and nononcogene dependencies in diverse human cancers. Acetyl-CoA-competitive HAT inhibitors have emerged as potential cancer therapeutics and the first clinical trial for this class of drugs is ongoing (NCT04606446). Despite these developments, the potential mechanisms of therapeutic response and evolved drug resistance remain poorly understood. Having discovered that multiple regulators of de novo coenzyme A (CoA) biosynthesis can modulate sensitivity to CBP/p300 HAT inhibition (PANK3, PANK4 and SLC5A6), we determined that elevated acetyl-CoA concentrations can outcompete drug-target engagement to elicit acquired drug resistance. This not only affects structurally diverse CBP/p300 HAT inhibitors, but also agents related to an investigational KAT6A/B HAT inhibitor that is currently in Phase 1 clinical trials. Altogether, this work uncovers CoA metabolism as an unexpected liability of anticancer HAT inhibitors and will therefore buoy future efforts to optimize the efficacy of this new form of targeted therapy.
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Affiliation(s)
- Timothy R Bishop
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Chitra Subramanian
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Eric M Bilotta
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Anissa R Ramos
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Yuxiang Zhang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Joshua N Asiaban
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Christopher J Ott
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael A Erb
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
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4
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Li AM, He B, Karagiannis D, Li Y, Jiang H, Srinivasan P, Ramirez Y, Zhou MN, Curtis C, Gruber JJ, Lu C, Rankin EB, Ye J. Serine starvation silences estrogen receptor signaling through histone hypoacetylation. Proc Natl Acad Sci U S A 2023; 120:e2302489120. [PMID: 37695911 PMCID: PMC10515173 DOI: 10.1073/pnas.2302489120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 08/07/2023] [Indexed: 09/13/2023] Open
Abstract
Loss of estrogen receptor (ER) pathway activity promotes breast cancer progression, yet how this occurs remains poorly understood. Here, we show that serine starvation, a metabolic stress often found in breast cancer, represses estrogen receptor alpha (ERα) signaling by reprogramming glucose metabolism and epigenetics. Using isotope tracing and time-resolved metabolomic analyses, we demonstrate that serine is required to maintain glucose flux through glycolysis and the TCA cycle to support acetyl-CoA generation for histone acetylation. Consequently, limiting serine depletes histone H3 lysine 27 acetylation (H3K27ac), particularly at the promoter region of ER pathway genes including the gene encoding ERα, ESR1. Mechanistically, serine starvation impairs acetyl-CoA-dependent gene expression by inhibiting the entry of glycolytic carbon into the TCA cycle and down-regulating the mitochondrial citrate exporter SLC25A1, a critical enzyme in the production of nucleocytosolic acetyl-CoA from glucose. Consistent with this model, total H3K27ac and ERα expression are suppressed by SLC25A1 inhibition and restored by acetate, an alternate source of acetyl-CoA, in serine-free conditions. We thus uncover an unexpected role for serine in sustaining ER signaling through the regulation of acetyl-CoA metabolism.
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Affiliation(s)
- Albert M Li
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305
| | - Bo He
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
| | - Dimitris Karagiannis
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032
| | - Yang Li
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
| | - Haowen Jiang
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
| | - Preethi Srinivasan
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Yaniel Ramirez
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
| | - Meng-Ning Zhou
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
| | - Christina Curtis
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Joshua J Gruber
- Department of Internal Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75235
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032
| | - Erinn B Rankin
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Jiangbin Ye
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305
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5
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Sasaki K, Suzuki M, Sonoda T, Schneider-Poetsch T, Ito A, Takagi M, Fujishiro S, Sohtome Y, Dodo K, Umehara T, Aburatani H, Shin-Ya K, Nakao Y, Sodeoka M, Yoshida M. Visualization of the dynamic interaction between nucleosomal histone H3K9 tri-methylation and HP1α chromodomain in living cells. Cell Chem Biol 2022; 29:1153-1161.e5. [PMID: 35728598 DOI: 10.1016/j.chembiol.2022.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/05/2022] [Accepted: 05/23/2022] [Indexed: 11/26/2022]
Abstract
Histone lysine methylation is an epigenetic mark that can control gene expression. In particular, H3K9me3 contributes to transcriptional repression by regulating chromatin structure. Successful mitotic progression requires correct timing of chromatin structure changes, including epigenetic marks. However, spatiotemporal information on histone modifications in living cells remains limited. In this study, we created an FRET-based probe for live-cell imaging based on the HP1α chromodomain (HP1αCD), which binds to H3K9me3. The probe was incorporated into chromatin and the emission ratio decreased after treatment with histone methyltransferase inhibitors, indicating that it successfully traced dynamic changes in H3K9me3. Upon entry into mitosis, the probe's emission ratio transiently increased with a concomitant increase in H3K9me3, then exhibited a stepwise decrease, probably due to loss of HP1αCD binding caused by phosphorylation of H3S10 and demethylation of H3K9me3. This probe will be a useful tool for detecting dynamic changes in chromatin structure associated with HP1α.
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Affiliation(s)
- Kazuki Sasaki
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan.
| | - Michihiro Suzuki
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Department of Chemistry and Biochemistry, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Takeshi Sonoda
- Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Tilman Schneider-Poetsch
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Akihiro Ito
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Motoki Takagi
- Japan Biological Informatics Consortium (JBIC), Koto-ku, Tokyo, 135-0064, Japan
| | - Shinya Fujishiro
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Yoshihiro Sohtome
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; Catalysis and Integrated Research Group, RIKEN Center for Sustainable Research Science, Wako, Saitama 351-0198, Japan
| | - Kosuke Dodo
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; Catalysis and Integrated Research Group, RIKEN Center for Sustainable Research Science, Wako, Saitama 351-0198, Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroyuki Aburatani
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan; Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yoichi Nakao
- Department of Chemistry and Biochemistry, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan; Research Institute for Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; Catalysis and Integrated Research Group, RIKEN Center for Sustainable Research Science, Wako, Saitama 351-0198, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
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6
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Malinee M, Pandian GN, Sugiyama H. Targeted epigenetic induction of mitochondrial biogenesis enhances antitumor immunity in mouse model. Cell Chem Biol 2021; 29:463-475.e6. [PMID: 34520746 DOI: 10.1016/j.chembiol.2021.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 06/04/2021] [Accepted: 08/01/2021] [Indexed: 11/25/2022]
Abstract
Considering the potential of combinatorial therapies in overcoming existing limitations of cancer immunotherapy, there is an increasing need to identify small-molecule modulators of immune cells capable of augmenting the effect of programmed cell death protein 1 (PD-1) blockade, leading to better cancer treatment. Although epigenetic drugs showed potential in combination therapy, the lack of sequence specificity is a major concern. Here, we identify and develop a DNA-based epigenetic activator with tri-arginine vector called EnPGC-1 that can trigger the targeted induction of the peroxisome proliferator-activated receptor-gamma coactivator 1 alpha/beta (PGC-1α/β), a regulator of mitochondrial biogenesis. EnPGC-1 enhances mitochondrial activation, energy metabolism, proliferation of CD8+ T cells in vitro, and, in particular, enhances oxidative phosphorylation, a feature of long-lived memory T cells. Genome-wide gene analysis suggests that EnPGC-1 and not the control compounds can regulate T cell activation as a major biological process. EnPGC-1 also synergizes with PD-1 blockade to enhance antitumor immunity and improved host survival.
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Affiliation(s)
- Madhu Malinee
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ganesh Namasivayam Pandian
- Institute of Integrated Cell Material Sciences (iCeMS), Kyoto University of Advanced Study, Kyoto, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan.
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7
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Shanmugam MK, Dharmarajan A, Warrier S, Bishayee A, Kumar AP, Sethi G, Ahn KS. Role of histone acetyltransferase inhibitors in cancer therapy. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 125:149-191. [PMID: 33931138 DOI: 10.1016/bs.apcsb.2020.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The development of cancer is a complex phenomenon driven by various extrinsic as well as intrinsic risk factors including epigenetic modifications. These post-translational modifications are encountered in diverse cancer cells and appear for a relatively short span of time. These changes can significantly affect various oncogenic genes and proteins involved in cancer initiation and progression. Histone lysine acetylation and deacetylation processes are controlled by two opposing classes of enzymes that modulate gene regulation either by adding an acetyl moiety on a histone lysine residue by histone lysine acetyltransferases (KATs) or via removing it by histone deacetylases (KDACs). Deregulated KAT activity has been implicated in the development of several diseases including cancer and can be targeted for the development of anti-neoplastic drugs. Here, we describe the predominant epigenetic changes that can affect key KAT superfamily members during carcinogenesis and briefly highlight the pharmacological potential of employing lysine acetyltransferase inhibitors (KATi) for cancer therapy.
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Affiliation(s)
- Muthu K Shanmugam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Arunasalam Dharmarajan
- Department of Biomedical Sciences, Faculty of Biomedical Sciences Technology and Research, Sri Ramachandra Institute of Higher Education & Research, Chennai, India
| | - Sudha Warrier
- Division of Cancer Stem Cells and Cardiovascular Regeneration, Manipal Institute of Regenerative Medicine, Manipal University, Bangalore, India
| | - Anupam Bishayee
- Lake Erie College of Osteopathic Medicine, Bradenton, FL, United States
| | - Alan Prem Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Kwang Seok Ahn
- Department of Science in Korean Medicine, College of Korean Medicine, Kyung Hee University, Seoul, Republic of Korea.
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8
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Current development of CBP/p300 inhibitors in the last decade. Eur J Med Chem 2020; 209:112861. [PMID: 33045661 DOI: 10.1016/j.ejmech.2020.112861] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 01/10/2023]
Abstract
CBP/p300, functioning as histone acetyltransferases and transcriptional co-factors, represents an attractive target for various diseases, including malignant tumor. The development of small-molecule inhibitors targeting the bromodomain and HAT domains of CBP/p300 has aroused broad interests of medicinal chemist in expectation of providing new hope for anti-cancer treatment. In particular, the CBP/p300 bromodomain inhibitor CCS1477, identified by CellCentric, is currently undergone clinical evaluation for the treatment of haematological malignancies and prostate cancer. In this review, we depict the development of CBP/p300 inhibitors reported from 2010 to 2020 and particularly highlight their structure-activity relationships (SARs), binding modes, selectivity and pharmacological functions with the aim to facilitate rational design and development of CBP/p300 inhibitors.
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9
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Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
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Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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10
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Magudeeswaran S, Poomani K. Binding mechanism of spinosine and venenatine molecules with p300 HAT enzyme: Molecular screening, molecular dynamics and free-energy analysis. J Cell Biochem 2019; 121:1759-1777. [PMID: 31633226 DOI: 10.1002/jcb.29412] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 10/04/2019] [Indexed: 12/25/2022]
Abstract
The chromatin modification is regulated by the histone acetyltransferase (HAT) and histone deacetyltransferase (HDAC) enzymes; abnormal function of these enzymes leads to several malignant diseases. The inhibition of these enzymes using natural ligand molecules is an emerging technique to cure these diseases. The in vitro analysis of natural molecules, venenatine, spinosine, palmatine and taxodione are giving the best inhibition rate against p300 HAT enzyme. However, the detailed understanding of binding and the stability of these molecules with p300 HAT is not yet known. The aim of the present study is focused to determine the binding strength of the molecules from molecular dynamics simulation analysis. The docking analysis confirms that, the venenatine (-6.97 kcal/mol - conformer 8), spinosine (-6.52 kcal/mol conformer -10), palmatine (-5.72 kcal/mol conformer-3) and taxodione (-4.99 kcal/mol conformer-4) molecules form strong hydrogen bonding interactions with the key amino acid residues (Arg1410, Thr1411 and Trp1466) present in the active site of p300. In the molecular dynamics (MD) simulation, the spinosine retain these key interactions with the active site amino acid residues (Arg1410, Thr1411, and Trp1466) than venenatine and are stable throughout the simulation. The RMSD value of spinosine (0.5 to 1.3 Å) and venenatine (0.3 to 1.3 Å) are almost equal during the MD simulation. However, during the MD simulation, the intermolecular interaction between venenatine and the active site amino acid residues (Arg1410, Thr1411, and Trp1466) decreased on comparing with the spinosine-p300 interaction. The binding free energy of the spinosine (-15.30 kcal/mol) is relatively higher than the venenatine (-11.8 kcal/mol); this increment is attributed to the strong hydrogen bonding interactions of spinosine molecule with the active site amino acid residues of p300.
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Affiliation(s)
- Sivanandam Magudeeswaran
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Kumaradhas Poomani
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
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11
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Kim E, Zucconi BE, Wu M, Nocco SE, Meyers DJ, McGee JS, Venkatesh S, Cohen DL, Gonzalez EC, Ryu B, Cole PA, Alani RM. MITF Expression Predicts Therapeutic Vulnerability to p300 Inhibition in Human Melanoma. Cancer Res 2019; 79:2649-2661. [PMID: 30910803 PMCID: PMC6522293 DOI: 10.1158/0008-5472.can-18-2331] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 12/27/2018] [Accepted: 03/21/2019] [Indexed: 01/17/2023]
Abstract
Histone modifications, largely regulated by histone acetyltransferases (HAT) and histone deacetylases, have been recognized as major regulatory mechanisms governing human diseases, including cancer. Despite significant effort and recent advances, the mechanism by which the HAT and transcriptional coactivator p300 mediates tumorigenesis remains unclear. Here, we use a genetic and chemical approach to identify the microphthalmia-associated transcription factor (MITF) as a critical downstream target of p300 driving human melanoma growth. Direct transcriptional control of MITF by p300-dependent histone acetylation within proximal gene regulatory regions was coupled to cellular proliferation, suggesting a significant growth regulatory axis. Further analysis revealed forkhead box M1 (FOXM1) as a key effector of the p300-MITF axis driving cell growth that is selectively activated in human melanomas. Targeted chemical inhibition of p300 acetyltransferase activity using a potent and selective catalytic p300/CBP inhibitor demonstrated significant growth inhibitory effects in melanoma cells expressing high levels of MITF. Collectively, these data confirm the critical role of the p300-MITF-FOXM1 axis in melanoma and support p300 as a promising novel epigenetic therapeutic target in human melanoma. SIGNIFICANCE: These results show that MITF is a major downstream target of p300 in human melanoma whose expression is predictive of melanoma response to small-molecule inhibition of p300 HAT activity.
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Affiliation(s)
- Edward Kim
- Department of Dermatology, Boston University School of Medicine, 609 Albany Street, Boston, MA 02118
| | - Beth E. Zucconi
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Muzhou Wu
- Department of Dermatology, Boston University School of Medicine, 609 Albany Street, Boston, MA 02118
| | - Sarah E. Nocco
- Department of Dermatology, Boston University School of Medicine, 609 Albany Street, Boston, MA 02118
| | - David J. Meyers
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, 725 N. Wolfe Street, 316 Hunterian Building, Baltimore, Maryland 21205
| | - Jean S. McGee
- Department of Dermatology, Boston University School of Medicine, 609 Albany Street, Boston, MA 02118
| | - Samantha Venkatesh
- Department of Dermatology, Boston University School of Medicine, 609 Albany Street, Boston, MA 02118
| | - Daniel L. Cohen
- Department of Dermatology, Boston University School of Medicine, 609 Albany Street, Boston, MA 02118
| | - Estela C. Gonzalez
- Department of Dermatology, Boston University School of Medicine, 609 Albany Street, Boston, MA 02118
| | - Byungwoo Ryu
- Department of Dermatology, Boston University School of Medicine, 609 Albany Street, Boston, MA 02118
| | - Philip A. Cole
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115;,Corresponding Authors: Rhoda M. Alani 617-638-5517, Department of Dermatology, Boston University School of Medicine, 609 Albany Street, Boston, MA 02118 (Lead Contact), Philip A. Cole 617-525-5208, Division of Genetics, Department of Medicine, Brigham and Women’s Hospital; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Rhoda M. Alani
- Department of Dermatology, Boston University School of Medicine, 609 Albany Street, Boston, MA 02118;,Corresponding Authors: Rhoda M. Alani 617-638-5517, Department of Dermatology, Boston University School of Medicine, 609 Albany Street, Boston, MA 02118 (Lead Contact), Philip A. Cole 617-525-5208, Division of Genetics, Department of Medicine, Brigham and Women’s Hospital; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
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12
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Wang L, Beier UH, Akimova T, Dahiya S, Han R, Samanta A, Levine MH, Hancock WW. Histone/protein deacetylase inhibitor therapy for enhancement of Foxp3+ T-regulatory cell function posttransplantation. Am J Transplant 2018; 18:1596-1603. [PMID: 29603600 PMCID: PMC6035084 DOI: 10.1111/ajt.14749] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/20/2018] [Accepted: 03/22/2018] [Indexed: 01/25/2023]
Abstract
T-regulatory (Treg) cells are like other cells present throughout the body in being subject to biochemical modifications in response to extracellular signals. An important component of these responses involves changes in posttranslational modifications (PTMs) of histones and many nonhistone proteins, including phosphorylation/dephosphorylation, ubiquitination/deubiquitination, and acetylation/deacetylation. Foxp3, the key transcription factor of Tregs, is constantly being rapidly turned over, and a number of these PTMs determine its level of expression and activity. Of interest in the transplant setting, modulation of the acetylation or deacetylation of key lysine residues in Foxp3 can promote the stability and function, leading to increased Treg production and increased Treg suppressive activity. This mini-review focuses on recent data concerning the roles that histone/protein deacetylases (HDACs) play in control of Treg function, and how small molecule HDAC inhibitors can be used to promote Treg-dependent allograft survival in experimental models. These data are discussed in the light of increasing interest in the identification and clinical evaluation of isoform-selective HDAC inhibitors, and their potential application as tools to modulate Foxp3+ Treg cell numbers and function in transplant recipients.
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Affiliation(s)
- L. Wang
- Division of Transplant Immunology, Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - U. H. Beier
- Division of Nephrology, Department of Pediatrics, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA 19104, USA
| | - T. Akimova
- Division of Transplant Immunology, Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA,Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - S. Dahiya
- Division of Transplant Immunology, Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - R. Han
- Division of Transplant Immunology, Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - A. Samanta
- Division of Transplant Immunology, Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - M. H. Levine
- Division of Transplant Surgery, Department of Surgery, University of Pennsylvania, and Department of Surgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - W. W. Hancock
- Division of Transplant Immunology, Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA,Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
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13
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Lysine acetyltransferase inhibitors: structure-activity relationships and potential therapeutic implications. Future Med Chem 2018; 10:1067-1091. [PMID: 29676588 DOI: 10.4155/fmc-2017-0244] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Lysine acetylation is a post-translational modification of both histone and nonhistone proteins that is catalyzed by lysine acetyltransferases and plays a key role in numerous biological contexts. The dysregulation of this enzyme activity is implicated in many human pathologies such as cancer, neurological and inflammatory disorders. Many lysine acetyltransferase inhibitors (KATi) have been developed so far, but there is still the need for new, more potent, metabolically stable and selective KATi as chemical tools for studying KAT biology and/or as potential therapeutic agents. This review will examine the features of KAT enzymes and related diseases, with particular emphasis on KATi (bisubstrate analogs, natural compounds and synthetic derivatives), analyzing their mechanism of action, structure-activity relationships, pharmacokinetic/pharmacodynamic properties and potential future applications.
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14
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Shrimp JH, Grose C, Widmeyer SRT, Thorpe AL, Jadhav A, Meier JL. Chemical Control of a CRISPR-Cas9 Acetyltransferase. ACS Chem Biol 2018; 13:455-460. [PMID: 29309117 PMCID: PMC6320253 DOI: 10.1021/acschembio.7b00883] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Lysine acetyltransferases (KATs) play a critical role in the regulation of transcription and other genomic functions. However, a persistent challenge is the development of assays capable of defining KAT activity directly in living cells. Toward this goal, here we report the application of a previously reported dCas9-p300 fusion as a transcriptional reporter of KAT activity. First, we benchmark the activity of dCas9-p300 relative to other dCas9-based transcriptional activators and demonstrate its compatibility with second generation short guide RNA architectures. Next, we repurpose this technology to rapidly identify small molecule inhibitors of acetylation-dependent gene expression. These studies validate a recently reported p300 inhibitor chemotype and reveal a role for p300s bromodomain in dCas9-p300-mediated transcriptional activation. Comparison with other CRISPR-Cas9 transcriptional activators highlights the inherent ligand tunable nature of dCas9-p300 fusions, suggesting new opportunities for orthogonal gene expression control. Overall, our studies highlight dCas9-p300 as a powerful tool for studying gene expression mechanisms in which acetylation plays a causal role and provide a foundation for future applications requiring spatiotemporal control over acetylation at specific genomic loci.
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Affiliation(s)
- Jonathan H Shrimp
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Frederick, Maryland 21702, United States
| | - Carissa Grose
- Protein Expression Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. , Frederick, Maryland 21702, United States
| | - Stephanie R T Widmeyer
- Protein Expression Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. , Frederick, Maryland 21702, United States
| | - Abigail L Thorpe
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Frederick, Maryland 21702, United States
| | - Ajit Jadhav
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health , Rockville, Maryland 20850, United States
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Frederick, Maryland 21702, United States
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15
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He M, Han Z, Liu L, Zheng YG. Untersuchung der epigenetischen Funktionen von Lysin‐Acetyltransferasen mit Methoden der chemischen Biologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Maomao He
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics University of Georgia Athens Georgia 30602 USA
| | - Zhen Han
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics University of Georgia Athens Georgia 30602 USA
| | - Liang Liu
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics University of Georgia Athens Georgia 30602 USA
| | - Y. George Zheng
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics University of Georgia Athens Georgia 30602 USA
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16
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He M, Han Z, Liu L, Zheng YG. Chemical Biology Approaches for Investigating the Functions of Lysine Acetyltransferases. Angew Chem Int Ed Engl 2017; 57:1162-1184. [PMID: 28786225 DOI: 10.1002/anie.201704745] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Indexed: 12/20/2022]
Abstract
The side-chain acetylation of lysine residues in histones and non-histone proteins catalyzed by lysine acetyltransferases (KATs) represents a widespread posttranslational modification (PTM) in the eukaryotic cells. Lysine acetylation plays regulatory roles in major cellular pathways inside and outside the nucleus. In particular, KAT-mediated histone acetylation has an effect on all DNA-templated epigenetic processes. Aberrant expression and activation of KATs are commonly observed in human diseases, especially cancer. In recent years, the study of KAT functions in biology and disease has greatly benefited from chemical biology tools and strategies. In this Review, we present the past and current accomplishments in the design of chemical biology approaches for the interrogation of KAT activity and function. These methods and probes are classified according to their mechanisms of action and respective applications, with both strengths and limitations discussed.
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Affiliation(s)
- Maomao He
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics, University of Georgia, Athens, Georgia, 30602 (U, SA
| | - Zhen Han
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics, University of Georgia, Athens, Georgia, 30602 (U, SA
| | - Liang Liu
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics, University of Georgia, Athens, Georgia, 30602 (U, SA
| | - Y George Zheng
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics, University of Georgia, Athens, Georgia, 30602 (U, SA
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17
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CBP Regulates Recruitment and Release of Promoter-Proximal RNA Polymerase II. Mol Cell 2017; 68:491-503.e5. [PMID: 29056321 DOI: 10.1016/j.molcel.2017.09.031] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 07/13/2017] [Accepted: 09/21/2017] [Indexed: 11/21/2022]
Abstract
Transcription activation involves RNA polymerase II (Pol II) recruitment and release from the promoter into productive elongation, but how specific chromatin regulators control these steps is unclear. Here, we identify a novel activity of the histone acetyltransferase p300/CREB-binding protein (CBP) in regulating promoter-proximal paused Pol II. We find that Drosophila CBP inhibition results in "dribbling" of Pol II from the pause site to positions further downstream but impedes transcription through the +1 nucleosome genome-wide. Promoters strongly occupied by CBP and GAGA factor have high levels of paused Pol II, a unique chromatin signature, and are highly expressed regardless of cell type. Interestingly, CBP activity is rate limiting for Pol II recruitment to these highly paused promoters through an interaction with TFIIB but for transit into elongation by histone acetylation at other genes. Thus, CBP directly stimulates both Pol II recruitment and the ability to traverse the first nucleosome, thereby promoting transcription of most genes.
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18
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Role of the CBP catalytic core in intramolecular SUMOylation and control of histone H3 acetylation. Proc Natl Acad Sci U S A 2017. [PMID: 28630323 DOI: 10.1073/pnas.1703105114] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The histone acetyl transferases CREB-binding protein (CBP) and its paralog p300 play a critical role in numerous cellular processes. Dysregulation of their catalytic activity is associated with several human diseases. Previous work has elucidated the regulatory mechanisms of p300 acetyltransferase activity, but it is not known whether CBP activity is controlled similarly. Here, we present the crystal structure of the CBP catalytic core encompassing the bromodomain (BRD), CH2 (comprising PHD and RING), HAT, and ZZ domains at 2.4-Å resolution. The BRD, PHD, and HAT domains form an integral structural unit to which the RING and ZZ domains are flexibly attached. The structure of the apo-CBP HAT domain is similar to that of acyl-CoA-bound p300 HAT complexes and shows that the acetyl-CoA binding site is stably formed in the absence of cofactor. The BRD, PHD, and ZZ domains interact with small ubiquitin-like modifier 1 (SUMO-1) and Ubc9, and function as an intramolecular E3 ligase for SUMOylation of the cell cycle regulatory domain 1 (CRD1) of CBP, which is located adjacent to the BRD. In vitro HAT assays suggest that the RING domain, the autoregulatory loop (AL) within the HAT domain, and the ZZ domain do not directly influence catalytic activity, whereas the BRD is essential for histone H3 acetylation in nucleosomal substrates. Several lysine residues in the intrinsically disordered AL are autoacetylated by the HAT domain. Upon autoacetylation, acetyl-K1596 (Ac-K1596) binds intramolecularly to the BRD, competing with histones for binding to the BRD and acting as a negative regulator that inhibits histone H3 acetylation.
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19
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Haak AJ, Girtman MA, Ali MF, Carmona EM, Limper AH, Tschumperlin DJ. Phenylpyrrolidine structural mimics of pirfenidone lacking antifibrotic activity: A new tool for mechanism of action studies. Eur J Pharmacol 2017; 811:87-92. [PMID: 28576410 DOI: 10.1016/j.ejphar.2017.05.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 05/24/2017] [Accepted: 05/29/2017] [Indexed: 12/21/2022]
Abstract
Pirfenidone recently received FDA approval as one of the first two drugs designed to treat idiopathic pulmonary fibrosis. While the clinical data continues to support the efficacy of pirfenidone, the specific molecular mechanism of action of this drug has not been fully defined. From a chemical perspective the comparatively simple and lipophilic structure of pirfenidone combined with its administration at high doses, both experimentally and clinically, complicates some of the basic tenants of drug action and drug design. Our objective here was to identify a commercially available structural mimic of pirfenidone which retains key aspects of its physical chemical properties but does not display any of its antifibrotic effects. We tested these molecules using lung fibroblasts derived from patients with idiopathic pulmonary fibrosis and found phenylpyrrolidine based analogs of pirfenidone that were non-toxic and lacked antifibrotic activity even when applied at millimolar concentrations. Based on our findings, these molecules represent pharmacological tools for future studies delineating pirfenidone's mechanism of action.
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Affiliation(s)
- Andrew J Haak
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, United States
| | - Megan A Girtman
- Division of Pulmonary Critical Care and Internal Medicine, Department of Medicine, Mayo Clinic and Foundation, Rochester, MN 55905, United States
| | - Mohamed F Ali
- Thoracic Diseases Research Unit, Department of Medicine, Mayo Clinic and Foundation, Rochester, MN 55905, United States
| | - Eva M Carmona
- Thoracic Diseases Research Unit, Department of Medicine, Mayo Clinic and Foundation, Rochester, MN 55905, United States; Division of Pulmonary Critical Care and Internal Medicine, Department of Medicine, Mayo Clinic and Foundation, Rochester, MN 55905, United States
| | - Andrew H Limper
- Thoracic Diseases Research Unit, Department of Medicine, Mayo Clinic and Foundation, Rochester, MN 55905, United States; Division of Pulmonary Critical Care and Internal Medicine, Department of Medicine, Mayo Clinic and Foundation, Rochester, MN 55905, United States
| | - Daniel J Tschumperlin
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, United States.
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20
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Bolbat A, Schultz C. Recent developments of genetically encoded optical sensors for cell biology. Biol Cell 2016; 109:1-23. [PMID: 27628952 DOI: 10.1111/boc.201600040] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/06/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022]
Abstract
Optical sensors are powerful tools for live cell research as they permit to follow the location, concentration changes or activities of key cellular players such as lipids, ions and enzymes. Most of the current sensor probes are based on fluorescence which provides great spatial and temporal precision provided that high-end microscopy is used and that the timescale of the event of interest fits the response time of the sensor. Many of the sensors developed in the past 20 years are genetically encoded. There is a diversity of designs leading to simple or sometimes complicated applications for the use in live cells. Genetically encoded sensors began to emerge after the discovery of fluorescent proteins, engineering of their improved optical properties and the manipulation of their structure through application of circular permutation. In this review, we will describe a variety of genetically encoded biosensor concepts, including those for intensiometric and ratiometric sensors based on single fluorescent proteins, Forster resonance energy transfer-based sensors, sensors utilising bioluminescence, sensors using self-labelling SNAP- and CLIP-tags, and finally tetracysteine-based sensors. We focus on the newer developments and discuss the current approaches and techniques for design and application. This will demonstrate the power of using optical sensors in cell biology and will help opening the field to more systematic applications in the future.
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Affiliation(s)
- Andrey Bolbat
- European Molecular Biology Laboratory (EMBL), Cell Biology & Biophysics Unit, Heidelberg, 69117, Germany
| | - Carsten Schultz
- European Molecular Biology Laboratory (EMBL), Cell Biology & Biophysics Unit, Heidelberg, 69117, Germany
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21
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Lamparter CL, Winn LM. Valproic acid exposure decreases Cbp/p300 protein expression and histone acetyltransferase activity in P19 cells. Toxicol Appl Pharmacol 2016; 306:69-78. [PMID: 27381264 DOI: 10.1016/j.taap.2016.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/17/2016] [Accepted: 07/01/2016] [Indexed: 12/13/2022]
Abstract
The teratogenicity of the antiepileptic drug valproic acid (VPA) is well established and its inhibition of histone deacetylases (HDAC) is proposed as an initiating factor. Recently, VPA-mediated HDAC inhibition was demonstrated to involve transcriptional downregulation of histone acetyltransferases (HATs), which was proposed to compensate for the increased acetylation resulting from HDAC inhibition. Cbp and p300 are HATs required for embryonic development and deficiencies in either are associated with congenital malformations and embryolethality. The objective of the present study was to characterize Cbp/p300 following VPA exposure in P19 cells. Consistent with previous studies, exposure to 5mM VPA over 24h induced a moderate decrease in Cbp/p300 mRNA, which preceded a strong decrease in total cellular protein mediated by ubiquitin-proteasome degradation. Nuclear Cbp/p300 protein was also decreased following VPA exposure, although to a lesser extent. Total cellular and nuclear p300 HAT activity was reduced proportionately to p300 protein levels, however while total cellular HAT activity also decreased, nuclear HAT activity was unaffected. Using the Cbp/p300 HAT inhibitor C646, we demonstrated that HAT inhibition similarly affected many of the same endpoints as VPA, including increased reactive oxygen species and caspase-3 cleavage, the latter of which could be attenuated by pre-treatment with the antioxidant catalase. C646 exposure also decreased NF-κB/p65 protein, which was not due to reduced mRNA and was not attenuated with catalase pre-treatment. This study provides support for an adaptive HAT response following VPA exposure and suggests that reduced Cbp/p300 HAT activity could contribute to VPA-mediated alterations.
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Affiliation(s)
- Christina L Lamparter
- Department of Biomedical and Molecular Sciences, Graduate Program in Pharmacology and Toxicology, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Louise M Winn
- Department of Biomedical and Molecular Sciences, Graduate Program in Pharmacology and Toxicology, Queen's University, Kingston, Ontario K7L 3N6, Canada; School of Environmental Studies, Queen's University, Kingston, Ontario K7L 3N6, Canada.
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22
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Zucconi BE, Luef B, Xu W, Henry RA, Nodelman IM, Bowman GD, Andrews AJ, Cole PA. Modulation of p300/CBP Acetylation of Nucleosomes by Bromodomain Ligand I-CBP112. Biochemistry 2016; 55:3727-34. [PMID: 27332697 DOI: 10.1021/acs.biochem.6b00480] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The histone acetyltransferase (HAT) enzymes p300 and CBP are closely related paralogs that serve as transcriptional coactivators and have been found to be dysregulated in cancer and other diseases. p300/CBP is a multidomain protein and possesses a highly conserved bromodomain that has been shown to bind acetylated Lys residues in both proteins and various small molecules, including I-CBP112 and CBP30. Here we show that the ligand I-CBP112 can stimulate nucleosome acetylation up to 3-fold while CBP30 does not. Activation of p300/CBP by I-CBP112 is not observed with the isolated histone H3 substrate but requires a nucleosome substrate. I-CBP112 does not impact nucleosome acetylation by the isolated p300 HAT domain, and the effects of I-CBP112 on p300/CBP can be neutralized by CBP30, suggesting that I-CBP112 likely allosterically activates p300/CBP through bromodomain interactions. Using mass spectrometry and Western blots, we have found that I-CBP112 particularly stimulates acetylation of Lys18 of histone H3 (H3K18) in nucleosomes, an established in vivo site of p300/CBP. In addition, we show that I-CBP112 enhances H3K18 acetylation in acute leukemia and prostate cancer cells in a concentration range commensurate with its antiproliferative effects. Our findings extend the known pharmacology of bromodomain ligands in the regulation of p300/CBP and suggest a novel approach to modulating histone acetylation in cancer.
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Affiliation(s)
- Beth E Zucconi
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine , Baltimore, Maryland 21205, United States
| | - Birgit Luef
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine , Baltimore, Maryland 21205, United States
| | - Wei Xu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine , Baltimore, Maryland 21205, United States
| | - Ryan A Henry
- Department of Cancer Biology, Fox Chase Cancer Center , Philadelphia, Pennsylvania 19111, United States
| | - Ilana M Nodelman
- Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Gregory D Bowman
- Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Andrew J Andrews
- Department of Cancer Biology, Fox Chase Cancer Center , Philadelphia, Pennsylvania 19111, United States
| | - Philip A Cole
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine , Baltimore, Maryland 21205, United States
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23
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Montgomery DC, Garlick JM, Kulkarni RA, Kennedy S, Allali-Hassani A, Kuo YM, Andrews AJ, Wu H, Vedadi M, Meier JL. Global Profiling of Acetyltransferase Feedback Regulation. J Am Chem Soc 2016; 138:6388-91. [PMID: 27149119 DOI: 10.1021/jacs.6b03036] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lysine acetyltransferases (KATs) are key mediators of cell signaling. Methods capable of providing new insights into their regulation thus constitute an important goal. Here we report an optimized platform for profiling KAT-ligand interactions in complex proteomes using inhibitor-functionalized capture resins. This approach greatly expands the scope of KATs, KAT complexes, and CoA-dependent enzymes accessible to chemoproteomic methods. This enhanced profiling platform is then applied in the most comprehensive analysis to date of KAT inhibition by the feedback metabolite CoA. Our studies reveal that members of the KAT superfamily possess a spectrum of sensitivity to CoA and highlight NAT10 as a novel KAT that may be susceptible to metabolic feedback inhibition. This platform provides a powerful tool to define the potency and selectivity of reversible stimuli, such as small molecules and metabolites, that regulate KAT-dependent signaling.
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Affiliation(s)
- David C Montgomery
- 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
| | - Rhushikesh A Kulkarni
- Chemical Biology Laboratory, National Cancer Institute , Frederick, Maryland 21702, United States
| | - Steven Kennedy
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario MG5 1L7, Canada
| | | | - Yin-Ming Kuo
- Fox Chase Cancer Institute , Philadelphia, Pennsylvania 19111, United States
| | - Andrew J Andrews
- Fox Chase Cancer Institute , Philadelphia, Pennsylvania 19111, United States
| | - Hong Wu
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario MG5 1L7, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario MG5 1L7, Canada
| | - Jordan L Meier
- Chemical Biology Laboratory, National Cancer Institute , Frederick, Maryland 21702, United States.,Department of Pharmacology and Toxicology, University of Toronto , Toronto, Ontario, M5S 1A8, Canada
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24
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Nakaoka S, Sasaki K, Ito A, Nakao Y, Yoshida M. A Genetically Encoded FRET Probe to Detect Intranucleosomal Histone H3K9 or H3K14 Acetylation Using BRD4, a BET Family Member. ACS Chem Biol 2016; 11:729-33. [PMID: 25946208 DOI: 10.1021/cb501046t] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Acetylation is a well-characterized histone modification, which plays important roles in controlling epigenetic gene expression, and its malfunction is tightly associated with cancer. By taking advantage of the specific binding of BRD4 to acetylated lysine residues, we developed a FRET-based probe for visualizing histone H3 acetylation in living cells. BRD4, a protein known to be involved in acute myeloid leukemia and nuclear protein in testis midline carcinoma, recognizes the acetylation of histone H3 via its bromodomains. The probe exhibited a significant change in FRET signaling that was dependent on histone H3 acetylation. Mutagenesis studies revealed that an increase in the emission ratio reflected the acetylation of either K9 or K14 of histone H3 within the probe. Since BRD4 has increasingly drawn attention as a new anticancer drug target, we demonstrated that the developed fluorescent probe will also serve as a powerful tool to evaluate BRD4 inhibitors in living cells.
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Affiliation(s)
- Shiho Nakaoka
- Chemical
Genetics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Department
of Chemistry and Biochemistry, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Kazuki Sasaki
- Chemical
Genetics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Chemical Genomics Research Group, RIKEN Center for
Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akihiro Ito
- Chemical
Genetics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Chemical Genomics Research Group, RIKEN Center for
Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoichi Nakao
- Department
of Chemistry and Biochemistry, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Minoru Yoshida
- Chemical
Genetics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Chemical Genomics Research Group, RIKEN Center for
Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- JST, CREST Research Project, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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25
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Li P, Han Y, Li Y, Zhu R, Wang H, Nie Z, Yao S. Bioanalytical approaches for the detection of protein acetylation-related enzymes. Anal Bioanal Chem 2016; 408:2659-68. [DOI: 10.1007/s00216-016-9304-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/26/2015] [Accepted: 01/04/2016] [Indexed: 10/22/2022]
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26
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Simon RP, Robaa D, Alhalabi Z, Sippl W, Jung M. KATching-Up on Small Molecule Modulators of Lysine Acetyltransferases. J Med Chem 2016; 59:1249-70. [PMID: 26701186 DOI: 10.1021/acs.jmedchem.5b01502] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The reversible acetylation of lysines is one of the best characterized epigenetic modifications. Its involvement in many key physiological and pathological processes has been documented in numerous studies. Lysine deacetylases (KDACs) and acetyltransferases (KATs) maintain the acetylation equilibrium at histones but also many other proteins. Besides acetylation, also other acyl groups are reversibly installed at the side chain of lysines in proteins. Because of their involvement in disease, KDACs and KATs were proposed to be promising drug targets, and for KDACs, indeed, five inhibitors are now approved for human use. While there is a similar level of evidence for the potential of KATs as drug targets, no inhibitor is in clinical trials. Here, we review the evidence for the diverse roles of KATs in disease pathology, provide an overview of structural features and the available modulators, including those targeting the bromodomains of KATs, and present an outlook.
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Affiliation(s)
- Roman P Simon
- Institute of Pharmaceutical Sciences, University of Freiburg , Albertstraße 25, Freiburg 79104, Germany
| | - Dina Robaa
- Department of Pharmaceutical Chemistry, University Halle-Wittenberg , Halle/Saale 06120, Germany
| | - Zayan Alhalabi
- Department of Pharmaceutical Chemistry, University Halle-Wittenberg , Halle/Saale 06120, Germany
| | - Wolfgang Sippl
- Department of Pharmaceutical Chemistry, University Halle-Wittenberg , Halle/Saale 06120, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg , Albertstraße 25, Freiburg 79104, Germany
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27
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Han Y, Li H, Hu Y, Li P, Wang H, Nie Z, Yao S. Time-Resolved Luminescence Biosensor for Continuous Activity Detection of Protein Acetylation-Related Enzymes Based on DNA-Sensitized Terbium(III) Probes. Anal Chem 2015; 87:9179-85. [DOI: 10.1021/acs.analchem.5b01338] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yitao Han
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People’s Republic of China
| | - Hao Li
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People’s Republic of China
| | - Yufang Hu
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People’s Republic of China
| | - Pei Li
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People’s Republic of China
| | - Huixia Wang
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People’s Republic of China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People’s Republic of China
| | - Shouzhuo Yao
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People’s Republic of China
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28
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Affiliation(s)
| | - Philip A. Cole
- Department
of Pharmacology
and Molecular Sciences, The Johns Hopkins
University School of Medicine, 725 North Wolfe Street, Hunterian 316, Baltimore, Maryland 21205, United States
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29
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Milite C, Feoli A, Sasaki K, La Pietra V, Balzano AL, Marinelli L, Mai A, Novellino E, Castellano S, Tosco A, Sbardella G. A novel cell-permeable, selective, and noncompetitive inhibitor of KAT3 histone acetyltransferases from a combined molecular pruning/classical isosterism approach. J Med Chem 2015; 58:2779-98. [PMID: 25730130 DOI: 10.1021/jm5019687] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Selective inhibitors of the two paralogue KAT3 acetyltransferases (CBP and p300) may serve not only as precious chemical tools to investigate the role of these enzymes in physiopathological mechanisms but also as lead structures for the development of further antitumor agents. After the application of a molecular pruning approach to the hardly optimizable and not very cell-permeable garcinol core structure, we prepared many analogues that were screened for their inhibitory effects using biochemical and biophysical (SPR) assays. Further optimization led to the discovery of the benzylidenebarbituric acid derivative 7h (EML425) as a potent and selective reversible inhibitor of CBP/p300, noncompetitive versus both acetyl-CoA and a histone H3 peptide, and endowed with good cell permeability. Furthermore, in human leukemia U937 cells, it induced a marked and time-dependent reduction in the acetylation of lysine H4K5 and H3K9, a marked arrest in the G0/G1 phase and a significant increase in the hypodiploid nuclei percentage.
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Affiliation(s)
- Ciro Milite
- †Epigenetic Med Chem Lab, Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
| | - Alessandra Feoli
- †Epigenetic Med Chem Lab, Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
| | - Kazuki Sasaki
- ‡Chemical Genetics Laboratory, RIKEN Advanced Science Institute, Wako, Saitama 351-0198, Japan.,§Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Valeria La Pietra
- ∥Dipartimento di Farmacia, Università di Napoli "Federico II" Via D. Montesano 49, I-80131 Naples, Italy
| | - Amodio Luca Balzano
- †Epigenetic Med Chem Lab, Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
| | - Luciana Marinelli
- ∥Dipartimento di Farmacia, Università di Napoli "Federico II" Via D. Montesano 49, I-80131 Naples, Italy
| | - Antonello Mai
- ⊥Dipartimento di Chimica e Tecnologie del Farmaco, "Sapienza" Università di Roma, P.le A. Moro 5, I-00185 Rome, Italy
| | - Ettore Novellino
- ∥Dipartimento di Farmacia, Università di Napoli "Federico II" Via D. Montesano 49, I-80131 Naples, Italy
| | - Sabrina Castellano
- †Epigenetic Med Chem Lab, Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy.,#Dipartimento di Medicina e Chirurgia, Università degli Studi di Salerno, Via Salvador Allende, I-84081 Baronissi, Salerno, Italy
| | - Alessandra Tosco
- †Epigenetic Med Chem Lab, Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
| | - Gianluca Sbardella
- †Epigenetic Med Chem Lab, Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
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30
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Dahlin JL, Nissink JWM, Strasser JM, Francis S, Higgins L, Zhou H, Zhang Z, Walters MA. PAINS in the assay: chemical mechanisms of assay interference and promiscuous enzymatic inhibition observed during a sulfhydryl-scavenging HTS. J Med Chem 2015; 58:2091-113. [PMID: 25634295 PMCID: PMC4360378 DOI: 10.1021/jm5019093] [Citation(s) in RCA: 244] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Significant resources in early drug discovery are spent unknowingly pursuing artifacts and promiscuous bioactive compounds, while understanding the chemical basis for these adverse behaviors often goes unexplored in pursuit of lead compounds. Nearly all the hits from our recent sulfhydryl-scavenging high-throughput screen (HTS) targeting the histone acetyltransferase Rtt109 were such compounds. Herein, we characterize the chemical basis for assay interference and promiscuous enzymatic inhibition for several prominent chemotypes identified by this HTS, including some pan-assay interference compounds (PAINS). Protein mass spectrometry and ALARM NMR confirmed these compounds react covalently with cysteines on multiple proteins. Unfortunately, compounds containing these chemotypes have been published as screening actives in reputable journals and even touted as chemical probes or preclinical candidates. Our detailed characterization and identification of such thiol-reactive chemotypes should accelerate triage of nuisance compounds, guide screening library design, and prevent follow-up on undesirable chemical matter.
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Affiliation(s)
- Jayme L Dahlin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine , Rochester, Minnesota 55905, United States
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31
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Abstract
![]()
Long
known for their role in histone acetylation, recent studies
have demonstrated that lysine acetyltransferases also carry out distinct
“orphan” functions. These activities impact a wide range
of biological phenomena including metabolism, RNA modification, nuclear
morphology, and mitochondrial function. Here, we review the discovery
and characterization of orphan lysine acetyltransferase functions.
In addition to highlighting the evidence and biological role for these
functions in human disease, we discuss the part emerging chemical
tools may play in investigating this versatile enzyme superfamily.
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Affiliation(s)
- David C. Montgomery
- National Cancer Institute, Chemical Biology Laboratory, Frederick, Maryland 21702-1201, United States
| | - Alexander W. Sorum
- National Cancer Institute, Chemical Biology Laboratory, Frederick, Maryland 21702-1201, United States
| | - Jordan L. Meier
- National Cancer Institute, Chemical Biology Laboratory, Frederick, Maryland 21702-1201, United States
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32
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Castellano S, Milite C, Feoli A, Viviano M, Mai A, Novellino E, Tosco A, Sbardella G. Identification of structural features of 2-alkylidene-1,3-dicarbonyl derivatives that induce inhibition and/or activation of histone acetyltransferases KAT3B/p300 and KAT2B/PCAF. ChemMedChem 2014; 10:144-57. [PMID: 25333655 DOI: 10.1002/cmdc.201402371] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Indexed: 12/23/2022]
Abstract
Dysregulation of the activity of lysine acetyltransferases (KATs) is related to a variety of diseases and/or pathological cellular states; however, their role remains unclear. Therefore, the development of selective modulators of these enzymes is of paramount importance, because these molecules could be invaluable tools for assessing the importance of KATs in several pathologies. We recently found that diethyl pentadecylidenemalonate (SPV106) possesses a previously unobserved inhibitor/activator activity profile against protein acetyltransferases. Herein, we report that manipulation of the carbonyl functions of a series of analogues of SPV106 yielded different activity profiles against KAT2B and KAT3B (pure KAT2B activator, pan-inhibitor, or mixed KAT2B activator/KAT3B inhibitor). Among the novel compounds, a few derivatives may be useful chemical tools for studying the mechanism of lysine acetylation and its implications in physiological and/or pathological processes.
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Affiliation(s)
- Sabrina Castellano
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (SA) (Italy)
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33
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Cîrneci D, Silaghi-Dumitrescu R. Learning tasks as a possible treatment for DNA lesions induced by oxidative stress in hippocampal neurons. Neural Regen Res 2014; 8:3063-70. [PMID: 25206627 PMCID: PMC4146205 DOI: 10.3969/j.issn.1673-5374.2013.32.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 09/26/2013] [Indexed: 11/18/2022] Open
Abstract
Reactive oxygen species have been implicated in conditions ranging from cardiovascular dysfunc-tion, arthritis, cancer, to aging and age-related disorders. The organism developed several path-ways to counteract these effects, with base excision repair being responsible for repairing one of the major base lesions (8-oxoG) in all organisms. Epidemiological evidence suggests that cognitive stimulation makes the brain more resilient to damage or degeneration. Recent studies have linked enriched environment to reduction of oxidative stressin neurons of mice with Alzheimer's dis-ease-like disease, but given its complexity it is not clear what specific aspect of enriched environ-ment has therapeutic effects. Studies from molecular biology have shown that the protein p300, which is a transcription co-activator required for consolidation of memories during specific learning tasks, is at the same time involved in DNA replication and repair, playing a central role in the long-patch pathway of base excision repair. Based on the evidence, we propose that learning tasks such as novel object recognition could be tested as possible methods of base excision repair faci-litation, hence inducing DNA repair in the hippocampal neurons. If this method proves to be effective, it could be the start for designing similar tasks for humans, as a behavioral therapeutic complement to the classical drug-based therapy in treating neurodegenerative disorders. This review presents the current status of therapeutic methods used in treating neurodegenerative diseases induced by reactive oxygen species and proposes a new approach based on existing data.
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Affiliation(s)
- Dragoş Cîrneci
- Brain Research Institute, Synergon Consulting, Bucharest 010094, Romania
| | - Radu Silaghi-Dumitrescu
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj Napoca, 400165, Romania
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34
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Sato Y, Mukai M, Ueda J, Muraki M, Stasevich TJ, Horikoshi N, Kujirai T, Kita H, Kimura T, Hira S, Okada Y, Hayashi-Takanaka Y, Obuse C, Kurumizaka H, Kawahara A, Yamagata K, Nozaki N, Kimura H. Genetically encoded system to track histone modification in vivo. Sci Rep 2014; 3:2436. [PMID: 23942372 PMCID: PMC3743053 DOI: 10.1038/srep02436] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 07/29/2013] [Indexed: 01/25/2023] Open
Abstract
Post-translational histone modifications play key roles in gene regulation, development, and differentiation, but their dynamics in living organisms remain almost completely unknown. To address this problem, we developed a genetically encoded system for tracking histone modifications by generating fluorescent modification-specific intracellular antibodies (mintbodies) that can be expressed in vivo. To demonstrate, an H3 lysine 9 acetylation specific mintbody (H3K9ac-mintbody) was engineered and stably expressed in human cells. In good agreement with the localization of its target acetylation, H3K9ac-mintbody was enriched in euchromatin, and its kinetics measurably changed upon treatment with a histone deacetylase inhibitor. We also generated transgenic fruit fly and zebrafish stably expressing H3K9ac-mintbody for in vivo tracking. Dramatic changes in H3K9ac-mintbody localization during Drosophila embryogenesis could highlight enhanced acetylation at the start of zygotic transcription around mitotic cycle 7. Together, this work demonstrates the broad potential of mintbody and lays the foundation for epigenetic analysis in vivo.
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Affiliation(s)
- Yuko Sato
- 1] Graduate School of Frontier Biosciences, Osaka University, Suita. 565-0871, Japan [2] JST, CREST, Suita. 565-0871, Japan
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35
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Hertel F, Zhang J. Monitoring of post-translational modification dynamics with genetically encoded fluorescent reporters. Biopolymers 2014; 101:180-7. [PMID: 23576192 PMCID: PMC3883948 DOI: 10.1002/bip.22254] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 04/01/2013] [Indexed: 11/06/2022]
Abstract
Post-translational modifications (PTMs) of proteins are essential mechanisms for virtually all dynamic processes within cellular signaling networks. Genetically encoded reporters based on fluorescent proteins (FPs) are powerful tools for spatiotemporal visualization of cellular parameters. Consequently, commonly used modular biosensor designs have been adapted to generate several protein-based indicators for monitoring various PTMs or the activity of corresponding enzymes in living cells, providing new biological insights into dynamics and regulatory functions of individual PTMs. In this review, we describe the application of general design strategies focusing on PTMs and discuss important considerations for engineering feasible indicators depending on the purpose. Moreover, we present developments and enhancements of PTM biosensors from selected studies and give an outlook on future perspectives of this versatile approach.
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Affiliation(s)
- Fabian Hertel
- The Johns Hopkins University School of Medicine, Department of Pharmacology and Molecular Sciences, Baltimore, MD 21205, USA
| | - Jin Zhang
- The Johns Hopkins University School of Medicine, Department of Pharmacology and Molecular Sciences, Baltimore, MD 21205, USA
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36
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Abstract
Chromatin modifications have been well-established to play a critical role in the regulation of genome function. Many of these modifications are introduced and removed by enzymes that utilize cofactors derived from primary metabolism. Recently, it has been shown that endogenous cofactors and metabolites can regulate the activity of chromatin-modifying enzymes, providing a direct link between the metabolic state of the cell and epigenetics. Here we review metabolic mechanisms of epigenetic regulation with an emphasis on their role in cancer. Focusing on three core mechanisms, we detail and draw parallels between metabolic and chemical strategies to modulate epigenetic signaling, and highlight opportunities for chemical biologists to help shape our knowledge of this emerging phenomenon. Continuing to integrate our understanding of metabolic and genomic regulatory mechanisms may help elucidate the role of nutrition in diseases such as cancer, while also providing a basis for new approaches to modulate epigenetic signaling for therapeutic benefit.
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Affiliation(s)
- Jordan L. Meier
- Chemical
Genomics Section,
Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
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37
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Schneider A, Chatterjee S, Bousiges O, Selvi BR, Swaminathan A, Cassel R, Blanc F, Kundu TK, Boutillier AL. Acetyltransferases (HATs) as targets for neurological therapeutics. Neurotherapeutics 2013; 10:568-88. [PMID: 24006237 PMCID: PMC3805875 DOI: 10.1007/s13311-013-0204-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The acetylation of histone and non-histone proteins controls a great deal of cellular functions, thereby affecting the entire organism, including the brain. Acetylation modifications are mediated through histone acetyltransferases (HAT) and deacetylases (HDAC), and the balance of these enzymes regulates neuronal homeostasis, maintaining the pre-existing acetyl marks responsible for the global chromatin structure, as well as regulating specific dynamic acetyl marks that respond to changes and facilitate neurons to encode and strengthen long-term events in the brain circuitry (e.g., memory formation). Unfortunately, the dysfunction of these finely-tuned regulations might lead to pathological conditions, and the deregulation of the HAT/HDAC balance has been implicated in neurological disorders. During the last decade, research has focused on HDAC inhibitors that induce a histone hyperacetylated state to compensate acetylation deficits. The use of these inhibitors as a therapeutic option was efficient in several animal models of neurological disorders. The elaboration of new cell-permeant HAT activators opens a new era of research on acetylation regulation. Although pathological animal models have not been tested yet, HAT activator molecules have already proven to be beneficial in ameliorating brain functions associated with learning and memory, and adult neurogenesis in wild-type animals. Thus, HAT activator molecules contribute to an exciting area of research.
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Affiliation(s)
- Anne Schneider
- />Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR7364, Université de Strasbourg-CNRS, GDR CNRS 2905, Faculté de Psychologie, 12 rue Goethe, 67000 Strasbourg, France
| | - Snehajyoti Chatterjee
- />Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR7364, Université de Strasbourg-CNRS, GDR CNRS 2905, Faculté de Psychologie, 12 rue Goethe, 67000 Strasbourg, France
| | - Olivier Bousiges
- />Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR7364, Université de Strasbourg-CNRS, GDR CNRS 2905, Faculté de Psychologie, 12 rue Goethe, 67000 Strasbourg, France
| | - B. Ruthrotha Selvi
- />Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064 India
| | - Amrutha Swaminathan
- />Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064 India
| | - Raphaelle Cassel
- />Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR7364, Université de Strasbourg-CNRS, GDR CNRS 2905, Faculté de Psychologie, 12 rue Goethe, 67000 Strasbourg, France
| | - Frédéric Blanc
- />Service de Neuropsychologie and CMRR (Centre Mémoire de Ressources et de recherche) Laboratoire ICube, Université de Strasbourg, CNRS, équipe IMIS-Neurocrypto, 1, place de l’Hôpital, 67000 Strasbourg, France
| | - Tapas K. Kundu
- />Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064 India
| | - Anne-Laurence Boutillier
- />Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR7364, Université de Strasbourg-CNRS, GDR CNRS 2905, Faculté de Psychologie, 12 rue Goethe, 67000 Strasbourg, France
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38
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Modak R, Basha J, Bharathy N, Maity K, Mizar P, Bhat AV, Vasudevan M, Rao VK, Kok WK, Natesh N, Taneja R, Kundu TK. Probing p300/CBP associated factor (PCAF)-dependent pathways with a small molecule inhibitor. ACS Chem Biol 2013; 8:1311-23. [PMID: 23570531 DOI: 10.1021/cb4000597] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PCAF (KAT2B) belongs to the GNAT family of lysine acetyltransferases (KAT) and specifically acetylates the histone H3K9 residue and several nonhistone proteins. PCAF is also a transcriptional coactivator. Due to the lack of a PCAF KAT-specific small molecule inhibitor, the exclusive role of the acetyltransferase activity of PCAF is not well understood. Here, we report that a natural compound of the hydroxybenzoquinone class, embelin, specifically inhibits H3Lys9 acetylation in mice and inhibits recombinant PCAF-mediated acetylation with near complete specificity in vitro. Furthermore, using embelin, we have identified the gene networks that are regulated by PCAF during muscle differentiation, further highlighting the broader regulatory functions of PCAF in muscle differentiation in addition to the regulation via MyoD acetylation.
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Affiliation(s)
- Rahul Modak
- Transcription
and Disease Laboratory,
Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore,
India 560064
| | - Jeelan Basha
- Transcription
and Disease Laboratory,
Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore,
India 560064
| | - Narendra Bharathy
- Department
of Physiology, Yong
Loo Lin School of Medicine, Block MD9, 2 Medical Drive, National University of Singapore, Singapore 117597
| | - Koustav Maity
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Pushpak Mizar
- Transcription
and Disease Laboratory,
Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore,
India 560064
| | - Akshay V. Bhat
- Transcription
and Disease Laboratory,
Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore,
India 560064
| | - Madavan Vasudevan
- Bionivid Technology [P] Ltd, 401 - 4 AB Cross, 1st Main, Kasturi Nagar,
East of NGEF, Bangalore, India 560043
| | - Vinay Kumar Rao
- Department
of Physiology, Yong
Loo Lin School of Medicine, Block MD9, 2 Medical Drive, National University of Singapore, Singapore 117597
| | - Wai Kay Kok
- Department
of Physiology, Yong
Loo Lin School of Medicine, Block MD9, 2 Medical Drive, National University of Singapore, Singapore 117597
| | - Nagashayana Natesh
- Central Government Health Scheme
Dispensary Number 3, Basavanagudi, Bangalore, India
| | - Reshma Taneja
- Department
of Physiology, Yong
Loo Lin School of Medicine, Block MD9, 2 Medical Drive, National University of Singapore, Singapore 117597
| | - Tapas K. Kundu
- Transcription
and Disease Laboratory,
Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore,
India 560064
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39
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Socher E, Grossmann TN. Chemical biology 2012: from drug targets to biological systems and back. Chembiochem 2013. [PMID: 23184865 DOI: 10.1002/cbic.201200697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Multiple sites sharing a common target: This year's EMBO conference on chemical biology encouraged over 340 researchers to come to Heidelberg, Germany, and discuss the use of diverse chemical strategies and tools to investigate biological questions and better understand cellular processes.
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Affiliation(s)
- Elke Socher
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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