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Discovery of cysteine-targeting covalent histone methyltransferase inhibitors. Eur J Med Chem 2023; 246:115028. [PMID: 36528996 DOI: 10.1016/j.ejmech.2022.115028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/02/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022]
Abstract
Post-translational methylation of histone lysine or arginine residues by histone methyltransferases (HMTs) plays crucial roles in gene regulation and diverse physiological processes and is implicated in a plethora of human diseases, especially cancer. Therefore, histone methyltransferases have been increasingly recognized as potential therapeutic targets. Consequently, the discovery and development of histone methyltransferase inhibitors have been pursued with steadily increasing interest over the past decade. However, the disadvantages of limited clinical efficacy, moderate selectivity, and propensity for acquired resistance have hindered the development of HMTs inhibitors. Targeted covalent modification represents a proven strategy for kinase drug development and has gained increasing attention in HMTs drug discovery. In this review, we focus on the discovery, characterization, and biological applications of covalent inhibitors for HMTs with emphasis on advancements in the field. In addition, we identify the challenges and future directions in this fast-growing research area of drug discovery.
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2
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Roy A, Niharika, Chakraborty S, Mishra J, Singh SP, Patra SK. Mechanistic aspects of reversible methylation modifications of arginine and lysine of nuclear histones and their roles in human colon cancer. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:261-302. [PMID: 37019596 DOI: 10.1016/bs.pmbts.2023.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Developmental proceedings and maintenance of cellular homeostasis are regulated by the precise orchestration of a series of epigenetic events that eventually control gene expression. DNA methylation and post-translational modifications (PTMs) of histones are well-characterized epigenetic events responsible for fine-tuning gene expression. PTMs of histones bear molecular logic of gene expression at chromosomal territory and have become a fascinating field of epigenetics. Nowadays, reversible methylation on histone arginine and lysine is gaining increasing attention as a significant PTM related to reorganizing local nucleosomal structure, chromatin dynamics, and transcriptional regulation. It is now well-accepted and reported that histone marks play crucial roles in colon cancer initiation and progression by encouraging abnormal epigenomic reprogramming. It is becoming increasingly clear that multiple PTM marks at the N-terminal tails of the core histones cross-talk with one another to intricately regulate DNA-templated biological processes such as replication, transcription, recombination, and damage repair in several malignancies, including colon cancer. These functional cross-talks provide an additional layer of message, which spatiotemporally fine-tunes the overall gene expression regulation. Nowadays, it is evident that several PTMs instigate colon cancer development. How colon cancer-specific PTM patterns or codes are generated and how they affect downstream molecular events are uncovered to some extent. Future studies would address more about epigenetic communication, and the relationship between histone modification marks to define cellular functions in depth. This chapter will comprehensively highlight the importance of histone arginine and lysine-based methylation modifications and their functional cross-talk with other histone marks from the perspective of colon cancer development.
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3
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Brekker MA, Sartawi T, Sawatzky TM, Causey CP, Rehman FK, Knuckley B. A peptoid-based inhibitor of protein arginine methyltransferase 1 (PRMT1) induces apoptosis and autophagy in cancer cells. J Biol Chem 2022; 298:102205. [PMID: 35764172 PMCID: PMC9307946 DOI: 10.1016/j.jbc.2022.102205] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 01/11/2023] Open
Abstract
Protein arginine methyltransferases (PRMTs) are S-adenosylmethionine-dependent enzymes that transfer a methyl group to arginine residues within proteins, most notably histones. The nine characterized PRMT family members are divided into three types depending on the resulting methylated product: asymmetric dimethylarginine (Type I PRMT), symmetric dimethylarginine (Type II PRMT), or monomethylated arginine (Type III PRMT). In some cancers, the resulting product can lead to either increased or decreased transcription of cancer-related genes, suggesting PRMT family members may be valid therapeutic targets. Traditionally, peptide-based compounds have been employed to target this family of enzymes, which has resulted in multiple tool and lead compounds being developed. However, peptide-based therapeutics suffer from poor stability and short half-lives, as proteases can render them useless by hydrolytic degradation. Conversely, peptoids, which are peptide-mimetics composed of N-substituted glycine monomers, are less susceptible to hydrolysis, resulting in improved stability and longer half-lives. Herein, we report the development of a bioavailable, peptoid-based PRMT1 inhibitor that induces cell death in MDA468 and HCT116 cancer cell lines while not exhibiting any significant impact on nontumorigenic HepaRG or normal human mammary epithelial cells. Furthermore, the inhibitor described herein appears to induce both apoptosis and autophagy, suggesting it may be a less toxic cytostatic agent. In conclusion, we propose this peptoid-based inhibitor has significant anticancer and therapeutic potential by reducing cell viability, growth, and size in breast and colon cancer. Further experimentation will help determine the mechanism of action and downstream effects of this compound.
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Affiliation(s)
- Mollie A. Brekker
- Department of Chemistry, University of North Florida, Jacksonville, Florida, USA
| | - Tala Sartawi
- Department of Biology, University of North Florida, Jacksonville, Florida, USA
| | - Tina M. Sawatzky
- Department of Chemistry, University of North Florida, Jacksonville, Florida, USA
| | - Corey P. Causey
- Department of Chemistry, University of North Florida, Jacksonville, Florida, USA
| | | | - Bryan Knuckley
- Department of Chemistry, University of North Florida, Jacksonville, Florida, USA.
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4
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Structure, Activity and Function of the Protein Arginine Methyltransferase 6. Life (Basel) 2021; 11:life11090951. [PMID: 34575100 PMCID: PMC8470942 DOI: 10.3390/life11090951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/25/2022] Open
Abstract
Members of the protein arginine methyltransferase (PRMT) family methylate the arginine residue(s) of several proteins and regulate a broad spectrum of cellular functions. Protein arginine methyltransferase 6 (PRMT6) is a type I PRMT that asymmetrically dimethylates the arginine residues of numerous substrate proteins. PRMT6 introduces asymmetric dimethylation modification in the histone 3 at arginine 2 (H3R2me2a) and facilitates epigenetic regulation of global gene expression. In addition to histones, PRMT6 methylates a wide range of cellular proteins and regulates their functions. Here, we discuss (i) the biochemical aspects of enzyme kinetics, (ii) the structural features of PRMT6 and (iii) the diverse functional outcomes of PRMT6 mediated arginine methylation. Finally, we highlight how dysregulation of PRMT6 is implicated in various types of cancers and response to viral infections.
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5
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Benns HJ, Wincott CJ, Tate EW, Child MA. Activity- and reactivity-based proteomics: Recent technological advances and applications in drug discovery. Curr Opin Chem Biol 2020; 60:20-29. [PMID: 32768892 DOI: 10.1016/j.cbpa.2020.06.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 06/22/2020] [Indexed: 12/20/2022]
Abstract
Activity-based protein profiling (ABPP) is recognized as a powerful and versatile chemoproteomic technology in drug discovery. Central to ABPP is the use of activity-based probes to report the activity of specific enzymes or reactivity of amino acid types in complex biological systems. Over the last two decades, ABPP has facilitated the identification of new drug targets and discovery of lead compounds in human and infectious disease. Furthermore, as part of a sustained global effort to illuminate the druggable proteome, the repertoire of target classes addressable with activity-based probes has vastly expanded in recent years. Here, we provide an overview of ABPP and summarise the major technological advances with an emphasis on probe development.
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Affiliation(s)
- Henry James Benns
- Department of Life Sciences, London, UK; Department of Chemistry, Imperial College London, London, UK
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6
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Richart L, Margueron R. Drugging histone methyltransferases in cancer. Curr Opin Chem Biol 2020; 56:51-62. [DOI: 10.1016/j.cbpa.2019.11.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 02/06/2023]
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7
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Lin H, Wang M, Zhang YW, Tong S, Leal RA, Shetty R, Vaddi K, Luengo JI. Discovery of Potent and Selective Covalent Protein Arginine Methyltransferase 5 (PRMT5) Inhibitors. ACS Med Chem Lett 2019; 10:1033-1038. [PMID: 31312404 PMCID: PMC6627734 DOI: 10.1021/acsmedchemlett.9b00074] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/22/2019] [Indexed: 12/22/2022] Open
Abstract
Protein arginine methyltransferase 5 (PRMT5) is known to symmetrically dimethylate numerous cytosolic and nuclear proteins that are involved in a variety of cellular processes. Recent findings have revealed its potential as a cancer therapeutic target. PRMT5 possesses a cysteine (C449) in the active site, unique to PRMT5. Therefore, covalent PRMT5 inhibition is an attractive chemical approach. Herein, we report an exciting discovery of a series of novel hemiaminals that under physiological conditions can be converted to aldehydes and react with C449 to form covalent adducts, which presumably undergo an unprecedented elimination to form the thiol-vinyl ethers, as indicated by electron density in the co-crystal structure of the PRMT5/MEP50 complex.
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Affiliation(s)
- Hong Lin
- Prelude Therapeutics, 200 Powder Mill Road, Wilmington, Delaware 19803, United States
| | - Min Wang
- Prelude Therapeutics, 200 Powder Mill Road, Wilmington, Delaware 19803, United States
| | - Yang W. Zhang
- Prelude Therapeutics, 200 Powder Mill Road, Wilmington, Delaware 19803, United States
| | - Shuilong Tong
- VIVA Biotech Ltd., 334 Aidisheng Road, Zhangjiang High-Tech Park, Shanghai 201203, China
| | - Raul A. Leal
- Prelude Therapeutics, 200 Powder Mill Road, Wilmington, Delaware 19803, United States
| | - Rupa Shetty
- Prelude Therapeutics, 200 Powder Mill Road, Wilmington, Delaware 19803, United States
| | - Kris Vaddi
- Prelude Therapeutics, 200 Powder Mill Road, Wilmington, Delaware 19803, United States
| | - Juan I. Luengo
- Prelude Therapeutics, 200 Powder Mill Road, Wilmington, Delaware 19803, United States
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8
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Lin H, Luengo JI. Nucleoside protein arginine methyltransferase 5 (PRMT5) inhibitors. Bioorg Med Chem Lett 2019; 29:1264-1269. [PMID: 30956011 DOI: 10.1016/j.bmcl.2019.03.042] [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: 01/31/2019] [Revised: 03/23/2019] [Accepted: 03/25/2019] [Indexed: 12/21/2022]
Abstract
Protein Arginine Methyltransferase 5 (PRMT5) is known to symmetrically dimethylate numerous cytosolic and nuclear proteins that are involved in a variety of cellular processes. Recent findings have revealed its potential as a cancer therapeutic target. PRMT5 selective inhibitors, GSK3326595, a substrate competitive inhibitor, and JNJ64619178, a SAM (S-adenosyl-l-methionine) mimetic/competitive inhibitor, have entered clinic trials for multiple cancer types. This review focuses on the recent developments in SAM mimetic nucleoside PRMT5 inhibitors, their SAR and structural insight based on published co-crystal structures.
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Affiliation(s)
- Hong Lin
- Prelude Therapeutics, 200 Powder Mill Road, Wilmington, DE 19803, United States
| | - Juan I Luengo
- Prelude Therapeutics, 200 Powder Mill Road, Wilmington, DE 19803, United States
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9
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Giannios I, Serafimidis I, Anastasiou V, Pezzolla D, Lesche M, Andree C, Bickle M, Gavalas A. Protein Methyltransferase Inhibition Decreases Endocrine Specification Through the Upregulation of Aldh1b1 Expression. Stem Cells 2019; 37:640-651. [PMID: 30681750 PMCID: PMC6850398 DOI: 10.1002/stem.2979] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 12/04/2018] [Accepted: 12/22/2018] [Indexed: 12/17/2022]
Abstract
Understanding the mechanisms that promote the specification of pancreas progenitors and regulate their self-renewal and differentiation will help to maintain and expand pancreas progenitor cells derived from human pluripotent stem (hPS) cells. This will improve the efficiency of current differentiation protocols of hPS cells into β-cells and bring such cells closer to clinical applications for the therapy of diabetes. Aldehyde dehydrogenase 1b1 (Aldh1b1) is a mitochondrial enzyme expressed specifically in progenitor cells during mouse pancreas development, and we have shown that its functional inactivation leads to accelerated differentiation and deficient β-cells. In this report, we aimed to identify small molecule inducers of Aldh1b1 expression taking advantage of a mouse embryonic stem (mES) cell Aldh1b1 lacZ reporter line and a pancreas differentiation protocol directing mES cells into pancreatic progenitors. We identified AMI-5, a protein methyltransferase inhibitor, as an Aldh1b1 inducer and showed that it can maintain Aldh1b1 expression in embryonic pancreas explants. This led to a selective reduction in endocrine specification. This effect was due to a downregulation of Ngn3, and it was mediated through Aldh1b1 since the effect was abolished in Aldh1b1 null pancreata. The findings implicated methyltransferase activity in the regulation of endocrine differentiation and showed that methyltransferases can act through specific regulators during pancreas differentiation. Stem Cells 2019;37:640-651.
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Affiliation(s)
- Ioannis Giannios
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | | | - Vivian Anastasiou
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Daniela Pezzolla
- Center for Regenerative Therapies Dresden (CRTD), Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Mathias Lesche
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany.,Biotechnology Center (Biotec), TU Dresden, Dresden, Germany
| | - Cordula Andree
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Marc Bickle
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Anthony Gavalas
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany.,Center for Regenerative Therapies Dresden (CRTD), Faculty of Medicine, TU Dresden, Dresden, Germany
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10
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Smith E, Zhou W, Shindiapina P, Sif S, Li C, Baiocchi RA. Recent advances in targeting protein arginine methyltransferase enzymes in cancer therapy. Expert Opin Ther Targets 2018; 22:527-545. [PMID: 29781349 PMCID: PMC6311705 DOI: 10.1080/14728222.2018.1474203] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Exploration in the field of epigenetics has revealed the diverse roles of the protein arginine methyltransferase (PRMT) family of proteins in multiple disease states. These findings have led to the development of specific inhibitors and discovery of several new classes of drugs with potential to treat both benign and malignant conditions. Areas covered: We provide an overview on the role of PRMT enzymes in healthy and malignant cells, highlighting the role of arginine methylation in specific pathways relevant to cancer pathogenesis. Additionally, we describe structure and catalytic activity of PRMT and discuss the mechanisms of action of novel small molecule inhibitors of specific members of the arginine methyltransferase family. Expert opinion: As the field of PRMT biology advances, it's becoming clear that this class of enzymes is highly relevant to maintaining normal physiologic processes as well and disease pathogenesis. We discuss the potential impact of PRMT inhibitors as a broad class of drugs, including the pleiotropic effects, off target effects the need for more detailed PRMT-centric interactomes, and finally, the potential for targeting this class of enzymes in clinical development of experimental therapeutics for cancer.
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Affiliation(s)
- Emily Smith
- The Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Wei Zhou
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Polina Shindiapina
- The Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Said Sif
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Chenglong Li
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Robert A. Baiocchi
- The Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
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11
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Zhang Z, Obianyo O, Dall E, Du Y, Fu H, Liu X, Kang SS, Song M, Yu SP, Cabrele C, Schubert M, Li X, Wang JZ, Brandstetter H, Ye K. Inhibition of delta-secretase improves cognitive functions in mouse models of Alzheimer's disease. Nat Commun 2017; 8:14740. [PMID: 28345579 PMCID: PMC5378956 DOI: 10.1038/ncomms14740] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 01/26/2017] [Indexed: 12/21/2022] Open
Abstract
δ-secretase, also known as asparagine endopeptidase (AEP) or legumain, is a lysosomal cysteine protease that cleaves both amyloid precursor protein (APP) and tau, mediating the amyloid-β and tau pathology in Alzheimer's disease (AD). Here we report the therapeutic effect of an orally bioactive and brain permeable δ-secretase inhibitor in mouse models of AD. We performed a high-throughput screen and identified a non-toxic and selective δ-secretase inhibitor, termed compound 11, that specifically blocks δ-secretase but not other related cysteine proteases. Co-crystal structure analysis revealed a dual active site-directed and allosteric inhibition mode of this compound class. Chronic treatment of tau P301S and 5XFAD transgenic mice with this inhibitor reduces tau and APP cleavage, ameliorates synapse loss and augments long-term potentiation, resulting in protection of memory. Therefore, these findings demonstrate that this δ-secretase inhibitor may be an effective clinical therapeutic agent towards AD.
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Affiliation(s)
- Zhentao Zhang
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Obiamaka Obianyo
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Elfriede Dall
- Department of Molecular Biology, University of Salzburg, Salzburg A-5020, Austria
| | - Yuhong Du
- Department of Pharmacology, Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Haian Fu
- Department of Pharmacology, Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Xia Liu
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Seong Su Kang
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Mingke Song
- Department of Anesthesiology Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Shan-Ping Yu
- Department of Anesthesiology Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Chiara Cabrele
- Department of Molecular Biology, University of Salzburg, Salzburg A-5020, Austria
| | - Mario Schubert
- Department of Molecular Biology, University of Salzburg, Salzburg A-5020, Austria
| | - Xiaoguang Li
- Pathophysiology Department, School of Basic Medicine and the Collaborative Innovation Center for Brain Science, Key Laboratory of Ministry of Education of China for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jian-Zhi Wang
- Pathophysiology Department, School of Basic Medicine and the Collaborative Innovation Center for Brain Science, Key Laboratory of Ministry of Education of China for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Co-innovation Center of Neuroregeneration, Nantong 226001, China
| | - Hans Brandstetter
- Department of Molecular Biology, University of Salzburg, Salzburg A-5020, Austria
| | - Keqiang Ye
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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Abstract
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Post-translational
modifications of histones by protein methyltransferases
(PMTs) and histone demethylases (KDMs) play an important role in the
regulation of gene expression and transcription and are implicated
in cancer and many other diseases. Many of these enzymes also target
various nonhistone proteins impacting numerous crucial biological
pathways. Given their key biological functions and implications in
human diseases, there has been a growing interest in assessing these
enzymes as potential therapeutic targets. Consequently, discovering
and developing inhibitors of these enzymes has become a very active
and fast-growing research area over the past decade. In this review,
we cover the discovery, characterization, and biological application
of inhibitors of PMTs and KDMs with emphasis on key advancements in
the field. We also discuss challenges, opportunities, and future directions
in this emerging, exciting research field.
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Affiliation(s)
- H Ümit Kaniskan
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Michael L Martini
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Jian Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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13
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Knuhtsen A, Legrand B, Van der Poorten O, Amblard M, Martinez J, Ballet S, Kristensen JL, Pedersen DS. Conformationally Constrained Peptidomimetics as Inhibitors of the Protein Arginine Methyl Transferases. Chemistry 2016; 22:14022-14028. [DOI: 10.1002/chem.201602518] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Indexed: 01/16/2023]
Affiliation(s)
- Astrid Knuhtsen
- Faculty of Health and Medical Sciences; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Baptiste Legrand
- Institut des Biomolécules Max Mousseron (IBMM); UMR 5247 CNRS-Université Montpellier-ENSCM; 15 Avenue Charles Flahault 34093 Montpellier, cedex 5 France
| | - Olivier Van der Poorten
- Research Group of Organic Chemistry; Departments of Chemistry and Bio-engineering Sciences; Vrije Universiteit Brussel; Pleinlaan 2 1050 Brussels Belgium
| | - Muriel Amblard
- Institut des Biomolécules Max Mousseron (IBMM); UMR 5247 CNRS-Université Montpellier-ENSCM; 15 Avenue Charles Flahault 34093 Montpellier, cedex 5 France
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron (IBMM); UMR 5247 CNRS-Université Montpellier-ENSCM; 15 Avenue Charles Flahault 34093 Montpellier, cedex 5 France
| | - Steven Ballet
- Research Group of Organic Chemistry; Departments of Chemistry and Bio-engineering Sciences; Vrije Universiteit Brussel; Pleinlaan 2 1050 Brussels Belgium
| | - Jesper L. Kristensen
- Faculty of Health and Medical Sciences; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Daniel Sejer Pedersen
- Faculty of Health and Medical Sciences; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
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14
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Abstract
The post-translational modification of arginine residues represents a key mechanism for the epigenetic control of gene expression. Aberrant levels of histone arginine modifications have been linked to the development of several diseases including cancer. In recent years, great progress has been made in understanding the physiological role of individual arginine modifications and their effects on chromatin function. The present review aims to summarize the structural and functional aspects of histone arginine modifying enzymes and their impact on gene transcription. We will discuss the potential for targeting these proteins with small molecules in a variety of disease states.
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Affiliation(s)
- Jakob Fuhrmann
- Department
of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Paul R. Thompson
- Department
of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program
in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
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15
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Hu H, Qian K, Ho MC, Zheng YG. Small Molecule Inhibitors of Protein Arginine Methyltransferases. Expert Opin Investig Drugs 2016; 25:335-58. [PMID: 26789238 DOI: 10.1517/13543784.2016.1144747] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
INTRODUCTION Arginine methylation is an abundant posttranslational modification occurring in mammalian cells and catalyzed by protein arginine methyltransferases (PRMTs). Misregulation and aberrant expression of PRMTs are associated with various disease states, notably cancer. PRMTs are prominent therapeutic targets in drug discovery. AREAS COVERED The authors provide an updated review of the research on the development of chemical modulators for PRMTs. Great efforts are seen in screening and designing potent and selective PRMT inhibitors, and a number of micromolar and submicromolar inhibitors have been obtained for key PRMT enzymes such as PRMT1, CARM1, and PRMT5. The authors provide a focus on their chemical structures, mechanism of action, and pharmacological activities. Pros and cons of each type of inhibitors are also discussed. EXPERT OPINION Several key challenging issues exist in PRMT inhibitor discovery. Structural mechanisms of many PRMT inhibitors remain unclear. There lacks consistency in potency data due to divergence of assay methods and conditions. Physiologically relevant cellular assays are warranted. Substantial engagements are needed to investigate pharmacodynamics and pharmacokinetics of the new PRMT inhibitors in pertinent disease models. Discovery and evaluation of potent, isoform-selective, cell-permeable and in vivo-active PRMT modulators will continue to be an active arena of research in years ahead.
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Affiliation(s)
- Hao Hu
- a Department of Pharmaceutical and Biomedical Sciences , The University of Georgia , Athens , GA , USA
| | - Kun Qian
- a Department of Pharmaceutical and Biomedical Sciences , The University of Georgia , Athens , GA , USA
| | - Meng-Chiao Ho
- b Institute of Biological Chemistry , Academia Sinica , Nankang , Taipei , Taiwan
| | - Y George Zheng
- a Department of Pharmaceutical and Biomedical Sciences , The University of Georgia , Athens , GA , USA
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16
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Fuhrmann J, Clancy K, Thompson PR. Chemical biology of protein arginine modifications in epigenetic regulation. Chem Rev 2015; 115:5413-61. [PMID: 25970731 PMCID: PMC4463550 DOI: 10.1021/acs.chemrev.5b00003] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Indexed: 01/10/2023]
Affiliation(s)
- Jakob Fuhrmann
- Department
of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Kathleen
W. Clancy
- Department of Biochemistry and Molecular Pharmacology and Program in Chemical
Biology, University of Massachusetts Medical
School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
| | - Paul R. Thompson
- Department of Biochemistry and Molecular Pharmacology and Program in Chemical
Biology, University of Massachusetts Medical
School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
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17
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A selective inhibitor of PRMT5 with in vivo and in vitro potency in MCL models. Nat Chem Biol 2015; 11:432-7. [PMID: 25915199 DOI: 10.1038/nchembio.1810] [Citation(s) in RCA: 391] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 04/01/2015] [Indexed: 12/25/2022]
Abstract
Protein arginine methyltransferase-5 (PRMT5) is reported to have a role in diverse cellular processes, including tumorigenesis, and its overexpression is observed in cell lines and primary patient samples derived from lymphomas, particularly mantle cell lymphoma (MCL). Here we describe the identification and characterization of a potent and selective inhibitor of PRMT5 with antiproliferative effects in both in vitro and in vivo models of MCL. EPZ015666 (GSK3235025) is an orally available inhibitor of PRMT5 enzymatic activity in biochemical assays with a half-maximal inhibitory concentration (IC50) of 22 nM and broad selectivity against a panel of other histone methyltransferases. Treatment of MCL cell lines with EPZ015666 led to inhibition of SmD3 methylation and cell death, with IC50 values in the nanomolar range. Oral dosing with EPZ015666 demonstrated dose-dependent antitumor activity in multiple MCL xenograft models. EPZ015666 represents a validated chemical probe for further study of PRMT5 biology and arginine methylation in cancer and other diseases.
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18
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Yang P, Liu K. Activity-based protein profiling: recent advances in probe development and applications. Chembiochem 2015; 16:712-24. [PMID: 25652106 DOI: 10.1002/cbic.201402582] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Indexed: 11/08/2022]
Abstract
The completion of the human genome sequencing project has provided a wealth of new information regarding the genomic blueprint of the cell. Although, to date, there are roughly 20,000 genes in the human genome, the functions of only a handful of proteins are clear. The major challenge lies in translating genomic information into an understanding of their cellular functions. The recently developed activity-based protein profiling (ABPP) is an unconventional approach that is complementary for gene expression analysis and an ideal utensil in decoding this overflow of genomic information. This approach makes use of synthetic small molecules that covalently modify a set of related proteins and subsequently facilitates identification of the target protein, enabling rapid biochemical analysis and inhibitor discovery. This tutorial review introduces recent advances in the field of ABPP and its applications.
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Affiliation(s)
- Pengyu Yang
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037 (USA)
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19
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Hu H, Owens EA, Su H, Yan L, Levitz A, Zhao X, Henary M, Zheng YG. Exploration of cyanine compounds as selective inhibitors of protein arginine methyltransferases: synthesis and biological evaluation. J Med Chem 2015; 58:1228-43. [PMID: 25559100 PMCID: PMC4610307 DOI: 10.1021/jm501452j] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Protein arginine methyltransferase
1 (PRMT1) is involved in many biological activities, such as gene
transcription, signal transduction, and RNA processing. Overexpression
of PRMT1 is related to cardiovascular diseases, kidney diseases, and
cancers; therefore, selective PRMT1 inhibitors serve as chemical probes
to investigate the biological function of PRMT1 and drug candidates
for disease treatment. Our previous work found trimethine cyanine
compounds that effectively inhibit PRMT1 activity. In our present
study, we systematically investigated the structure–activity
relationship of cyanine structures. A pentamethine compound, E-84
(compound 50), showed inhibition on PRMT1 at the micromolar
level and 6- to 25-fold selectivity over CARM1, PRMT5, and PRMT8.
The cellular activity suggests that compound 50 permeated
the cellular membrane, inhibited cellular PRMT1 activity, and blocked
leukemia cell proliferation. Additionally, our molecular docking study
suggested compound 50 might act by occupying the cofactor
binding site, which provided a roadmap to guide further optimization
of this lead compound.
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Affiliation(s)
- Hao Hu
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia , Athens, Georgia 30602, United States
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20
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Xie Y, Zhou R, Lian F, Liu Y, Chen L, Shi Z, Zhang N, Zheng M, Shen B, Jiang H, Liang Z, Luo C. Virtual screening and biological evaluation of novel small molecular inhibitors against protein arginine methyltransferase 1 (PRMT1). Org Biomol Chem 2014; 12:9665-73. [PMID: 25348815 DOI: 10.1039/c4ob01591f] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Protein arginine methylation is a common post-translational modification which is crucial for a variety of biological processes. Dysregulation of protein arginine methyltransferases (PRMTs) activity has been implicated in cancer and other serious diseases. Thus, small molecule inhibitors against PRMT have great potential for therapeutic development. Herein, through the combination of virtual screening and bioassays, six small molecular compounds were identified as PRMT1 inhibitors. Amongst them, the binding affinity of compounds DCLX069 and DCLX078 with PRMT1 was further validated by T1ρ and saturation transfer difference (STD) NMR experiments. Most important of all, both compounds effectively blocked cell proliferation in breast cancer, liver cancer and acute myeloid leukemia cell lines. The binding mode analysis from molecular docking simulations theoretically indicated that both inhibitors occupied the SAM binding pocket to exert the inhibitory effect. Taken together, our compounds enriched the structural scaffolds as PRMT1 inhibitors and afforded clues for further optimization.
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Affiliation(s)
- Yiqian Xie
- Center for Systems Biology, Soochow University, Jiangsu 215006, China.
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21
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Targeting protein arginine N-methyltransferases with peptide-based inhibitors: opportunities and challenges. Future Med Chem 2013; 5:2199-206. [DOI: 10.4155/fmc.13.184] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Recently peptide-based inhibitors have been used to selectively inhibit a family of epigenetic enzymes called protein arginine N-methyltransferases (PRMTs), which has been implicated in different physiological processes and human diseases, such as heart disease and cancer. The diverse efforts to tease out subtle structural differences among PRMT enzymes in order to generate selective inhibitors as well as existing challenges in the field will be examined. The acquisition of PRMT substrate sequence preferences and structural information obtained from small-molecule inhibitors have helped in developing different peptide-based inhibitors that show great promise not only as inhibitors, but also as molecular probes to characterize PRMTs.
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22
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Fuhrmann J, Subramanian V, Thompson PR. Targeting the arginine phosphatase YwlE with a catalytic redox-based inhibitor. ACS Chem Biol 2013; 8:2024-32. [PMID: 23838530 DOI: 10.1021/cb4001469] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein phosphatases are critical regulators of cellular signaling in both eukaryotes and prokaryotes. The majority of protein phosphatases dephosphorylate phosphoserine/phosphothreonine or phosphotyrosine residues. Recently, however, YwlE, a member of the low-molecular weight protein tyrosine phosphatase (LMW-PTP) family, was shown to efficiently target phosphoarginine. YwlE shares several sequence motifs with this family including the C(X)4 CR(S/T) motif that is crucial for catalysis and redox regulation of the enzyme. Herein we confirm that Cys9 and Cys14 play important roles in YwlE catalysis and regulation. On the basis of these observations, we designed and synthesized a YwlE inhibitor, denoted cyc-SeCN-amidine, that irreversibly inhibits YwlE (kinact/KI = 310 M(-1) min(-1)) by inducing disulfide bond formation between the two active site cysteine residues. Interestingly, inactivation appears to be catalytic, since the compound is neither destroyed nor altered after enzyme inhibition. Although the exact mechanism of disulfide induction remains elusive, we propose several potential mechanisms accounting for the cyc-SeCN-amidine mediated inhibition of YwlE. These findings could stimulate the design of similar selenium-based compounds targeting other redox-sensitive enzymes.
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Affiliation(s)
- Jakob Fuhrmann
- Department
of Chemistry and ‡The Kellogg School of Science and Technology, The Scripps Research Institute, 130 Scripps Way, Jupiter,
Florida 33458, United States
| | - Venkataraman Subramanian
- Department
of Chemistry and ‡The Kellogg School of Science and Technology, The Scripps Research Institute, 130 Scripps Way, Jupiter,
Florida 33458, United States
| | - Paul R. Thompson
- Department
of Chemistry and ‡The Kellogg School of Science and Technology, The Scripps Research Institute, 130 Scripps Way, Jupiter,
Florida 33458, United States
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23
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Castellano S, Spannhoff A, Milite C, Dal Piaz F, Cheng D, Tosco A, Viviano M, Yamani A, Cianciulli A, Sala M, Cura V, Cavarelli J, Novellino E, Mai A, Bedford MT, Sbardella G. Identification of small-molecule enhancers of arginine methylation catalyzed by coactivator-associated arginine methyltransferase 1. J Med Chem 2012; 55:9875-90. [PMID: 23095008 PMCID: PMC3508294 DOI: 10.1021/jm301097p] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Arginine methylation is a common post-translational modification that is crucial in modulating gene expression at multiple critical levels. The arginine methyltransferases (PRMTs) are envisaged as promising druggable targets, but their role in physiological and pathological pathways is far from being clear due to the limited number of modulators reported to date. In this effort, enzyme activators can be invaluable tools useful as gain-of-function reagents to interrogate the biological roles in cells and in vivo of PRMTs. Yet the identification of such molecules is rarely pursued. Herein we describe a series of aryl ureido acetamido indole carboxylates (dubbed "uracandolates"), able to increase the methylation of histone (H3) or nonhistone (polyadenylate-binding protein 1, PABP1) substrates induced by coactivator-associated arginine methyltransferase 1 (CARM1), both in in vitro and cellular settings. To the best of our knowledge, this is the first report of compounds acting as CARM1 activators.
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Affiliation(s)
- Sabrina Castellano
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Astrid Spannhoff
- University of Texas M.D. Anderson Cancer Center, Science Park-Research Division, Smithville, Texas 78957, USA
| | - Ciro Milite
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Fabrizio Dal Piaz
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Donghang Cheng
- University of Texas M.D. Anderson Cancer Center, Science Park-Research Division, Smithville, Texas 78957, USA
| | - Alessandra Tosco
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Monica Viviano
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Abdellah Yamani
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Agostino Cianciulli
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Marina Sala
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Vincent Cura
- Département de Biologie Structurale Intégrative, IGBMC (Institut de Génétique et Biologie Moléculaire et Cellulaire), UDS, CNRS, INSERM, 67404 Illkirch Cedex, France
| | - Jean Cavarelli
- Département de Biologie Structurale Intégrative, IGBMC (Institut de Génétique et Biologie Moléculaire et Cellulaire), UDS, CNRS, INSERM, 67404 Illkirch Cedex, France
| | - Ettore Novellino
- Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano 49, I-80131 Napoli, Italy
| | - Antonello Mai
- Istituto Pasteur – Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, P.le A. Moro 5, I-00185 Roma, Italy
| | - Mark T. Bedford
- University of Texas M.D. Anderson Cancer Center, Science Park-Research Division, Smithville, Texas 78957, USA
| | - Gianluca Sbardella
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
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24
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Hobley G, McKelvie JC, Harmer JE, Howe J, Oyston PC, Roach PL. Development of rationally designed DNA N6 adenine methyltransferase inhibitors. Bioorg Med Chem Lett 2012; 22:3079-82. [DOI: 10.1016/j.bmcl.2012.03.072] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 03/16/2012] [Accepted: 03/19/2012] [Indexed: 01/12/2023]
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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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Obianyo O, Thompson PR. Kinetic mechanism of protein arginine methyltransferase 6 (PRMT6). J Biol Chem 2012; 287:6062-71. [PMID: 22219200 DOI: 10.1074/jbc.m111.333609] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The protein arginine methyltransferases (PRMTs) are a family of enzymes that catalyze the mono- and dimethylation of arginine residues in a variety of proteins. Although these enzymes play important roles in a variety of cellular processes, aberrant PRMT activity is associated with several disease states, including heart disease and cancer. In an effort to guide the development of inhibitors targeting individual PRMTs, we initiated studies to characterize the molecular mechanisms of PRMT catalysis. Herein, we report studies on the kinetic mechanism of PRMT6. Initial velocity, product inhibition, and dead-end analog inhibition studies with the AcH4-21 and R1 peptides, as well as their monomethylated versions, indicate, in contrast to a previous report, that PRMT6 utilizes a rapid equilibrium random mechanism with dead-end EAP and EBQ complexes.
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Affiliation(s)
- Obiamaka Obianyo
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, USA
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27
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Obianyo O, Causey CP, Jones JE, Thompson PR. Activity-based protein profiling of protein arginine methyltransferase 1. ACS Chem Biol 2011; 6:1127-35. [PMID: 21838253 DOI: 10.1021/cb2001473] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The protein arginine methyltransferases (PRMTs) are SAM-dependent enzymes that catalyze the mono- and dimethylation of peptidyl arginine residues. PRMT1 is the founding member of the PRMT family, and this isozyme is responsible for methylating ∼85% of the arginine residues in mammalian cells. Additionally, PRMT1 activity is aberrantly upregulated in heart disease and cancer. As a part of a program to develop isozyme-specific PRMT inhibitors, we recently described the design and synthesis of C21, a chloroacetamidine bearing histone H4 tail analogue that acts as an irreversible PRMT1 inhibitor. Given the covalent nature of the interaction, we set out to develop activity-based probes (ABPs) that could be used to characterize the physiological roles of PRMT1. Herein, we report the design, synthesis, and characterization of fluorescein-conjugated C21 (F-C21) and biotin-conjugated C21 (B-C21) as PRMT1-specific ABPs. Additionally, we provide the first evidence that PRMT1 activity is negatively regulated in a spatial and temporal fashion.
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Affiliation(s)
- Obiamaka Obianyo
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter St, Columbia, South Carolina 29208, United States
| | - Corey P. Causey
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter St, Columbia, South Carolina 29208, United States
| | - Justin E. Jones
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Paul R. Thompson
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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28
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Dowden J, Pike RA, Parry RV, Hong W, Muhsen UA, Ward SG. Small molecule inhibitors that discriminate between protein arginine N-methyltransferases PRMT1 and CARM1. Org Biomol Chem 2011; 9:7814-21. [PMID: 21952734 DOI: 10.1039/c1ob06100c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein arginine N-methyltransferases (PRMTs) selectively replace N-H for N-CH(3) at substrate protein guanidines, a post-translational modification important for a range of biological processes, such as epigenetic regulation, signal transduction and cancer progression. Selective chemical probes are required to establish the dynamic function of individual PRMTs. Herein, model inhibitors designed to occupy PRMT binding sites for an arginine substrate and S-adenosylmethionine (AdoMet) co-factor are described. Expedient access to such compounds by modular synthesis is detailed. Remarkably, biological evaluation revealed some compounds to be potent inhibitors of PRMT1, but inactive against CARM1. Docking studies show how prototype compounds may occupy the binding sites for a co-factor and arginine substrate. Overlay of PRMT1 and CARM1 binding sites suggest a difference in a single amino acid that may be responsible for the observed selectivity.
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Affiliation(s)
- James Dowden
- School of Chemistry, University of Nottingham, University Park, Nottingham, UK NG7 2RD.
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29
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't Hart P, Lakowski TM, Thomas D, Frankel A, Martin NI. Peptidic partial bisubstrates as inhibitors of the protein arginine N-methyltransferases. Chembiochem 2011; 12:1427-32. [PMID: 21560220 DOI: 10.1002/cbic.201100074] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Indexed: 11/10/2022]
Affiliation(s)
- Peter 't Hart
- Department of Medicinal Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
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30
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Rust HL, Zurita-Lopez CI, Clarke S, Thompson PR. Mechanistic studies on transcriptional coactivator protein arginine methyltransferase 1. Biochemistry 2011; 50:3332-45. [PMID: 21417440 PMCID: PMC3582369 DOI: 10.1021/bi102022e] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein arginine methyltransferases (PRMTs) catalyze the transfer of methyl groups from S-adenosylmethionine (SAM) to the guanidinium group of arginine residues in a number of important cell signaling proteins. PRMT1 is the founding member of this family, and its activity appears to be dysregulated in heart disease and cancer. To begin to characterize the catalytic mechanism of this isozyme, we assessed the effects of mutating a number of highly conserved active site residues (i.e., Y39, R54, E100, E144, E153, M155, and H293), which are believed to play key roles in SAM recognition, substrate binding, and catalysis. The results of these studies, as well as pH-rate studies, and the determination of solvent isotope effects (SIEs) indicate that M155 plays a critical role in both SAM binding and the processivity of the reaction but is not responsible for the regiospecific formation of asymmetrically dimethylated arginine (ADMA). Additionally, mutagenesis studies on H293, combined with pH studies and the lack of a normal SIE, do not support a role for this residue as a general base. Furthermore, the lack of a normal SIE with either the wild type or catalytically impaired mutants suggests that general acid/base catalysis is not important for promoting methyl transfer. This result, combined with the fact that the E144A/E153A double mutant retains considerably more activity then the single mutants alone, suggests that the PRMT1-catalyzed reaction is primarily driven by bringing the substrate guanidinium into the proximity of the S-methyl group of SAM and that the prior deprotonation of the substrate guanidinium is not required for methyl transfer.
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Affiliation(s)
- Heather L. Rust
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458
- Department of Chemistry & Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208
| | - Cecilia I. Zurita-Lopez
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095
| | - Steven Clarke
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095
| | - Paul R. Thompson
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458
- Department of Chemistry & Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208
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31
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Cheng D, Bedford MT. Xenoestrogens regulate the activity of arginine methyltransferases. Chembiochem 2011; 12:323-9. [PMID: 21243720 PMCID: PMC3142315 DOI: 10.1002/cbic.201000522] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Indexed: 11/08/2022]
Abstract
Arginine methylation is a common post-translational modification that has been strongly implicated in transcriptional regulation. The arginine methyltransferases (PRMTs) were first reported as transcriptional coactivators for the estrogen and androgen receptors. Compounds that inhibit these enzymes will provide us with valuable tools for dissecting the roles of these enzymes in cells, and will possibly also have therapeutic applications. In order to identify such inhibitors of the PRMTs, we have previously performed a high-throughput screen using a small molecule library. These compounds were named arginine methyltransferase inhibitors (AMIs). The majority of these inhibitors were polyphenols, and one in particular (AMI-18) shared additional features with a group of known xenoestrogens. We, thus, tested a panel of xenoestrogens and found that a number of them possess the ability to inhibit PRMT activity, in vitro. These inhibitors primarily target CARM1, and include licochalcone A, kepone, benzyl 4-hydroxybenzoate, and tamoxifen. We developed a cell-based reporter system for CARM1 activity, and showed that tamoxifen (IC(50) =30 μM) inhibits this PRMT. The ability of these compounds to regulate the activity of transcriptional coactivators may be an unappreciated mechanism of action for xenoestrogens, and might also explain the efficacy of high-dose tamoxifen treatment on estrogen receptor negative cancers.
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Affiliation(s)
- Donghang Cheng
- Department of Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas, 78957, USA
| | - Mark T. Bedford
- Department of Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas, 78957, USA
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32
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Lakowski TM, ’t Hart P, Ahern CA, Martin NI, Frankel A. Nη-substituted arginyl peptide inhibitors of protein arginine N-methyltransferases. ACS Chem Biol 2010; 5:1053-63. [PMID: 20701328 DOI: 10.1021/cb100161u] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Protein arginine N-methyltransferases (PRMTs) catalyze the post-translational methylation of arginine residues within substrate proteins. Their roles in the epigenetic regulation of gene expression make them viable targets for drug discovery. Peptides containing a single arginine residue substituted at the guanidino nitrogen (N(η)) with an ethyl group bearing zero to three fluorine atoms (R1-1, -2, -3, and -4) have been synthesized and tested for methylation and inhibition activity with PRMT1, PRMT6, and CARM1. Only the nonfluorinated R1-1 peptide is methylated by PRMT1, demonstrating that the N(η)-substituted arginine is accommodated by its active site. The R1-1 ethyl-substituted guanidine N(η) was further identified as the methylation site via mass spectrometry. Although weak inhibitors of CARM1, R1-1, -2, -3, and -4 are potent inhibitors of PRMT1 and PRMT6. These peptides are more potent against PRMT1 than product inhibitor peptides, showing that N(η)-substituted arginyl peptides do not work by a purely product inhibitor mechanism. A trend of increasing potency with an increase in the number of fluorine atoms is observed for PRMT1, which may result from the corresponding change in the guanidino dipole moment. Modeling of the ethyl-arginine moiety of the R1-1 peptide demonstrates that the active site of PRMT1 accommodates such modifications. N(η)-Substituted arginyl peptides represent lead compounds for the further development of inhibitors that target the methyl-acceptor binding site of PRMTs.
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Affiliation(s)
- Ted M. Lakowski
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter ’t Hart
- Department of Medicinal Chemistry & Chemical Biology, University of Utrecht, Utrecht, The Netherlands
| | - Christopher A. Ahern
- Department of Anaesthesiology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Nathaniel I. Martin
- Department of Medicinal Chemistry & Chemical Biology, University of Utrecht, Utrecht, The Netherlands
| | - Adam Frankel
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
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33
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Bicker KL, Obianyo O, Rust HL, Thompson PR. A combinatorial approach to characterize the substrate specificity of protein arginine methyltransferase 1. MOLECULAR BIOSYSTEMS 2010; 7:48-51. [PMID: 20607165 DOI: 10.1039/c0mb00015a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dysregulation of protein arginine methyltransferases (PRMTs) is implicated in a wide variety of disease states. Here we report the design, synthesis, and screening of a combinatorial peptide library used to characterize the substrate specificity of PRMT1. The information gained from this approach was used to develop a PRMT1 inhibitor with enhanced selectivity.
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Affiliation(s)
- Kevin L Bicker
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter St, Columbia, South Carolina, USA
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