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Hendrickson-Rebizant T, Sudhakar SRN, Rowley MJ, Frankel A, Davie JR, Lakowski TM. Structure, Function, and Activity of Small Molecule and Peptide Inhibitors of Protein Arginine Methyltransferase 1. J Med Chem 2024; 67:15931-15946. [PMID: 39250434 DOI: 10.1021/acs.jmedchem.4c00490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Protein arginine N-methyltransferases (PRMT) are a family of S-adenosyl-l-methionine (SAM)-dependent enzymes that transfer methyl-groups to the ω-N of arginyl residues in proteins. PRMTs are involved in regulating gene expression, RNA splicing, and other activities. PRMT1 is responsible for most cellular arginine methylation, and its dysregulation is involved in many cancers. Accordingly, many groups have targeted PRMT1 using small molecules and peptide inhibitors. In this Perspective, we discuss the structure and function of selected peptide and small molecule inhibitors of PRMT1. We examine inhibitors that target the substrate arginyl peptide, SAM, or both binding sites, and the type of inhibition that results. Small molecules, and peptides that are bisubstrate, and/or PRMT transition state mimic inhibitors as well as inhibitors that alkylate PRMTs will be discussed. We define a structure-activity relationship for the aromatic/heteroaromatic N-methylethylenediamine inhibitors of PRMT1 and review current progress of PRMT1 inhibitors in clinical trials.
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Affiliation(s)
- Thordur Hendrickson-Rebizant
- Pharmaceutical analysis Laboratory, College of Pharmacy, University of Manitoba, 750 McDermot Avenue West, Winnipeg, Manitoba R3E 0T5, Canada
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0 V9, Canada
| | - Sadhana R N Sudhakar
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0 V9, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Michael J Rowley
- Faculty of Pharmaceutical Sciences, The University of British Columbia, 2405 Wesbrook Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Adam Frankel
- Faculty of Pharmaceutical Sciences, The University of British Columbia, 2405 Wesbrook Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - James R Davie
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0 V9, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Ted M Lakowski
- Pharmaceutical analysis Laboratory, College of Pharmacy, University of Manitoba, 750 McDermot Avenue West, Winnipeg, Manitoba R3E 0T5, Canada
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0 V9, Canada
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2
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Structural and biochemical evaluation of bisubstrate inhibitors of protein arginine N-methyltransferases PRMT1 and CARM1 (PRMT4). Biochem J 2020; 477:787-800. [PMID: 32011657 PMCID: PMC7054760 DOI: 10.1042/bcj20190826] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 12/28/2022]
Abstract
Attenuating the function of protein arginine methyltransferases (PRMTs) is an objective for the investigation and treatment of several diseases including cardiovascular disease and cancer. Bisubstrate inhibitors that simultaneously target binding sites for arginine substrate and the cofactor (S-adenosylmethionine (SAM)) have potential utility, but structural information on their binding is required for their development. Evaluation of bisubstrate inhibitors featuring an isosteric guanidine replacement with two prominent enzymes PRMT1 and CARM1 (PRMT4) by isothermal titration calorimetry (ITC), activity assays and crystallography are reported. Key findings are that 2-aminopyridine is a viable replacement for guanidine, providing an inhibitor that binds more strongly to CARM1 than PRMT1. Moreover, a residue around the active site that differs between CARM1 (Asn-265) and PRMT1 (Tyr-160) is identified that affects the side chain conformation of the catalytically important neighbouring glutamate in the crystal structures. Mutagenesis data supports its contribution to the difference in binding observed for this inhibitor. Structures of CARM1 in complex with a range of seven inhibitors reveal the binding modes and show that inhibitors with an amino acid terminus adopt a single conformation whereas the electron density for equivalent amine-bearing inhibitors is consistent with preferential binding in two conformations. These findings inform the molecular basis of CARM1 ligand binding and identify differences between CARM1 and PRMT1 that can inform drug discovery efforts.
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3
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Alim K, Lefranc B, Sopkova-de Oliveira Santos J, Dubessy C, Picot M, Boutin JA, Vaudry H, Chartrel N, Vaudry D, Chuquet J, Leprince J. Design, Synthesis, Molecular Dynamics Simulation, and Functional Evaluation of a Novel Series of 26RFa Peptide Analogues Containing a Mono- or Polyalkyl Guanidino Arginine Derivative. J Med Chem 2018; 61:10185-10197. [PMID: 30358997 DOI: 10.1021/acs.jmedchem.8b01332] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
26RFa, the endogenous QRFPR ligand, is implicated in several physiological and pathological conditions such as the regulation of glucose homeostasis and bone mineralization; hence, QRFPR ligands display therapeutic potential. At the molecular level, functional interaction occurs between residues Arg25 of 26RFa and Gln125 of QRFPR. We have designed 26RFa(20-26) analogues incorporating arginine derivatives modified by alkylated substituents. We found that the Arg25 side chain length was necessary to retain the activity of 26RFa(20-26) and that N-monoalkylation of arginine was accommodated by the QRFPR active site. In particular, [(Me)ωArg25]26RFa(20-26) (5b, LV-2186) appeared to be 25-fold more potent than 26RFa(20-26) and displayed a position in a QRFPR homology model slightly different to that of the unmodified heptapeptide. Other peptides were less potent than 26RFa(20-26), exhibited partial agonistic activity, or were totally inactive in accordance to different ligand-bound structures. In vivo, [(Me)ωArg25]26RFa(20-26) exerted a delayed 26RFa-like hypoglycemic effect. Finally, N-methyl substituted arginine-containing peptides represent lead compounds for further development of QRFPR agonists.
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Affiliation(s)
- Karima Alim
- INSERM U1239, Laboratory of Neuronal and Neuroendocrine Differentiation and Communication , Normandy University , 76000 Rouen , France
| | - Benjamin Lefranc
- INSERM U1239, Laboratory of Neuronal and Neuroendocrine Differentiation and Communication , Normandy University , 76000 Rouen , France.,Cell Imaging Platform of Normandy (PRIMACEN) , Normandy University , 76000 Rouen , France
| | | | - Christophe Dubessy
- INSERM U1239, Laboratory of Neuronal and Neuroendocrine Differentiation and Communication , Normandy University , 76000 Rouen , France.,Cell Imaging Platform of Normandy (PRIMACEN) , Normandy University , 76000 Rouen , France
| | - Marie Picot
- INSERM U1239, Laboratory of Neuronal and Neuroendocrine Differentiation and Communication , Normandy University , 76000 Rouen , France
| | - Jean A Boutin
- Institut de Recherches Internationales Servier , 50 rue Carnot , 92150 Suresnes , France
| | - Hubert Vaudry
- INSERM U1239, Laboratory of Neuronal and Neuroendocrine Differentiation and Communication , Normandy University , 76000 Rouen , France.,Cell Imaging Platform of Normandy (PRIMACEN) , Normandy University , 76000 Rouen , France
| | - Nicolas Chartrel
- INSERM U1239, Laboratory of Neuronal and Neuroendocrine Differentiation and Communication , Normandy University , 76000 Rouen , France
| | - David Vaudry
- INSERM U1239, Laboratory of Neuronal and Neuroendocrine Differentiation and Communication , Normandy University , 76000 Rouen , France.,Cell Imaging Platform of Normandy (PRIMACEN) , Normandy University , 76000 Rouen , France
| | - Julien Chuquet
- INSERM U1239, Laboratory of Neuronal and Neuroendocrine Differentiation and Communication , Normandy University , 76000 Rouen , France
| | - Jérôme Leprince
- INSERM U1239, Laboratory of Neuronal and Neuroendocrine Differentiation and Communication , Normandy University , 76000 Rouen , France.,Cell Imaging Platform of Normandy (PRIMACEN) , Normandy University , 76000 Rouen , France
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4
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Transition state mimics are valuable mechanistic probes for structural studies with the arginine methyltransferase CARM1. Proc Natl Acad Sci U S A 2017; 114:3625-3630. [PMID: 28330993 DOI: 10.1073/pnas.1618401114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Coactivator associated arginine methyltransferase 1 (CARM1) is a member of the protein arginine methyltransferase (PRMT) family and methylates a range of proteins in eukaryotic cells. Overexpression of CARM1 is implicated in a number of cancers, and it is therefore seen as a potential therapeutic target. Peptide sequences derived from the well-defined CARM1 substrate poly(A)-binding protein 1 (PABP1) were covalently linked to an adenosine moiety as in the AdoMet cofactor to generate transition state mimics. These constructs were found to be potent CARM1 inhibitors and also formed stable complexes with the enzyme. High-resolution crystal structures of CARM1 in complex with these compounds confirm a mode of binding that is indeed reflective of the transition state at the CARM1 active site. Given the transient nature of PRMT-substrate complexes, such transition state mimics represent valuable chemical tools for structural studies aimed at deciphering the regulation of arginine methylation mediated by the family of arginine methyltransferases.
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5
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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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6
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Morales Y, Cáceres T, May K, Hevel JM. Biochemistry and regulation of the protein arginine methyltransferases (PRMTs). Arch Biochem Biophys 2015; 590:138-152. [PMID: 26612103 DOI: 10.1016/j.abb.2015.11.030] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/14/2015] [Accepted: 11/15/2015] [Indexed: 12/27/2022]
Abstract
Many key cellular processes can be regulated by the seemingly simple addition of one, or two, methyl groups to arginine residues by the nine known mammalian protein arginine methyltransferases (PRMTs). The impact that arginine methylation has on cellular well-being is highlighted by the ever growing evidence linking PRMT dysregulation to disease states, which has marked the PRMTs as prominent pharmacological targets. This review is meant to orient the reader with respect to the structural features of the PRMTs that account for catalytic activity, as well as provide a framework for understanding how these enzymes are regulated. An overview of what we understand about substrate recognition and binding is provided. Control of product specificity and enzyme processivity are introduced as necessary but flexible features of the PRMTs. Precise control of PRMT activity is a critical component to eukaryotic cell health, especially given that an arginine demethylase has not been identified. We therefore conclude the review with a comprehensive discussion of how protein arginine methylation is regulated.
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Affiliation(s)
- Yalemi Morales
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322, United States
| | - Tamar Cáceres
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322, United States
| | - Kyle May
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322, United States
| | - Joan M Hevel
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322, United States.
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7
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van Haren M, van Ufford LQ, Moret EE, Martin NI. Synthesis and evaluation of protein arginine N-methyltransferase inhibitors designed to simultaneously occupy both substrate binding sites. Org Biomol Chem 2015; 13:549-60. [PMID: 25380215 DOI: 10.1039/c4ob01734j] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The protein arginine N-methyltransferases (PRMTs) are a family of enzymes that function by specifically transferring a methyl group from the cofactor S-adenosyl-L-methionine (AdoMet) to the guanidine group of arginine residues in target proteins. The most notable is the PRMT-mediated methylation of arginine residues that are present in histone proteins which can lead to chromatin remodelling and influence gene transcription. A growing body of evidence now implicates dysregulated PRMT activity in a number of diseases including various forms of cancer. The development of PRMT inhibitors may therefore hold potential as a means of developing new therapeutics. We here report the synthesis and evaluation of a series of small molecule PRMT inhibitors designed to simultaneously occupy the binding sites of both the guanidino substrate and AdoMet cofactor. Potent inhibition and surprising selectivity were observed when testing these compounds against a panel of methyltransferases.
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Affiliation(s)
- Matthijs van Haren
- Medicinal Chemistry & Chemical Biology Group, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands.
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8
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Lakowski TM, Pak ML, Szeitz A, Thomas D, Vhuiyan MI, Clement B, Frankel A. Arginine methylation in yeast proteins during stationary-phase growth and heat shock. Amino Acids 2015; 47:2561-71. [DOI: 10.1007/s00726-015-2047-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 07/08/2015] [Indexed: 11/29/2022]
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9
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Bonnefond L, Stojko J, Mailliot J, Troffer-Charlier N, Cura V, Wurtz JM, Cianférani S, Cavarelli J. Functional insights from high resolution structures of mouse protein arginine methyltransferase 6. J Struct Biol 2015; 191:175-83. [PMID: 26094878 DOI: 10.1016/j.jsb.2015.06.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 03/19/2015] [Accepted: 06/18/2015] [Indexed: 01/15/2023]
Abstract
PRMT6 is a protein arginine methyltransferase involved in transcriptional regulation, human immunodeficiency virus pathogenesis, DNA base excision repair, and cell cycle progression. Like other PRMTs, PRMT6 is overexpressed in several cancer types and is therefore considered as a potential anti-cancer drug target. In the present study, we described six crystal structures of PRMT6 from Mus musculus, solved and refined at 1.34 Å for the highest resolution structure. The crystal structures revealed that the folding of the helix αX is required to stabilize a productive active site before methylation of the bound peptide can occur. In the absence of cofactor, metal cations can be found in the catalytic pocket at the expected position of the guanidinium moiety of the target arginine substrate. Using mass spectrometry under native conditions, we show that PRMT6 dimer binds two cofactor and a single H4 peptide molecules. Finally, we characterized a new site of in vitro automethylation of mouse PRMT6 at position 7.
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Affiliation(s)
- Luc Bonnefond
- Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR7104, INSERM U964, 1 rue Laurent Fries, Illkirch, F-67404, France
| | - Johann Stojko
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC-DSA, Université de Strasbourg, CNRS, UMR7178, 25 rue Becquerel, Strasbourg 67087, France
| | - Justine Mailliot
- Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR7104, INSERM U964, 1 rue Laurent Fries, Illkirch, F-67404, France
| | - Nathalie Troffer-Charlier
- Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR7104, INSERM U964, 1 rue Laurent Fries, Illkirch, F-67404, France
| | - Vincent Cura
- Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR7104, INSERM U964, 1 rue Laurent Fries, Illkirch, F-67404, France
| | - Jean-Marie Wurtz
- Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR7104, INSERM U964, 1 rue Laurent Fries, Illkirch, F-67404, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC-DSA, Université de Strasbourg, CNRS, UMR7178, 25 rue Becquerel, Strasbourg 67087, France
| | - Jean Cavarelli
- Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR7104, INSERM U964, 1 rue Laurent Fries, Illkirch, F-67404, France.
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10
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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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11
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Thomas D, Koopmans T, Lakowski TM, Kreinin H, Vhuiyan MI, Sedlock SA, Bui JM, Martin NI, Frankel A. Protein Arginine N-Methyltransferase Substrate Preferences for Different Nη-Substituted Arginyl Peptides. Chembiochem 2014; 15:1607-13. [DOI: 10.1002/cbic.201402045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Indexed: 01/08/2023]
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12
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Liu Y, Liu K, Qin S, Xu C, Min J. Epigenetic targets and drug discovery: part 1: histone methylation. Pharmacol Ther 2014; 143:275-94. [PMID: 24704322 DOI: 10.1016/j.pharmthera.2014.03.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 03/24/2014] [Indexed: 01/10/2023]
Abstract
Dynamic chromatin structure is modulated by post-translational modifications on histones, such as acetylation, phosphorylation and methylation. Research on histone methylation has become the most flourishing area of epigenetics in the past fourteen years, and a large amount of data has been accumulated regarding its biology and disease implications. Correspondingly, a lot of efforts have been made to develop small molecule compounds that can specifically modulate histone methyltransferases and methylation reader proteins, aiming for potential therapeutic drugs. Here, we summarize recent progress in chemical probe and drug discovery of histone methyltransferases and methylation reader proteins. For each target, we will review their biological/biochemical functions first, and then focus on their disease implications and drug discovery. We can also see that structure-based compound design and optimization plays a critical role in facilitating the development of highly potent and selective chemical probes and inhibitors for these targets.
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Affiliation(s)
- Yanli Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Su Qin
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Chao Xu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada; Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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13
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Guo H, Wang R, Zheng W, Chen Y, Blum G, Deng H, Luo M. Profiling substrates of protein arginine N-methyltransferase 3 with S-adenosyl-L-methionine analogues. ACS Chem Biol 2014; 9:476-84. [PMID: 24320160 DOI: 10.1021/cb4008259] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Protein arginine N-methyltransferase 3 (PRMT3) belongs to the family of type I PRMTs and harbors the activity to use S-adenosyl-l-methionine (SAM) as a methyl-donor cofactor for protein arginine labeling. However, PRMT3's functions remain elusive with the lacked knowledge of its target scope in cellular settings. Inspired by the emerging Bioorthogonal Profiling of Protein Methylation (BPPM) using engineered methyltransferases and SAM analogues for target identification, the current work documents the endeavor to systematically explore the SAM-binding pocket of PRMT3 and identify suitable PRMT3 variants for BPPM. The M233G single point mutation transforms PRMT3 into a promiscuous alkyltransferase using sp(2)-β-sulfonium-containing SAM analogues as cofactor surrogates. Here the conserved methionine was defined as a hot spot that can be engineered alone or in combination with nearby residues to render cofactor promiscuity of multiple type I PRMTs. With this promiscuous variant and the matched 4-propargyloxy-but-2-enyl (Pob)-SAM analogue as the BPPM reagents, more than 80 novel proteins were readily uncovered as potential targets of PRMT3 in the cellular context. Subsequent target validation and functional analysis correlated the PRMT3 methylation to several biological processes such as cytoskeleton dynamics, whose roles might be compensated by other PRMTs. These BPPM-revealed substrates are primarily localized but not restricted in cytoplasm, the preferred site of PRMT3. The broad localization pattern may implicate the diverse roles of PRMT3 in the cellular setting. The revelation of PRMT3 targets and the transformative character of BPPM for other PRMTs present unprecedented pathways toward elucidating physiological and pathological roles of diverse PRMTs.
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Affiliation(s)
| | - Rui Wang
- Program
of Pharmacology, Weill Graduate School of Medical Science, Cornell University, New York, New York 10021, United States
| | | | - Yuling Chen
- School
of Life Sciences, Tsinghua University, Beijing 100084, China
| | | | - Haiteng Deng
- School
of Life Sciences, Tsinghua University, Beijing 100084, China
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14
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Alegre-Requena JV, Marqués-López E, Herrera RP. Guanidine Motif in Biologically Active Peptides. Aust J Chem 2014. [DOI: 10.1071/ch14043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In the past decade, guanidines have attracted attention as valuable hydrogen bond-based catalysts while they have long been considered as organic superbases with a broad scope of synthetic applicability. Their easy modification has also expanded their capacity to form complexes with a wide range of metal salts as effective metal scavengers. All these attractive aspects have promoted a huge growth in the field of organic synthesis involving guanidines and examples of such reactions have been collected in numerous reviews and some books. Moreover, this structural motif is also present in a large number of natural products and biologically active compounds that exhibit appealing properties and play important roles in medicinal chemistry. In this highlight, we will only cover the synthesis and properties of biologically active guanidine-containing peptides reported in the past 3 years.
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15
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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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16
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Singhroy DN, Mesplède T, Sabbah A, Quashie PK, Falgueyret JP, Wainberg MA. Automethylation of protein arginine methyltransferase 6 (PRMT6) regulates its stability and its anti-HIV-1 activity. Retrovirology 2013; 10:73. [PMID: 23866860 PMCID: PMC3750301 DOI: 10.1186/1742-4690-10-73] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 07/09/2013] [Indexed: 01/10/2023] Open
Abstract
Background Protein arginine methyltransferase 6 (PRMT6) is a nuclear enzyme that methylates arginine residues on histones and transcription factors. In addition, PRMT6 inhibits HIV-1 replication in cell culture by directly methylating and interfering with the functions of several HIV-1 proteins, i.e. Tat, Rev and nucleocapsid (NC). PRMT6 also displays automethylation capacity but the role of this post-translational modification in its antiretroviral activity remains unknown. Results Here we report the identification by liquid chromatography-mass spectrometry of R35 within PRMT6 as the target residue for automethylation and have confirmed this by site-directed mutagenesis and in vitro and in vivo methylation assays. We further show that automethylation at position 35 greatly affects PRMT6 stability and is indispensable for its antiretroviral activity, as demonstrated in HIV-1 single-cycle TZM-bl infectivity assays. Conclusion These results show that PRMT6 automethylation plays a role in the stability of this protein and that this event is indispensible for its anti-HIV-1 activity.
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Affiliation(s)
- Diane N Singhroy
- McGill University AIDS Centre, Lady Davis for Medical Research, Jewish General Hospital, 3755 Cote Sainte Catherine, Montreal, QC, H3T 1E2, Canada
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17
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Patananan AN, Palmer JM, Garvey GS, Keller NP, Clarke SG. A novel automethylation reaction in the Aspergillus nidulans LaeA protein generates S-methylmethionine. J Biol Chem 2013; 288:14032-14045. [PMID: 23532849 PMCID: PMC3656261 DOI: 10.1074/jbc.m113.465765] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The filamentous fungi in the genus Aspergillus are opportunistic plant and animal pathogens that can adapt to their environment by producing various secondary metabolites, including lovastatin, penicillin, and aflatoxin. The synthesis of these small molecules is dependent on gene clusters that are globally regulated by the LaeA protein. Null mutants of LaeA in all pathogenic fungi examined to date show decreased virulence coupled with reduced secondary metabolism. Although the amino acid sequence of LaeA contains the motifs characteristic of seven-β-strand methyltransferases, a methyl-accepting substrate of LaeA has not been identified. In this work we did not find a methyl-accepting substrate in Aspergillus nidulans with various assays, including in vivo S-adenosyl-[methyl-(3)H]methionine labeling, targeted in vitro methylation experiments using putative protein substrates, or in vitro methylation assays using whole cell extracts grown under different conditions. However, in each experiment LaeA was shown to self-methylate. Amino acid hydrolysis of radioactively labeled LaeA followed by cation exchange and reverse phase chromatography identified methionine as the modified residue. Point mutations show that the major site of modification of LaeA is on methionine 207. However, in vivo complementation showed that methionine 207 is not required for the biological function of LaeA. LaeA is the first protein to exhibit automethylation at a methionine residue. These findings not only indicate LaeA may perform novel chemistry with S-adenosylmethionine but also provide new insights into the physiological function of LaeA.
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Affiliation(s)
- Alexander N. Patananan
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California 90095 and
| | | | | | - Nancy P. Keller
- the Departments of Medical Microbiology and Immunology and ,Bacteriology, University of Wisconsin, Madison, Wisconsin 53706
| | - Steven G. Clarke
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California 90095 and , To whom correspondence should be addressed: Dept. of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, 607 Charles E. Young Dr. East, Los Angeles, CA. Tel.: 310-825-8754; Fax: 310-825-1968; E-mail:
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18
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Lakowski TM, Szeitz A, Pak ML, Thomas D, Vhuiyan MI, Kotthaus J, Clement B, Frankel A. MS³ fragmentation patterns of monomethylarginine species and the quantification of all methylarginine species in yeast using MRM³. J Proteomics 2013; 80:43-54. [PMID: 23333926 DOI: 10.1016/j.jprot.2013.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/07/2013] [Accepted: 01/08/2013] [Indexed: 01/06/2023]
Abstract
Protein arginine methylation is one of the epigenetic modifications to proteins that is studied in yeast and is known to be involved in a number of human diseases. All eukaryotes produce Nη-monomethylarginine (ηMMA), asymmetric Nη1, Nη1-dimethylarginine (aDMA), and most produce symmetric Nη1, Nη2-dimethylarginine (sDMA) on proteins, but only yeast produce Nδ-monomethylarginine (δMMA). It has proven difficult to differentiate among all of these methylarginines using mass spectrometry. Accordingly, we demonstrated that the two forms of MMA have indistinguishable primary product ion spectra. However, the secondary product ion spectra of δMMA and ηMMA exhibited distinct patterns of ions. Using incorporation of deuterated methyl-groups in yeast, we determined which secondary product ions were methylated and their structures. Utilizing distinct secondary product ions, a triple quadrupole multiple reaction monitoring cubed (MRM(3)) assay was developed to measure δMMA, ηMMA, sDMA and aDMA derived from hydrolyzed protein. As a proof-of-concept, δMMA and ηMMA were measured using the MRM(3) method in wild type and mutant strains of Saccharomyces cerevisiae and compared to the total MMA measured using an existing assay. The MRM(3) assay represents the only method to directly quantify δMMA and the only method to simultaneously quantify all yeast methylarginines.
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Affiliation(s)
- Ted M Lakowski
- Faculty of Pharmacy, The University of Manitoba, Winnipeg, Manitoba, Canada.
| | - András Szeitz
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Magnolia L Pak
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Dylan Thomas
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Mynol I Vhuiyan
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Joscha Kotthaus
- Pharmaceutical Institute, Gutenbergstr. 76, 24118 Kiel, Germany
| | - Bernd Clement
- Pharmaceutical Institute, Gutenbergstr. 76, 24118 Kiel, Germany
| | - Adam Frankel
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada.
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19
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Theillet FX, Smet-Nocca C, Liokatis S, Thongwichian R, Kosten J, Yoon MK, Kriwacki RW, Landrieu I, Lippens G, Selenko P. Cell signaling, post-translational protein modifications and NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2012; 54:217-36. [PMID: 23011410 PMCID: PMC4939263 DOI: 10.1007/s10858-012-9674-x] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 09/07/2012] [Indexed: 05/13/2023]
Abstract
Post-translationally modified proteins make up the majority of the proteome and establish, to a large part, the impressive level of functional diversity in higher, multi-cellular organisms. Most eukaryotic post-translational protein modifications (PTMs) denote reversible, covalent additions of small chemical entities such as phosphate-, acyl-, alkyl- and glycosyl-groups onto selected subsets of modifiable amino acids. In turn, these modifications induce highly specific changes in the chemical environments of individual protein residues, which are readily detected by high-resolution NMR spectroscopy. In the following, we provide a concise compendium of NMR characteristics of the main types of eukaryotic PTMs: serine, threonine, tyrosine and histidine phosphorylation, lysine acetylation, lysine and arginine methylation, and serine, threonine O-glycosylation. We further delineate the previously uncharacterized NMR properties of lysine propionylation, butyrylation, succinylation, malonylation and crotonylation, which, altogether, define an initial reference frame for comprehensive PTM studies by high-resolution NMR spectroscopy.
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Affiliation(s)
- Francois-Xavier Theillet
- Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), In-cell NMR Group, Robert-Roessle Strasse 10, 13125 Berlin, German
| | - Caroline Smet-Nocca
- CNRS UMR 8576, Universite Lille Nord de France, 59655 Villeneuve d’Ascq, France
| | - Stamatios Liokatis
- Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), In-cell NMR Group, Robert-Roessle Strasse 10, 13125 Berlin, German
| | - Rossukon Thongwichian
- Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), In-cell NMR Group, Robert-Roessle Strasse 10, 13125 Berlin, German
| | - Jonas Kosten
- Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), In-cell NMR Group, Robert-Roessle Strasse 10, 13125 Berlin, German
| | - Mi-Kyung Yoon
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Richard W. Kriwacki
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Isabelle Landrieu
- CNRS UMR 8576, Universite Lille Nord de France, 59655 Villeneuve d’Ascq, France
| | - Guy Lippens
- CNRS UMR 8576, Universite Lille Nord de France, 59655 Villeneuve d’Ascq, France
| | - Philipp Selenko
- Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), In-cell NMR Group, Robert-Roessle Strasse 10, 13125 Berlin, German
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20
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Dillon MBC, Bachovchin DA, Brown SJ, Finn MG, Rosen H, Cravatt BF, Mowen KA. Novel inhibitors for PRMT1 discovered by high-throughput screening using activity-based fluorescence polarization. ACS Chem Biol 2012; 7:1198-204. [PMID: 22506763 DOI: 10.1021/cb300024c] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein arginine methyltransferases (PRMTs) catalyze the posttranslational methylation of arginine using S-adenosylmethionine (SAM) as a methyl-donor. The PRMT family is widely expressed and has been implicated in biological functions such as RNA splicing, transcriptional control, signal transduction, and DNA repair. Therefore, specific inhibitors of individual PRMTs have potentially significant research and therapeutic value. In particular, PRMT1 is responsible for >85% of arginine methyltransferase activity, but currently available inhibitors of PRMT1 lack specificity, efficacy, and bioavailability. To address this limitation, we developed a high-throughput screening assay for PRMT1 that utilizes a hyper-reactive cysteine within the active site, which is lacking in almost all other PRMTs. This assay, which monitors the kinetics of the fluorescence polarization signal increase upon PRMT1 labeling by a rhodamine-containing cysteine-reactive probe, successfully identified two novel inhibitors selective for PRMT1 over other SAM-dependent methyltransferases.
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Affiliation(s)
- Myles B. C. Dillon
- Department
of Chemical Physiology and ‡Department of Chemistry, The Scripps Research Institute, 10550 North Torrey
Pines Road, La Jolla, California 92037, United States
| | - Daniel A. Bachovchin
- Department
of Chemical Physiology and ‡Department of Chemistry, The Scripps Research Institute, 10550 North Torrey
Pines Road, La Jolla, California 92037, United States
| | - Steven J. Brown
- Department
of Chemical Physiology and ‡Department of Chemistry, The Scripps Research Institute, 10550 North Torrey
Pines Road, La Jolla, California 92037, United States
| | - M. G. Finn
- Department
of Chemical Physiology and ‡Department of Chemistry, The Scripps Research Institute, 10550 North Torrey
Pines Road, La Jolla, California 92037, United States
| | - Hugh Rosen
- Department
of Chemical Physiology and ‡Department of Chemistry, The Scripps Research Institute, 10550 North Torrey
Pines Road, La Jolla, California 92037, United States
| | - Benjamin F. Cravatt
- Department
of Chemical Physiology and ‡Department of Chemistry, The Scripps Research Institute, 10550 North Torrey
Pines Road, La Jolla, California 92037, United States
| | - Kerri A. Mowen
- Department
of Chemical Physiology and ‡Department of Chemistry, The Scripps Research Institute, 10550 North Torrey
Pines Road, La Jolla, California 92037, United States
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21
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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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22
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Abstract
This review focuses on the progress in the development of the second generation of epigenetic modifiers able to modulate histone marks, and restore normal gene transcription.
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Affiliation(s)
- Philip Jones
- Institute for Applied Cancer Sciences
- MD Anderson Cancer Center
- Houston
- USA
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23
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't Hart P, Thomas D, van Ommeren R, Lakowski TM, Frankel A, Martin NI. Analogues of the HIV-Tat peptide containing Nη-modified arginines as potent inhibitors of protein arginine N-methyltransferases. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20161e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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24
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Role of estrogen receptor signaling in breast cancer metastasis. Int J Breast Cancer 2011; 2012:654698. [PMID: 22295247 PMCID: PMC3262597 DOI: 10.1155/2012/654698] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 09/16/2011] [Accepted: 09/19/2011] [Indexed: 12/21/2022] Open
Abstract
Metastatic breast cancer is a life-threatening stage of cancer and is the leading cause of death in advanced breast cancer patients. Estrogen signaling and the estrogen receptor (ER) are implicated in breast cancer progression, and the majority of the human breast cancers start out as estrogen dependent. Accumulating evidence suggests that ER signaling is complex, involving coregulatory proteins and extranuclear actions. ER-coregualtory proteins are tightly regulated under normal conditions with miss expression primarily reported in cancer. Deregulation of ER coregualtors or ER extranuclear signaling has potential to promote metastasis in ER-positive breast cancer cells. This review summarizes the emerging role of ER signaling in promoting metastasis of breast cancer cells, discusses the molecular mechanisms by which ER signaling contributes to metastasis, and explores possible therapeutic targets to block ER-driven metastasis.
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25
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Flemer S, Madalengoitia JS. On-resin synthesis of novel arginine-isostere peptides bearing substituted amidine headgroups. J Pept Sci 2011; 18:30-6. [PMID: 22034042 DOI: 10.1002/psc.1412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/02/2011] [Accepted: 08/11/2011] [Indexed: 11/12/2022]
Abstract
A methodology is presented for the facile synthesis of Arg-containing peptides modified at the guanidine headgroup as substituted amidine cores. This process allows for the iterative construction of these Arg isosteres while the peptide is being built out on the solid support, providing a high potential for diversity in substitution pattern in the resulting peptide. A series of N-Pmc-substituted thioamides were condensed with deprotected δ-N Orn-bearing peptides while attached to the solid support using Mukaiyama's reagent as coupling reagent, yielding isosteric Arg-containing analogs. Peptides were cleaved using trimethylsilyl trifluoromethanesulfonate/TFA and analyzed in their crude form in order to illustrate the amenability of this process toward production of peptide isolates in high crude purity. Arg-containing peptides having a single Arg isostere were utilized to show the general utility of this approach as well as a multiple-Arg-containing construct, illustrating the amenability of this method toward stepwise construction of differently substituted amidine headgroups within the same peptide.
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Affiliation(s)
- Stevenson Flemer
- Department of Chemistry, University of Vermont, A232 Cook Physical Sciences Building, 82 University Place, Burlington, VT 05405, USA
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26
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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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27
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Wang R, Ibáñez G, Islam K, Zheng W, Blum G, Sengelaub C, Luo M. Formulating a fluorogenic assay to evaluate S-adenosyl-L-methionine analogues as protein methyltransferase cofactors. MOLECULAR BIOSYSTEMS 2011; 7:2970-81. [PMID: 21866297 DOI: 10.1039/c1mb05230f] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein methyltransferases (PMTs) catalyze arginine and lysine methylation of diverse histone and nonhistone targets. These posttranslational modifications play essential roles in regulating multiple cellular events in an epigenetic manner. In the recent process of defining PMT targets, S-adenosyl-L-methionine (SAM) analogues have emerged as powerful small molecule probes to label and profile PMT targets. To examine efficiently the reactivity of PMTs and their variants on SAM analogues, we transformed a fluorogenic PMT assay into a ready high throughput screening (HTS) format. The reformulated fluorogenic assay is featured by its uncoupled but more robust character with the first step of accumulation of the commonly-shared reaction byproduct S-adenosyl-L-homocysteine (SAH), followed by SAH-hydrolase-mediated fluorogenic quantification. The HTS readiness and robustness of the assay were demonstrated by its excellent Z' values of 0.83-0.95 for the so-far-examined 8 human PMTs with SAM as a cofactor (PRMT1, PRMT3, CARM1, SUV39H2, SET7/9, SET8, G9a and GLP1). The fluorogenic assay was further implemented to screen the PMTs against five SAM analogues (allyl-SAM, propargyl-SAM, (E)-pent-2-en-4-ynyl-SAM (EnYn-SAM), (E)-hex-2-en-5-ynyl-SAM (Hey-SAM) and 4-propargyloxy-but-2-enyl-SAM (Pob-SAM)). Among the examined 8 × 5 pairs of PMTs and SAM analogues, native SUV39H2, G9a and GLP1 showed promiscuous activity on allyl-SAM. In contrast, the bulky SAM analogues, such as EnYn-SAM, Hey-SAM and Pob-SAM, are inert toward the panel of human PMTs. These findings therefore provide the useful structure-activity guidance to further evolve PMTs and SAM analogues for substrate labeling. The current assay format is ready to screen methyltransferase variants on structurally-diverse SAM analogues.
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Affiliation(s)
- Rui Wang
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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28
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Gui S, Wooderchak WL, Daly MP, Porter PJ, Johnson SJ, Hevel JM. Investigation of the molecular origins of protein-arginine methyltransferase I (PRMT1) product specificity reveals a role for two conserved methionine residues. J Biol Chem 2011; 286:29118-29126. [PMID: 21697082 DOI: 10.1074/jbc.m111.224097] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein-arginine methyltransferases aid in the regulation of many biological processes by methylating specific arginyl groups within targeted proteins. The varied nature of the response to methylation is due in part to the diverse product specificity displayed by the protein-arginine methyltransferases. In addition to site location within a protein, biological response is also determined by the degree (mono-/dimethylation) and type of arginine dimethylation (asymmetric/symmetric). Here, we have identified two strictly conserved methionine residues in the PRMT1 active site that are not only important for activity but also control substrate specificity. Mutation of Met-155 or Met-48 results in a loss in activity and a change in distribution of mono- and dimethylated products. The altered substrate specificity of M155A and M48L mutants is also evidenced by automethylation. Investigation into the mechanistic basis of altered substrate recognition led us to consider each methyl transfer step separately. Single turnover experiments reveal that the rate of transfer of the second methyl group is much slower than transfer of the first methyl group in M48L, especially for arginine residues located in the center of the peptide substrate where turnover of the monomethylated species is negligible. Thus, altered product specificity in M48L originates from the differential effect of the mutation on the two rates. Characterization of the two active-site methionines provides the first insight into how the PRMT1 active site is engineered to control product specificity.
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Affiliation(s)
- Shanying Gui
- Chemistry and Biochemistry Department, Utah State University, Logan, Utah 84322 and
| | - Whitney L Wooderchak
- Chemistry and Biochemistry Department, Utah State University, Logan, Utah 84322 and
| | | | - Paula J Porter
- Chemistry and Biochemistry Department, Utah State University, Logan, Utah 84322 and
| | - Sean J Johnson
- Chemistry and Biochemistry Department, Utah State University, Logan, Utah 84322 and
| | - Joan M Hevel
- Chemistry and Biochemistry Department, Utah State University, Logan, Utah 84322 and.
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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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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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