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de Almeida LGN, Thode H, Eslambolchi Y, Chopra S, Young D, Gill S, Devel L, Dufour A. Matrix Metalloproteinases: From Molecular Mechanisms to Physiology, Pathophysiology, and Pharmacology. Pharmacol Rev 2022; 74:712-768. [PMID: 35738680 DOI: 10.1124/pharmrev.121.000349] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The first matrix metalloproteinase (MMP) was discovered in 1962 from the tail of a tadpole by its ability to degrade collagen. As their name suggests, matrix metalloproteinases are proteases capable of remodeling the extracellular matrix. More recently, MMPs have been demonstrated to play numerous additional biologic roles in cell signaling, immune regulation, and transcriptional control, all of which are unrelated to the degradation of the extracellular matrix. In this review, we will present milestones and major discoveries of MMP research, including various clinical trials for the use of MMP inhibitors. We will discuss the reasons behind the failures of most MMP inhibitors for the treatment of cancer and inflammatory diseases. There are still misconceptions about the pathophysiological roles of MMPs and the best strategies to inhibit their detrimental functions. This review aims to discuss MMPs in preclinical models and human pathologies. We will discuss new biochemical tools to track their proteolytic activity in vivo and ex vivo, in addition to future pharmacological alternatives to inhibit their detrimental functions in diseases. SIGNIFICANCE STATEMENT: Matrix metalloproteinases (MMPs) have been implicated in most inflammatory, autoimmune, cancers, and pathogen-mediated diseases. Initially overlooked, MMP contributions can be both beneficial and detrimental in disease progression and resolution. Thousands of MMP substrates have been suggested, and a few hundred have been validated. After more than 60 years of MMP research, there remain intriguing enigmas to solve regarding their biological functions in diseases.
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Affiliation(s)
- Luiz G N de Almeida
- Departments of Physiology and Pharmacology and Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada (L.G.N.d.A., Y.E., S.C., D.Y., A.D.); Department of Physiology and Pharmacology, University of Western Ontario, London, Canada (S.G., H.T.); and Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Santé, Gif-sur-Yvette, France (L.D.)
| | - Hayley Thode
- Departments of Physiology and Pharmacology and Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada (L.G.N.d.A., Y.E., S.C., D.Y., A.D.); Department of Physiology and Pharmacology, University of Western Ontario, London, Canada (S.G., H.T.); and Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Santé, Gif-sur-Yvette, France (L.D.)
| | - Yekta Eslambolchi
- Departments of Physiology and Pharmacology and Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada (L.G.N.d.A., Y.E., S.C., D.Y., A.D.); Department of Physiology and Pharmacology, University of Western Ontario, London, Canada (S.G., H.T.); and Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Santé, Gif-sur-Yvette, France (L.D.)
| | - Sameeksha Chopra
- Departments of Physiology and Pharmacology and Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada (L.G.N.d.A., Y.E., S.C., D.Y., A.D.); Department of Physiology and Pharmacology, University of Western Ontario, London, Canada (S.G., H.T.); and Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Santé, Gif-sur-Yvette, France (L.D.)
| | - Daniel Young
- Departments of Physiology and Pharmacology and Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada (L.G.N.d.A., Y.E., S.C., D.Y., A.D.); Department of Physiology and Pharmacology, University of Western Ontario, London, Canada (S.G., H.T.); and Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Santé, Gif-sur-Yvette, France (L.D.)
| | - Sean Gill
- Departments of Physiology and Pharmacology and Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada (L.G.N.d.A., Y.E., S.C., D.Y., A.D.); Department of Physiology and Pharmacology, University of Western Ontario, London, Canada (S.G., H.T.); and Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Santé, Gif-sur-Yvette, France (L.D.)
| | - Laurent Devel
- Departments of Physiology and Pharmacology and Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada (L.G.N.d.A., Y.E., S.C., D.Y., A.D.); Department of Physiology and Pharmacology, University of Western Ontario, London, Canada (S.G., H.T.); and Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Santé, Gif-sur-Yvette, France (L.D.)
| | - Antoine Dufour
- Departments of Physiology and Pharmacology and Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada (L.G.N.d.A., Y.E., S.C., D.Y., A.D.); Department of Physiology and Pharmacology, University of Western Ontario, London, Canada (S.G., H.T.); and Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Santé, Gif-sur-Yvette, France (L.D.)
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Menna M, Fiorentino F, Marrocco B, Lucidi A, Tomassi S, Cilli D, Romanenghi M, Cassandri M, Pomella S, Pezzella M, Del Bufalo D, Zeya Ansari MS, Tomašević N, Mladenović M, Viviano M, Sbardella G, Rota R, Trisciuoglio D, Minucci S, Mattevi A, Rotili D, Mai A. Novel non-covalent LSD1 inhibitors endowed with anticancer effects in leukemia and solid tumor cellular models. Eur J Med Chem 2022; 237:114410. [DOI: 10.1016/j.ejmech.2022.114410] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/22/2022]
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Jan S, Dar MI, Wani R, Sandey J, Mushtaq I, Lateef S, Syed SH. Targeting EHMT2/ G9a for cancer therapy: Progress and perspective. Eur J Pharmacol 2020; 893:173827. [PMID: 33347828 DOI: 10.1016/j.ejphar.2020.173827] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/12/2020] [Accepted: 12/16/2020] [Indexed: 12/11/2022]
Abstract
Euchromatic histone lysine methyltransferase-2, also known as G9a, is a ubiquitously expressed SET domain-containing histone lysine methyltransferase linked with both facultative and constitutive heterochromatin formation and transcriptional repression. It is an essential developmental gene and reported to play role in embryonic development, establishment of proviral silencing in ES cells, tumor cell growth, metastasis, T-cell immune response, cocaine induced neural plasticity and cognition and adaptive behavior. It is mainly responsible for carrying out mono, di and tri methylation of histone H3K9 in euchromatin. G9a levels are elevated in many cancers and its selective inhibition is known to reduce the cell growth and induce autophagy, apoptosis and senescence. We carried out a thorough search of online literature databases including Pubmed, Scopus, Journal websites, Clinical trials etc to gather the maximum possible information related to the G9a. The main messages from the cited papers are presented in a systematic manner. Chemical structures were drawn by Chemdraw software. In this review, we shed light on current understanding of structure and biological activity of G9a, the molecular events directing its targeting to genomic regions and its post-translational modification. Finally, we discuss the current strategies to target G9a in different cancers and evaluate the available compounds and agents used to inhibit G9a functions. The review provides the present status and future directions of research in targeting G9a and provides the basis to persuade the development of novel strategies to target G9a -related effects in cancer cells.
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Affiliation(s)
- Suraya Jan
- CSIR, Indian Institute of Integrative Medicine, Sanatnagar, 190005, Srinagar, Kashmir, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Mohd Ishaq Dar
- CSIR, Indian Institute of Integrative Medicine, Sanatnagar, 190005, Srinagar, Kashmir, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rubiada Wani
- CSIR, Indian Institute of Integrative Medicine, Sanatnagar, 190005, Srinagar, Kashmir, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jagjeet Sandey
- CSIR, Indian Institute of Integrative Medicine, Sanatnagar, 190005, Srinagar, Kashmir, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Iqra Mushtaq
- CSIR, Indian Institute of Integrative Medicine, Sanatnagar, 190005, Srinagar, Kashmir, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sammar Lateef
- CSIR, Indian Institute of Integrative Medicine, Sanatnagar, 190005, Srinagar, Kashmir, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sajad Hussain Syed
- CSIR, Indian Institute of Integrative Medicine, Sanatnagar, 190005, Srinagar, Kashmir, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Screening of inhibitors against histone demethylation jumonji domain-containing protein 3 by capillary electrophoresis. J Chromatogr A 2019; 1613:460625. [PMID: 31668999 DOI: 10.1016/j.chroma.2019.460625] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 11/21/2022]
Abstract
Jumonji domain-containing proteins (JMJDs) play an important role in the epigenetic regulation of gene expression. Aberrant regulation of histone modification has been observed in the progression of a variety of diseases, such as neurological disorders and cancer. Therefore, discovery of selective modulators of JMJDs is very attractive in new drug discovery. Herein, a simple capillary electrophoresis (CE) method was developed for screening of inhibitors against JMJD3. A known JMJD3 inhibitor GSK-J1, 5-carboxyfluorescein labeled substrate peptide with an amino acid sequence of KAPRKQLATKAARK(me3)SAPATGG (truncated from histone H3), as well as a small chemical library composed of 37 purified natural compounds and 30 natural extracts were used for method development and validation. The separation of substrate from its demethylated product was achieved by addition of polycation hexadimethrine bromide (HDB) in the running buffer. The enzyme activity was thus assayed accurately through separating the demethylated product from the substrate and then measuring the peak area of the product. The enzyme inhibition can be read out by comparing the peak area of the demethylated product obtained in the present of inhibitors and that of the negative control in the absence of any inhibitor. The merit of the method is proved by discovering two new JMJD3 inhibitors: salvianic acid A and puerarin 6''-O-xyloside.
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King SL, Goth CK, Eckhard U, Joshi HJ, Haue AD, Vakhrushev SY, Schjoldager KT, Overall CM, Wandall HH. TAILS N-terminomics and proteomics reveal complex regulation of proteolytic cleavage by O-glycosylation. J Biol Chem 2018; 293:7629-7644. [PMID: 29593093 PMCID: PMC5961060 DOI: 10.1074/jbc.ra118.001978] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/27/2018] [Indexed: 12/31/2022] Open
Abstract
Proteolytic processing is an irreversible post-translational modification functioning as a ubiquitous regulator of cellular activity. Protease activity is tightly regulated via control of gene expression, enzyme and substrate compartmentalization, zymogen activation, enzyme inactivation, and substrate availability. Emerging evidence suggests that proteolysis can also be regulated by substrate glycosylation and that glycosylation of individual sites on a substrate can decrease or, in rare cases, increase its sensitivity to proteolysis. Here, we investigated the relationship between site-specific, mucin-type (or GalNAc-type) O-glycosylation and proteolytic cleavage of extracellular proteins. Using in silico analysis, we found that O-glycosylation and cleavage sites are significantly associated with each other. We then used a positional proteomic strategy, terminal amine isotopic labeling of substrates (TAILS), to map the in vivo cleavage sites in HepG2 SimpleCells with and without one of the key initiating GalNAc transferases, GalNAc-T2, and after treatment with exogenous matrix metalloproteinase 9 (MMP9) or neutrophil elastase. Surprisingly, we found that loss of GalNAc-T2 not only increased cleavage, but also decreased cleavage across a broad range of other substrates, including key regulators of the protease network. We also found altered processing of several central regulators of lipid homeostasis, including apolipoprotein B and the phospholipid transfer protein, providing new clues to the previously reported link between GALNT2 and lipid homeostasis. In summary, we show that loss of GalNAc-T2 O-glycosylation leads to a general decrease in cleavage and that GalNAc-T2 O-glycosylation affects key regulators of the cellular proteolytic network, including multiple members of the serpin family.
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Affiliation(s)
- Sarah L King
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Christoffer K Goth
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Ulrich Eckhard
- the Centre for Blood Research, Department of Oral Biological and Medical Sciences, Faculty of Dentistry, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Hiren J Joshi
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Amalie D Haue
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Sergey Y Vakhrushev
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Katrine T Schjoldager
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Christopher M Overall
- the Centre for Blood Research, Department of Oral Biological and Medical Sciences, Faculty of Dentistry, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Hans H Wandall
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
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Vedadi M, Blazer L, Eram MS, Barsyte-Lovejoy D, Arrowsmith CH, Hajian T. Targeting human SET1/MLL family of proteins. Protein Sci 2017; 26:662-676. [PMID: 28160335 PMCID: PMC5368065 DOI: 10.1002/pro.3129] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/18/2017] [Accepted: 01/24/2017] [Indexed: 12/15/2022]
Abstract
The SET1 family of proteins, and in particular MLL1, are essential regulators of transcription and key mediators of normal development and disease. Here, we summarize the detailed characterization of the methyltransferase activity of SET1 complexes and the role of the key subunits, WDR5, RbBP5, ASH2L, and DPY30. We present new data on full kinetic characterization of human MLL1, MLL3, SET1A, and SET1B trimeric, tetrameric, and pentameric complexes to elaborate on substrate specificities and compare our findings with what has been reported before. We also review exciting recent work identifying potent inhibitors of oncogenic MLL1 function through disruption of protein–protein interactions within the MLL1 complex.
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Affiliation(s)
- Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8
| | - Levi Blazer
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7
| | - Mohammad S Eram
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7
| | | | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9
| | - Taraneh Hajian
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7
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Sorum AW, Shrimp JH, Roberts AM, Montgomery DC, Tiwari NK, Lal-Nag M, Simeonov A, Jadhav A, Meier JL. Microfluidic Mobility Shift Profiling of Lysine Acetyltransferases Enables Screening and Mechanistic Analysis of Cellular Acetylation Inhibitors. ACS Chem Biol 2016; 11:734-41. [PMID: 26428393 DOI: 10.1021/acschembio.5b00709] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Lysine acetyltransferases (KATs) are critical regulators of signaling in many diseases, including cancer. A major challenge in establishing the targetable functions of KATs in disease is a lack of well-characterized, cell-active KAT inhibitors. To confront this challenge, here we report a microfluidic mobility shift platform for the discovery and characterization of small molecule KAT inhibitors. Novel fluorescent peptide substrates were developed for four well-known KAT enzymes (p300, Crebbp, Morf, and Gcn5). Enzyme-catalyzed acetylation alters the electrophoretic mobility of these peptides in a microfluidic chip, allowing facile and direct monitoring of KAT activity. A pilot screen was used to demonstrate the utility of microfluidic mobility shift profiling to identify known and novel modulators of KAT activity. Real-time kinetic monitoring of KAT activity revealed that garcinol, a natural product KAT inhibitor used in cellular studies, exhibits time-dependent and detergent-sensitive inhibition, consistent with an aggregation-based mechanism. In contrast, the cell-permeable bisubstrate inhibitor Tat-CoA exhibited potent and time-independent KAT inhibition, highlighting its potential utility as a cellular inhibitor of KAT activity. These studies define microfluidic mobility shift profiling as a powerful platform for the discovery and characterization of small molecule inhibitors of KAT activity, and provide mechanistic insights potentially important for the application of KAT inhibitors in cellular contexts.
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Affiliation(s)
- Alexander W. Sorum
- Chemical
Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Jonathan H. Shrimp
- Chemical
Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Allison M. Roberts
- Chemical
Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - David C. Montgomery
- Chemical
Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Neil K. Tiwari
- Chemical
Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Madhu Lal-Nag
- Division
of Preclinical Innovation, National Center for Advancing Translational
Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Anton Simeonov
- Division
of Preclinical Innovation, National Center for Advancing Translational
Sciences, National Institutes of Health, Rockville, Maryland 20850, 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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Ma F, Zhang CY. Histone modifying enzymes: novel disease biomarkers and assay development. Expert Rev Mol Diagn 2016; 16:297-306. [DOI: 10.1586/14737159.2016.1135057] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Ma H, Howitz KT, Horiuchi KY, Wang Y. Histone Methyltransferase Activity Assays. EPIGENETICS FOR DRUG DISCOVERY 2015. [DOI: 10.1039/9781782628484-00267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Histone methyltransferases (HMTs) methylate either the lysine or arginine residues on histones and other proteins and play a crucial role in epigenetic regulation. Over 70 HMTs are encoded by the human genome, and many have been implicated in the aetiology of cancer, inflammatory diseases, neurodegenerative diseases and other conditions. There are currently about a dozen HMT activity assays available, and many of these assay formats are applicable to other epigenetic factors, such as histone acetyltransferases, histone deacetylases, and histone and DNA demethylases. Many factors need to be considered in selecting an HMT assay for drug discovery studies, including cost, adaptability to high-throughput screening, and rates of false positives and false negatives. This chapter describes the mechanisms of the major assay platforms available for HMT screening and profiling and presents the advantages and limitations associated with each.
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Affiliation(s)
- Haiching Ma
- Reaction Biology Corporation One Great Valley Parkway, Suite 2 Malvern PA 19355 USA
| | - Konrad T. Howitz
- Reaction Biology Corporation One Great Valley Parkway, Suite 2 Malvern PA 19355 USA
| | - Kurumi Y. Horiuchi
- Reaction Biology Corporation One Great Valley Parkway, Suite 2 Malvern PA 19355 USA
| | - Yuren Wang
- Reaction Biology Corporation One Great Valley Parkway, Suite 2 Malvern PA 19355 USA
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Horiuchi KY. Challenges in profiling and lead optimization of drug discovery for methyltransferases. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 18:62-68. [PMID: 26723894 DOI: 10.1016/j.ddtec.2015.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 10/12/2015] [Accepted: 10/13/2015] [Indexed: 06/05/2023]
Abstract
The importance of epigenetics in the initiation and progression of disease has attracted many investigators to incorporate this novel and exciting field in drug development. Protein methyltransferases are one of the target classes which have gained attention as potential therapeutic targets after promising results of inhibitors for EZH2 and DOT1L in clinical trials. There are many technologies developed in order to find small molecule inhibitors for protein methyltransferases. However, in contrast to high throughput screening, profiling against different methyltransferases is challenging since each enzyme has a different substrate preference so that it is hard to profile in one assay format. Here, different technologies for methyltransferase assays will be overviewed, and the advantages and disadvantages of each will be discussed.
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Affiliation(s)
- Kurumi Y Horiuchi
- Reaction Biology Corporation, One Great Valley Parkway, Suite 2, Malvern, PA 19355, USA.
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12
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Janzen WP. Screening technologies for small molecule discovery: the state of the art. ACTA ACUST UNITED AC 2015; 21:1162-70. [PMID: 25237860 DOI: 10.1016/j.chembiol.2014.07.015] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/14/2014] [Accepted: 07/16/2014] [Indexed: 01/24/2023]
Abstract
Screening, high-throughput screening, and ultra-high-throughput screening are all really just points on a spectrum that represent differing applications of the same process: the creation of biologically relevant assays that are relevant, reproducible, reliable, and robust. Whether the discovery program is developing a pharmaceutical, an academic probe, cosmetics, pesticides, or a toxicity monitoring assay, the development of a screen focuses on generating a method that will reliably deliver reproducible results over a period of weeks, months, or years and that will generate consistent results for every test along the way. This review provides both historical perspective on how this unique scientific discipline evolved and commentary on the current state of the art technologies and techniques.
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Affiliation(s)
- William P Janzen
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Wigle TJ, Swinger KK, Campbell JE, Scholle MD, Sherrill J, Admirand EA, Boriack-Sjodin PA, Kuntz KW, Chesworth R, Moyer MP, Scott MP, Copeland RA. A High-Throughput Mass Spectrometry Assay Coupled with Redox Activity Testing Reduces Artifacts and False Positives in Lysine Demethylase Screening. ACTA ACUST UNITED AC 2015; 20:810-20. [DOI: 10.1177/1087057115575689] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/06/2015] [Indexed: 11/17/2022]
Abstract
Demethylation of histones by lysine demethylases (KDMs) plays a critical role in controlling gene transcription. Aberrant demethylation may play a causal role in diseases such as cancer. Despite the biological significance of these enzymes, there are limited assay technologies for study of KDMs and few quality chemical probes available to interrogate their biology. In this report, we demonstrate the utility of self-assembled monolayer desorption/ionization (SAMDI) mass spectrometry for the investigation of quantitative KDM enzyme kinetics and for high-throughput screening for KDM inhibitors. SAMDI can be performed in 384-well format and rapidly allows reaction components to be purified prior to injection into a mass spectrometer, without a throughput-limiting liquid chromatography step. We developed sensitive and robust assays for KDM1A (LSD1, AOF2) and KDM4C (JMJD2C, GASC1) and screened 13,824 compounds against each enzyme. Hits were rapidly triaged using a redox assay to identify compounds that interfered with the catalytic oxidation chemistry used by the KDMs for the demethylation reaction. We find that overall this high-throughput mass spectrometry platform coupled with the elimination of redox active compounds leads to a hit rate that is manageable for follow-up work.
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A fluorescence resonance energy transfer-based method for histone methyltransferases. Anal Biochem 2015; 476:78-80. [PMID: 25703602 DOI: 10.1016/j.ab.2015.02.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 02/12/2015] [Indexed: 11/22/2022]
Abstract
A simple dye-quencher fluorescence resonance energy transfer (FRET)-based assay for methyltransferases was developed and used to determine kinetic parameters and inhibitory activity at EHMT1 and EHMT2. Peptides mimicking the truncated histone H3 tail were functionalized in each end with a dye and a quencher, respectively. When lysine-9 residues in the peptides were methylated, they were protected from cleavage by endoproteinase-EndoLysC, whereas unmethylated peptides were cleaved, resulting in an increase in fluorescent intensity.
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Yu W, Eram MS, Hajian T, Szykowska A, Burgess-Brown N, Vedadi M, Brown PJ. A scintillation proximity assay for histone demethylases. Anal Biochem 2014; 463:54-60. [DOI: 10.1016/j.ab.2014.06.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 06/22/2014] [Accepted: 06/28/2014] [Indexed: 10/25/2022]
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Ma A, Yu W, Li F, Bleich RM, Herold JM, Butler KV, Norris JL, Korboukh V, Tripathy A, Janzen WP, Arrowsmith CH, Frye SV, Vedadi M, Brown PJ, Jin J. Discovery of a selective, substrate-competitive inhibitor of the lysine methyltransferase SETD8. J Med Chem 2014; 57:6822-33. [PMID: 25032507 PMCID: PMC4136711 DOI: 10.1021/jm500871s] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The lysine methyltransferase SETD8 is the only known methyltransferase that catalyzes monomethylation of histone H4 lysine 20 (H4K20). Monomethylation of H4K20 has been implicated in regulating diverse biological processes including the DNA damage response. In addition to H4K20, SETD8 monomethylates non-histone substrates including proliferating cell nuclear antigen (PCNA) and promotes carcinogenesis by deregulating PCNA expression. However, selective inhibitors of SETD8 are scarce. The only known selective inhibitor of SETD8 to date is nahuoic acid A, a marine natural product, which is competitive with the cofactor. Here, we report the discovery of the first substrate-competitive inhibitor of SETD8, UNC0379 (1). This small-molecule inhibitor is active in multiple biochemical assays. Its affinity to SETD8 was confirmed by ITC (isothermal titration calorimetry) and SPR (surface plasmon resonance) studies. Importantly, compound 1 is selective for SETD8 over 15 other methyltransferases. We also describe structure-activity relationships (SAR) of this series.
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Affiliation(s)
- Anqi Ma
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, ‡Department of Pharmacology, School of Medicine, §Lineberger Comprehensive Cancer Center, and ∥Department of Biochemistry and Biophysics, UNC Macromolecular Interactions Facility, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
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17
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Kotzsch A, Skovgaard T, Buus U, Andersen S, Devkota K, Berthelsen J. A substrate-optimized electrophoretic mobility shift assay for ADAM12. Anal Biochem 2014; 452:34-42. [PMID: 24534253 DOI: 10.1016/j.ab.2014.02.008] [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: 11/01/2013] [Revised: 01/31/2014] [Accepted: 02/02/2014] [Indexed: 11/17/2022]
Abstract
ADAM12 belongs to the A disintegrin and metalloprotease (ADAM) family of secreted sheddases activating extracellular growth factors such as epidermal growth factor receptor (EGFR) ligands and tumor necrosis factor-alpha (TNF-α). ADAM proteases, most notably ADAM17 (TNF-α-converting enzyme), have long been investigated as pharmaceutical drug targets; however, due to lack of potency and in vivo side effects, none of the small-molecule inhibitors discovered so far has made it beyond clinical testing. Ongoing research on novel selective inhibitors of ADAMs requires reliable biochemical assays to validate molecular probes from large-scale screening efforts. Here we describe an electrophoretic mobility shift assay for ADAM12 based on the identification of an optimized peptide substrate that is characterized by excellent performance and reproducibility.
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Affiliation(s)
- Alexander Kotzsch
- Facility for Protein Purification and Function at the Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark.
| | - Tine Skovgaard
- Facility for Protein Purification and Function at the Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Uwe Buus
- Facility for Protein Purification and Function at the Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Simon Andersen
- Facility for Protein Purification and Function at the Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Kanchan Devkota
- Facility for Protein Purification and Function at the Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Jens Berthelsen
- Facility for Protein Purification and Function at the Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
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18
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Liu F, Barsyte-Lovejoy D, Li F, Xiong Y, Korboukh V, Huang XP, Allali-Hassani A, Janzen WP, Roth BL, Frye SV, Arrowsmith CH, Brown PJ, Vedadi M, Jin J. Discovery of an in vivo chemical probe of the lysine methyltransferases G9a and GLP. J Med Chem 2013; 56:8931-42. [PMID: 24102134 PMCID: PMC3880643 DOI: 10.1021/jm401480r] [Citation(s) in RCA: 192] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Among epigenetic "writers", "readers", and "erasers", the lysine methyltransferases G9a and GLP, which catalyze mono- and dimethylation of histone H3 lysine 9 (H3K9me2) and nonhistone proteins, have been implicated in a variety of human diseases. A "toolkit" of well-characterized chemical probes will allow biological and disease hypotheses concerning these proteins to be tested in cell-based and animal models with high confidence. We previously discovered potent and selective G9a/GLP inhibitors including the cellular chemical probe UNC0638, which displays an excellent separation of functional potency and cell toxicity. However, this inhibitor is not suitable for animal studies due to its poor pharmacokinetic (PK) properties. Here, we report the discovery of the first G9a and GLP in vivo chemical probe UNC0642, which not only maintains high in vitro and cellular potency, low cell toxicity, and excellent selectivity, but also displays improved in vivo PK properties, making it suitable for animal studies.
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Affiliation(s)
- Feng Liu
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Ontario, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Ontario, Canada
| | - Yan Xiong
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy
| | - Victoria Korboukh
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy
| | - Xi-Ping Huang
- National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Abdellah Allali-Hassani
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Ontario, Canada
| | - William P. Janzen
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy
| | - Bryan L. Roth
- National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Stephen V. Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Ontario, Canada
| | - Peter J. Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Ontario, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Ontario, Canada
| | - Jian Jin
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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19
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Ge C, Yu L, Fang Z, Zeng L. An Enhanced Strip Biosensor for Rapid and Sensitive Detection of Histone Methylation. Anal Chem 2013; 85:9343-9. [DOI: 10.1021/ac402202x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Chenchen Ge
- Key
Laboratory of Regenerative Biology, South China Institute for Stem
Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine
and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Luxin Yu
- Key
Laboratory of Regenerative Biology, South China Institute for Stem
Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine
and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Zhiyuan Fang
- Key
Laboratory of Regenerative Biology, South China Institute for Stem
Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine
and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Lingwen Zeng
- Key
Laboratory of Regenerative Biology, South China Institute for Stem
Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine
and Health, Chinese Academy of Sciences, Guangzhou 510530, China
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20
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Zeng H, Wu J, Bedford MT, Sbardella G, Hoffmann FM, Bi K, Xu W. A TR-FRET-based functional assay for screening activators of CARM1. Chembiochem 2013; 14:827-35. [PMID: 23585185 PMCID: PMC3828750 DOI: 10.1002/cbic.201300029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Indexed: 11/07/2022]
Abstract
Epigenetics is an emerging field that demands selective cell-permeable chemical probes to perturb, especially in vivo, the activity of specific enzymes involved in modulating the epigenetic codes. Coactivator-associated arginine methyltransferase 1 (CARM1) is a coactivator of estrogen receptor α (ERα), the main target in human breast cancer. We previously showed that twofold overexpression of CARM1 in MCF7 breast cancer cells increased the expression of ERα-target genes involved in differentiation and reduced cell proliferation, thus leading to the hypothesis that activating CARM1 by chemical activators might be therapeutically effective in breast cancer. Selective, potent, cell-permeable CARM1 activators will be essential to test this hypothesis. Here we report the development of a cell-based, time-resolved (TR) FRET assay that uses poly(A) binding protein 1 (PABP1) methylation to monitor cellular activity of CARM1. The LanthaScreen TR-FRET assay uses MCF7 cells expressing GFP-PABP1 fusion protein through BacMam gene delivery system, methyl-PABP1 specific antibody, and terbium-labeled secondary antibody. This assay has been validated as reflecting the expression and/or activity of CARM1 and optimized for high throughput screening to identify CARM1 allosteric activators. This TR-FRET platform serves as a generic tool for functional screening of cell-permeable, chemical modulators of CARM1 for elucidation of its in vivo functions.
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Affiliation(s)
- Hao Zeng
- Graduate Program in Cellular and Molecular Biology, McArdle Laboratory for Cancer Research and Carbone Comprehensive Cancer Center, University of Wisconsin, 1400 University Ave, Madison, WI 53706, USA
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21
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Horiuchi KY, Eason MM, Ferry JJ, Planck JL, Walsh CP, Smith RF, Howitz KT, Ma H. Assay development for histone methyltransferases. Assay Drug Dev Technol 2013; 11:227-36. [PMID: 23557020 DOI: 10.1089/adt.2012.480] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Epigenetic modifications play a crucial role in human diseases. Unlike genetic mutations, however, they do not change the underlying DNA sequences. Epigenetic phenomena have gained increased attention in the field of cancer research, with many studies indicating that they are significantly involved in tumor establishment and progression. Histone methyltransferases (HMTs) are a large group of enzymes that specifically methylate protein lysine and arginine residues, especially in histones, using S-adenosyl-L-methionine (SAM) as the methyl donor. However, in general, HMTs have no widely accepted high-throughput screening (HTS) assay format, and reference inhibitors are not available for many of the enzymes. In this study, we describe the application of a miniaturized, radioisotope-based reaction system: the HotSpot(SM) platform for methyltransferases. Since this platform employs tritiated SAM as a cofactor, it can be applied to the assay of any HMT. The key advantage of this format is that any substrate can be used, including peptides, proteins, or even nucleosomes, without the need for labeling or any other modifications. Using this platform, we have determined substrate specificities, characterized enzyme kinetics, performed compound profiling for both lysine and arginine methyltransferases, and carried out HTS for a small-library LOPAC against DOT1L. After hit confirmation and profiling, we found that suramin inhibited DOT1L, NSD2, and PRMT4 with IC₅₀ values at a low μM range.
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Affiliation(s)
- Kurumi Y Horiuchi
- Department of Biochemistry, Reaction Biology Corporation, One Great Valley Parkway, Suite 2, Malvern, PA 19355, USA.
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22
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Blancafort P, Jin J, Frye S. Writing and rewriting the epigenetic code of cancer cells: from engineered proteins to small molecules. Mol Pharmacol 2012; 83:563-76. [PMID: 23150486 DOI: 10.1124/mol.112.080697] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The epigenomic era has revealed a well-connected network of molecular processes that shape the chromatin landscape. These processes comprise abnormal methylomes, transcriptosomes, genome-wide histone post-transcriptional modifications patterns, histone variants, and noncoding RNAs. The mapping of these processes in large scale by chromatin immunoprecipitation sequencing and other methodologies in both cancer and normal cells reveals novel therapeutic opportunities for anticancer intervention. The goal of this minireview is to summarize pharmacological strategies to modify the epigenetic landscape of cancer cells. These approaches include the use of novel small molecule inhibitors of epigenetic processes specifically deregulated in cancer cells and the design of engineered proteins able to stably reprogram the epigenetic code in cancer cells in a way that is similar to normal cells.
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Affiliation(s)
- Pilar Blancafort
- School of Anatomy, Physiology, and Human Biology, M309, the University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia.
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23
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Hinge and chromoshadow of HP1α participate in recognition of K9 methylated histone H3 in nucleosomes. J Mol Biol 2012; 425:54-70. [PMID: 23142645 DOI: 10.1016/j.jmb.2012.10.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/26/2012] [Accepted: 10/28/2012] [Indexed: 11/22/2022]
Abstract
The majority of the genome in eukaryotes is packaged into transcriptionally inactive chromatin. Heterochromatin protein 1 (HP1) is a major player in the establishment and maintenance of heterochromatin. HP1 specifically recognizes a methylated lysine residue at position 9 in histone H3 through its N-terminal chromo domain (CD). To elucidate the binding properties of HP1α to nucleosomes in vitro, we reconstituted nucleosomes containing histone H3 trimethylated at lysine 9. HP1α exhibited high-affinity binding to nucleosomes containing methylated histone H3 in a nucleosome core-number-dependent manner. The hinge region (HR) connecting the CD and C-terminal chromoshadow domain (CSD), and the CSD contributed to the selective binding of HP1α to histone H3 with trimethylated lysine 9 through weak DNA binding and by suppressing the DNA binding, respectively. We propose that not only the specific recognition of lysine 9 methylation of histone H3 by the CD but also the HR and the CSD cooperatively contribute to the selective binding of HP1α to histone H3 lysine 9 methylated nucleosomes.
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24
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Francis NJ, Rowlands M, Workman P, Jones K, Aherne W. Small-molecule inhibitors of the protein methyltransferase SET7/9 identified in a high-throughput screen. JOURNAL OF BIOMOLECULAR SCREENING 2012; 17:1102-9. [PMID: 22772057 DOI: 10.1177/1087057112452137] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Aberrant expression of chromatin-modifying enzymes (CMEs) is associated with a range of human diseases, including cancer. CMEs are now an important target area in drug discovery. Although the role that histone and protein (lysine) methyltransferases (PMTs) play in the regulation of transcription and cell growth is increasingly recognized, few small-molecule inhibitors of this class of enzyme have been reported. Here we describe an assay suitable for primary compound screening for the identification of PMT inhibitors. The assay followed the methylation of histones in the presence of the PMT SET7/9 and the radioactive cofactor S-adenosyl-methionine using scintillating microplates (FlashPlate) and was used to screen approximately 65 000 compounds (% coefficient of variation = 10%; Z' = 0.6). The hits identified from a library of more than 63 000 diverse small molecules included a series of rhodanine compounds with micromolar activity. A screen of the National Cancer Institute Diversity Set (2000 compounds) identified an orsein derivative that inhibited SET7/9 (~20 µM) and showed modest growth inhibition associated with the expected cellular phenotype of reduced histone methylation in a human tumor cell line. The assay represents a useful tool for the identification of inhibitors of PMT activity.
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Affiliation(s)
- Nicola-Jane Francis
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, Haddow Laboratories, Sutton, UK
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25
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Luo M. Current chemical biology approaches to interrogate protein methyltransferases. ACS Chem Biol 2012; 7:443-63. [PMID: 22220966 DOI: 10.1021/cb200519y] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein methyltransferases (PMTs) play various physiological and pathological roles through methylating histone and nonhistone targets. However, most PMTs including more than 60 human PMTs remain to be fully characterized. The current approaches to elucidate the functions of PMTs have been diversified by many emerging chemical biology technologies. This review focuses on progress in these aspects and is organized into four discussion modules (assays, substrates, cofactors, and inhibitors) that are important to elucidate biological functions of PMTs. These modules are expected to provide general guidance and present emerging methods for researchers to select and combine suitable PMT-activity assays, well-defined substrates, novel SAM surrogates, and PMT inhibitors to interrogate PMTs.
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Affiliation(s)
- Minkui Luo
- Molecular Pharmacology
and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, New
York 10065, United States
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26
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Neelamegam R, Ricq EL, Malvaez M, Patnaik D, Norton S, Carlin SM, Hill IT, Wood MA, Haggarty SJ, Hooker JM. Brain-penetrant LSD1 inhibitors can block memory consolidation. ACS Chem Neurosci 2012; 3:120-128. [PMID: 22754608 DOI: 10.1021/cn200104y] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Modulation of histone modifications in the brain may represent a new mechanism for brain disorder therapy. Post-translational modifications of histones regulate gene expression, affecting major cellular processes such as proliferation, differentiation, and function. An important enzyme involved in one of these histone modifications is lysine specific demethylase 1 (LSD1). This enzyme is flavin-dependent and exhibits homology to amine oxidases. Parnate (2-phenylcyclopropylamine (2-PCPA); tranylcypromine) is a potent inhibitor of monoamine oxidases and derivatives of 2-PCPA have been used for development of selective LSD1 inhibitors based on the ability to form covalent adducts with flavin adenine dinucleotide (FAD). Here we report the synthesis and in vitro characterization of LSD1 inhibitors that bond covalently to FAD. The two most potent and selective inhibitors were used to demonstrate brain penetration when administered systemically to rodents. First, radiosynthesis of a positron-emitting analog was used to obtain preliminary bio-distribution data and whole brain time-activity curves. Second, we demonstrate that this series of LSD1 inhibitors is capable of producing a cognitive effect in a mouse model. By using a memory formation paradigm, novel object recognition, we show that LSD1 inhibition can abolish long-term memory formation without affecting short-term memory, providing further evidence for the importance of reversible histone methylation in the function of the nervous system.
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Affiliation(s)
- Ramesh Neelamegam
- Department
of Radiology, Athinoula
A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
02129, United States
| | - Emily L. Ricq
- Department
of Radiology, Athinoula
A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
02129, United States
- Department
of Chemistry and
Chemical Biology, Harvard University, 12
Oxford Street, Cambridge, Massachusetts 02138, United States
- Department of Neurology, Center
for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114,
United States
| | - Melissa Malvaez
- Department of Neurobiology and
Behavior, Center for the Neurobiology of Learning and Memory, University of California, Irvine, California 92697-3800,
United States
| | - Debasis Patnaik
- Department of Neurology, Center
for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114,
United States
| | - Stephanie Norton
- Department of Neurology, Center
for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114,
United States
| | - Stephen M. Carlin
- Department
of Radiology, Athinoula
A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
02129, United States
| | - Ian T. Hill
- Department
of Radiology, Athinoula
A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
02129, United States
| | - Marcelo A. Wood
- Department of Neurobiology and
Behavior, Center for the Neurobiology of Learning and Memory, University of California, Irvine, California 92697-3800,
United States
| | - Stephen J. Haggarty
- Department of Neurology, Center
for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114,
United States
- Stanley Center for Psychiatric Research at the Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Jacob M. Hooker
- Department
of Radiology, Athinoula
A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
02129, United States
- Brookhaven National Laboratory, Upton, New York 11973-5000, United
States
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27
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He Y, Korboukh I, Jin J, Huang J. Targeting protein lysine methylation and demethylation in cancers. Acta Biochim Biophys Sin (Shanghai) 2012; 44:70-9. [PMID: 22194015 DOI: 10.1093/abbs/gmr109] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
During the last decade, we saw an explosion of studies investigating the role of lysine methylation/demethylation of histones and non-histone proteins, such as p53, NF-kappaB, and E2F1. These 'Ying-Yang' post-translational modifications are important to fine-tuning the activity of these proteins. Lysine methylation and demethylation are catalyzed by protein lysine methyltransferases (PKMTs) and protein lysine demethylases (PKDMs). PKMTs, PKDMs, and their substrates have been shown to play important roles in cancers. Although the underlying mechanisms of tumorigenesis are still largely unknown, growing evidence is starting to link aberrant regulation of methylation to tumorigenesis. This review focuses on summarizing the recent progress in understanding of the function of protein lysine methylation, and in the discovery of small molecule inhibitors for PKMTs and PKDMs. We also discuss the potential and the caveats of targeting protein lysine methylation for the treatment of cancer.
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Affiliation(s)
- Yunlong He
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
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28
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Ahrens T, Bergner A, Sheppard D, Hafenbradl D. Efficient Hit-Finding Approaches for Histone Methyltransferases. ACTA ACUST UNITED AC 2011; 17:85-98. [DOI: 10.1177/1087057111422823] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
For many novel epigenetics targets the chemical ligand space and structural information were limited until recently and are still largely unknown for some targets. Hit-finding campaigns are therefore dependent on large and chemically diverse libraries. In the specific case of the histone methyltransferase G9a, the authors have been able to apply an efficient process of intelligent selection of compounds for primary screening, rather than screening the full diverse deck of 900 000 compounds to identify hit compounds. A number of different virtual screening methods have been applied for the compound selection, and the results have been analyzed in the context of their individual success rates. For the primary screening of 2112 compounds, a FlashPlate assay format and full-length histone H3.1 substrate were employed. Validation of hit compounds was performed using the orthogonal fluorescence lifetime technology. Rated by purity and IC50 value, 18 compounds (0.9% of compound screening deck) were finally considered validated primary G9a hits. The hit-finding approach has led to novel chemotypes being identified, which can facilitate hit-to-lead projects. This study demonstrates the power of virtual screening technologies for novel, therapeutically relevant epigenetics protein targets.
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29
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Allali-Hassani A, Wasney GA, Siarheyeva A, Hajian T, Arrowsmith CH, Vedadi M. Fluorescence-based methods for screening writers and readers of histone methyl marks. ACTA ACUST UNITED AC 2011; 17:71-84. [PMID: 21972038 DOI: 10.1177/1087057111422256] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The histone methyltransferase (HMT) family of proteins consists of enzymes that methylate lysine or arginine residues on histone tails as well as other proteins. Such modifications affect chromatin structure and play a significant regulatory role in gene expression. Many HMTs have been implicated in tumorigenesis and progression of multiple malignancies and play essential roles in embryonic development and stem cell renewal. Overexpression of some HMTs has been observed and is correlated positively with various types of cancer. Here the authors report development of a continuous fluorescence-based methyltransferase assay in a 384-well format and its application in determining kinetic parameters for EHMT1, G9a, PRMT3, SETD7, and SUV39H2 as well as for screening against libraries of small molecules to identify enzyme inhibitors. They also report the development of a peptide displacement assay using fluorescence polarization in a 384-well format to assay and screen protein peptide interactions such as those of WDR5 and EED, components of MLL and EZH2 methyltransferase complexes. Using these high-throughput screening methods, the authors have identified potent inhibitors and ligands for some of these proteins.
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30
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Hauser AT, Bissinger EM, Metzger E, Repenning A, Bauer UM, Mai A, Schüle R, Jung M. Screening assays for epigenetic targets using native histones as substrates. ACTA ACUST UNITED AC 2011; 17:18-26. [PMID: 21965113 DOI: 10.1177/1087057111423968] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In the past years, a lot of attention has been given to the identification and characterization of selective and potent inhibitors of chromatin-modifying enzymes to better understand their specific role in transcriptional regulation. As aberrant histone methylation is involved in different pathological processes, the search for methyltransferase and demethylase inhibitors has emerged as a crucial issue in current medicinal chemistry research. High-throughput in vitro assays are important tools for the identification of new methyltransferase or demethylase inhibitors. These usually use oligopeptide substrates derived from histone sequences, although in many cases, they are not good substrates for these enzymes. Here, the authors report about the setup and establishment of in vitro assays that use native core histones as substrates, enabling an assay environment that better resembles native conditions. They have applied these substrates for the known formaldehyde dehydrogenase assay for the histone demethylase LSD1 and have established two new antibody-based assays. For LSD1, a heterogeneous assay format was set up, and a homogeneous assay was used for the characterization of the arginine methyltransferase PRMT1. Validation of the system was achieved with reference inhibitors in each case.
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31
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Klink TA, Staeben M, Twesten K, Kopp AL, Kumar M, Dunn RS, Pinchard CA, Kleman-Leyer KM, Klumpp M, Lowery RG. Development and validation of a generic fluorescent methyltransferase activity assay based on the transcreener AMP/GMP assay. ACTA ACUST UNITED AC 2011; 17:59-70. [PMID: 21956169 DOI: 10.1177/1087057111421624] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Methylation is a ubiquitous covalent modification used to control the function of diverse biomolecules including hormones, neurotransmitters, xenobiotics, proteins, nucleic acids, and lipids. Histone methyltransferases (HMTs) are currently of high interest as drug targets because of their role in epigenetic regulation; however, most HMT assay methods are either not amenable to a high-throughput screening (HTS) environment or are applicable to a limited number of enzymes. The authors developed a generic methyltransferase assay method using fluorescent immunodetection of adenosine monophosphate (AMP), which is formed from the MT reaction product S-adenosylhomocysteine in a dual-enzyme coupling step. The detection range of the assay; its suitability for HTS, including stability of reagents following dispensing and after addition to reactions; and the potential for interference from drug-like molecules was investigated. In addition, the use of the assay for measuring inhibitor potencies with peptide or intact protein substrates was examined through pilot screening with selected reference enzymes including HMT G9a. By combining a novel enzymatic coupling step with the well-characterized Transcreener AMP/GMP assay, the authors have developed a robust HTS assay for HMTs that should be broadly applicable to other types of methyltransferases as well.
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Yost JM, Korboukh I, Liu F, Gao C, Jin J. Targets in epigenetics: inhibiting the methyl writers of the histone code. CURRENT CHEMICAL GENOMICS 2011; 5:72-84. [PMID: 21966347 PMCID: PMC3178896 DOI: 10.2174/1875397301005010072] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 07/11/2011] [Accepted: 07/18/2011] [Indexed: 01/11/2023]
Abstract
Growing evidence suggests that protein lysine methyltransferases (PKMTs) and protein arginine methyltransferases (PRMTs) are associated with the development of various human diseases, including cancer, inflammation, and psychiatric disorders. Given the significant role of these proteins in human disease, efforts to discover selective small-molecule inhibitors of these enzymes are quickly gaining momentum. In this review, we focus on the recent progress in the discovery of selective PKMT and PRMT inhibitors. A future perspective on developing methyltransferase inhibitors is also offered.
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Affiliation(s)
| | | | | | | | - Jian Jin
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Quinn AM, Simeonov A. Methods for Activity Analysis of the Proteins that Regulate Histone Methylation. CURRENT CHEMICAL GENOMICS 2011; 5:95-105. [PMID: 21966349 PMCID: PMC3180180 DOI: 10.2174/1875397301005010095] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 03/23/2011] [Accepted: 04/25/2011] [Indexed: 12/20/2022]
Abstract
The enzymes that regulate histone methylation states and the protein domains that recognize methylated histone residues have been implicated in a number of human diseases, including cancer, as a result of their ability to affect transcriptional changes by altering chromatin structure. These proteins are recognized as potential therapeutic targets for the treatment of diseases associated with epigenetic disruption; however, few inhibitors of their activity have been identified. The majority of histone demethylase and methyltransferase enzyme inhibitors have been discovered on the basis of their structural similarity to substrates or known inhibitors of enzymes with analogous mechanisms. The general lack of potency and specificity of these compounds indicates that novel chemotypes are needed to address the large number of recently discovered histone-modifying enzymes. High-throughput screening (HTS) allows rapid testing of chemically diverse small molecule libraries, provided assays amenable to HTS exist. Here we review the biochemical and cellular assays available for testing the proteins and enzymes that regulate histone methylation. Progress in the development of high-throughput, sensitive, and robust assays will enable discovery of small molecules for epigenetic therapy.
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Affiliation(s)
- Amy M Quinn
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-3370, USA
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Vedadi M, Barsyte-Lovejoy D, Liu F, Rival-Gervier S, Allali-Hassani A, Labrie V, Wigle TJ, Dimaggio PA, Wasney GA, Siarheyeva A, Dong A, Tempel W, Wang SC, Chen X, Chau I, Mangano TJ, Huang XP, Simpson CD, Pattenden SG, Norris JL, Kireev DB, Tripathy A, Edwards A, Roth BL, Janzen WP, Garcia BA, Petronis A, Ellis J, Brown PJ, Frye SV, Arrowsmith CH, Jin J. A chemical probe selectively inhibits G9a and GLP methyltransferase activity in cells. Nat Chem Biol 2011; 7:566-74. [PMID: 21743462 PMCID: PMC3184254 DOI: 10.1038/nchembio.599] [Citation(s) in RCA: 400] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Accepted: 04/27/2011] [Indexed: 12/12/2022]
Abstract
Protein lysine methyltransferases G9a and GLP modulate the transcriptional repression of a variety of genes via dimethylation of Lys9 on histone H3 (H3K9me2) as well as dimethylation of non-histone targets. Here we report the discovery of UNC0638, an inhibitor of G9a and GLP with excellent potency and selectivity over a wide range of epigenetic and non-epigenetic targets. UNC0638 treatment of a variety of cell lines resulted in lower global H3K9me2 levels, equivalent to levels observed for small hairpin RNA knockdown of G9a and GLP with the functional potency of UNC0638 being well separated from its toxicity. UNC0638 markedly reduced the clonogenicity of MCF7 cells, reduced the abundance of H3K9me2 marks at promoters of known G9a-regulated endogenous genes and disproportionately affected several genomic loci encoding microRNAs. In mouse embryonic stem cells, UNC0638 reactivated G9a-silenced genes and a retroviral reporter gene in a concentration-dependent manner without promoting differentiation.
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Affiliation(s)
- Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | - Feng Liu
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sylvie Rival-Gervier
- Developmental and Stem Cell Biology Program, SickKids Hospital, Toronto, Ontario, Canada
- INRa, UMR 1198 Biologie du Développement et Reproduction, Jouy en Josas, France
| | | | - Viviane Labrie
- Krembil Family Epigenetic Laboratory, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Tim J Wigle
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Peter A Dimaggio
- Department of Chemistry, Princeton University, Princeton, New Jersey, USA
| | - Gregory A Wasney
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Alena Siarheyeva
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Sun-Chong Wang
- Krembil Family Epigenetic Laboratory, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Institute of Systems Biology and Bioinformatics, National Central University, Jhongli City, Taiwan
| | - Xin Chen
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Irene Chau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Thomas J Mangano
- National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Xi-ping Huang
- National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Catherine D Simpson
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Samantha G Pattenden
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jacqueline L Norris
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dmitri B Kireev
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ashutosh Tripathy
- Department of Biochemistry and Biophysics, UNC Macromolecular Interactions Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Aled Edwards
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Bryan L Roth
- National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - William P Janzen
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Benjamin A Garcia
- Department of Chemistry, Princeton University, Princeton, New Jersey, USA
| | - Arturas Petronis
- Krembil Family Epigenetic Laboratory, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - James Ellis
- Developmental and Stem Cell Biology Program, SickKids Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Stephen V Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Ontario Cancer Institute, Campbell Family Cancer Research Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jian Jin
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Abstract
IMPORTANCE OF THE FIELD Fluorescence polarization (FP) is a homogeneous method that allows rapid and quantitative analysis of diverse molecular interactions and enzyme activities. This technique has been widely utilized in clinical and biomedical settings, including the diagnosis of certain diseases and monitoring therapeutic drug levels in body fluids. Recent developments in the field have been symbolized by the facile adoption of FP in high-throughput screening and small molecule drug discovery of an increasing range of target classes. AREAS COVERED IN THIS REVIEW The article provides a brief overview of the theoretical foundation of FP, followed by updates on recent advancements in its application for various drug target classes, including GPCRs, enzymes and protein-protein interactions. The strengths and weaknesses of this method, practical considerations in assay design, novel applications and future directions are also discussed. WHAT THE READER WILL GAIN The reader is informed of the most recent advancements and future directions of FP application to small molecule screening. TAKE HOME MESSAGE In addition to its continued utilization in high-throughput screening, FP has expanded into new disease and target areas and has been marked by increased use of labeled small molecule ligands for receptor-binding studies.
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Affiliation(s)
- Wendy A. Lea
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-3370, U.S.A
| | - Anton Simeonov
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-3370, U.S.A
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Auld D, Simeonov A, Lea W, Thomas C. Literature Search and Review. Assay Drug Dev Technol 2010. [DOI: 10.1089/adt.2010.0805.lr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Liu F, Chen X, Allali-Hassani A, Quinn AM, Wigle TJ, Wasney GA, Dong A, Senisterra G, Chau I, Siarheyeva A, Norris JL, Kireev DB, Jadhav A, Herold JM, Janzen WP, Arrowsmith CH, Frye SV, Brown PJ, Simeonov A, Vedadi M, Jin J. Protein lysine methyltransferase G9a inhibitors: design, synthesis, and structure activity relationships of 2,4-diamino-7-aminoalkoxy-quinazolines. J Med Chem 2010; 53:5844-57. [PMID: 20614940 PMCID: PMC2920043 DOI: 10.1021/jm100478y] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein lysine methyltransferase G9a, which catalyzes methylation of lysine 9 of histone H3 (H3K9) and lysine 373 (K373) of p53, is overexpressed in human cancers. Genetic knockdown of G9a inhibits cancer cell growth, and the dimethylation of p53 K373 results in the inactivation of p53. Initial SAR exploration of the 2,4-diamino-6,7-dimethoxyquinazoline template represented by 3a (BIX01294), a selective small molecule inhibitor of G9a and GLP, led to the discovery of 10 (UNC0224) as a potent G9a inhibitor with excellent selectivity. A high resolution X-ray crystal structure of the G9a-10 complex, the first cocrystal structure of G9a with a small molecule inhibitor, was obtained. On the basis of the structural insights revealed by this cocrystal structure, optimization of the 7-dimethylaminopropoxy side chain of 10 resulted in the discovery of 29 (UNC0321) (Morrison K(i) = 63 pM), which is the first G9a inhibitor with picomolar potency and the most potent G9a inhibitor to date.
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Affiliation(s)
- Feng Liu
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Xin Chen
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Abdellah Allali-Hassani
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Ontario, Canada
| | - Amy M. Quinn
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Tim J. Wigle
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Gregory A. Wasney
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Ontario, Canada
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Ontario, Canada
| | - Guillermo Senisterra
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Ontario, Canada
| | - Irene Chau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Ontario, Canada
| | - Alena Siarheyeva
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Ontario, Canada
| | - Jacqueline L. Norris
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Dmitri B. Kireev
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Ajit Jadhav
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - J. Martin Herold
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - William P. Janzen
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Ontario, Canada
| | - Stephen V. Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Peter J. Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Ontario, Canada
| | - Anton Simeonov
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Ontario, Canada
| | - Jian Jin
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Bissinger EM, Jung M. No Taste for Methyl: Methylation Sensitive Proteolysis in Drug Screening. ACTA ACUST UNITED AC 2010; 17:677-8. [DOI: 10.1016/j.chembiol.2010.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Abstract
Epigenetics refers to heritable changes that control how the genome is accessed in different cell-types and during development and differentiation. Even though each cell contains essentially the same genetic code, epigenetic mechanisms permit specialization of function between cells. The state of chromatin, the complex of histone proteins, RNA and DNA that efficiently package the genome, is largely regulated by specific modifications to histone proteins and DNA, and the recognition of these marks by other proteins and protein complexes. The enzymes that produce these modifications (the 'writers'), the proteins that recognize them (the 'readers'), and the enzymes that remove them (the 'erasers') are critical targets for manipulation in order to further understand the histone code and its role in biology and human disease.
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