1
|
Jensen M, Chandrasekaran V, García-Bonete MJ, Li S, Anindya AL, Andersson K, Erlandsson MC, Oparina NY, Burmann BM, Brath U, Panchenko AR, Bokarewa I. M, Katona G. Survivin prevents the polycomb repressor complex 2 from methylating histone 3 lysine 27. iScience 2023; 26:106976. [PMID: 37534134 PMCID: PMC10391610 DOI: 10.1016/j.isci.2023.106976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/27/2023] [Accepted: 04/17/2023] [Indexed: 08/04/2023] Open
Abstract
This study investigates the role of survivin in epigenetic control of gene transcription through interaction with the polycomb repressive complex 2 (PRC2). PRC2 is responsible for silencing gene expression by trimethylating lysine 27 on histone 3. We observed differential expression of PRC2 subunits in CD4+ T cells with varying levels of survivin expression, and ChIP-seq results indicated that survivin colocalizes with PRC2 along DNA. Inhibition of survivin resulted in a significant increase in H3K27 trimethylation, implying that survivin prevents PRC2 from functioning. Peptide microarray showed that survivin interacts with peptides from PRC2 subunits, and machine learning revealed that amino acid composition contains relevant information for predicting survivin interaction. NMR and BLI experiments supported the interaction of survivin with PRC2 subunit EZH2. Finally, protein-protein docking revealed that the survivin-EZH2 interaction interface overlaps with catalytic residues of EZH2, potentially inhibiting its H3K27 methylation activity. These findings suggest that survivin inhibits PRC2 function.
Collapse
Affiliation(s)
- Maja Jensen
- Department of Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Venkataragavan Chandrasekaran
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Box 480, 40530 Gothenburg, Sweden
| | - María-José García-Bonete
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden
| | - Shuxiang Li
- Department of Pathology and Molecular Medicine, School of Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Atsarina Larasati Anindya
- Department of Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Karin Andersson
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Box 480, 40530 Gothenburg, Sweden
| | - Malin C. Erlandsson
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Box 480, 40530 Gothenburg, Sweden
| | - Nina Y. Oparina
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Box 480, 40530 Gothenburg, Sweden
| | - Björn M. Burmann
- Department of Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Ulrika Brath
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Anna R. Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Maria Bokarewa I.
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Box 480, 40530 Gothenburg, Sweden
- Rheumatology Clinic, Sahlgrenska University Hospital, Gröna stråket 16, 41346 Gothenburg, Sweden
| | - Gergely Katona
- Department of Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| |
Collapse
|
2
|
Weng HR, Taing K, Chen L, Penney A. EZH2 Methyltransferase Regulates Neuroinflammation and Neuropathic Pain. Cells 2023; 12:1058. [PMID: 37048131 PMCID: PMC10093242 DOI: 10.3390/cells12071058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Recent studies by us and others have shown that enhancer of zeste homolog-2 (EZH2), a histone methyltransferase, in glial cells regulates the genesis of neuropathic pain by modulating the production of proinflammatory cytokines and chemokines. In this review, we summarize recent advances in this research area. EZH2 is a subunit of polycomb repressive complex 2 (PRC2), which primarily serves as a histone methyltransferase to catalyze methylation of histone 3 on lysine 27 (H3K27), ultimately resulting in transcriptional repression. Animals with neuropathic pain exhibit increased EZH2 activity and neuroinflammation of the injured nerve, spinal cord, and anterior cingulate cortex. Inhibition of EZH2 with DZNep or GSK-126 ameliorates neuroinflammation and neuropathic pain. EZH2 protein expression increases upon activation of Toll-like receptor 4 and calcitonin gene-related peptide receptors, downregulation of miR-124-3p and miR-378 microRNAs, or upregulation of Lncenc1 and MALAT1 long noncoding RNAs. Genes suppressed by EZH2 include suppressor of cytokine signaling 3 (SOCS3), nuclear factor (erythroid-derived 2)-like-2 factor (NrF2), miR-29b-3p, miR-146a-5p, and brain-specific angiogenesis inhibitor 1 (BAI1). Pro-inflammatory mediators facilitate neuronal activation along pain-signaling pathways by sensitizing nociceptors in the periphery, as well as enhancing excitatory synaptic activities and suppressing inhibitory synaptic activities in the CNS. These studies collectively reveal that EZH2 is implicated in signaling pathways known to be key players in the process of neuroinflammation and genesis of neuropathic pain. Therefore, targeting the EZH2 signaling pathway may open a new avenue to mitigate neuroinflammation and neuropathic pain.
Collapse
Affiliation(s)
- Han-Rong Weng
- Department of Basic Sciences, California Northstate University College of Medicine, Elk Grove, CA 95757, USA
| | | | | | | |
Collapse
|
3
|
Fındık V, Varınca Gerçik BT, Sinek Ö, Erdem SS, Ruiz-López MF. Mechanistic Investigation of Lysine-Targeted Covalent Inhibition of PI3Kδ via ONIOM QM:QM Computations. J Chem Inf Model 2022; 62:6775-6787. [PMID: 35980989 DOI: 10.1021/acs.jcim.2c00569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Phosphoinositide 3-kinase (PI3K) enzymes are important drug targets, especially in oncology, and several inhibitors are currently under investigation in clinical trials for the treatment of lymphocytic leukemia, follicular lymphoma, breast, thyroid, colorectal, and lung cancer. Targeted covalent inhibitors hold significant promise for drug discovery research especially for kinases. Targeting the lysine residues attracts attention as a new strategy in designing targeted covalent inhibitors, since the lysine residue provides several advantages over the traditional cysteine residue. Recently, new highly selective covalent inhibitors of PI3Kδ with activated ester warheads, targeting the conserved Lys779 residue, were reported. Based on the observed kinetics, a covalent inhibition mechanism was proposed, but the atomistic details of the reaction are still not understood. Therefore, in the present work, we have conducted quantum chemical ONIOM M06-2X/6-31+G(d,p):PM6 calculations on the active site cluster structure of PI3Kδ to elucidate the microscopic details of the mechanism of the aminolysis reaction between Lys779 and the ester inhibitors. Our calculations clearly discriminate the noncovalent methyl ester inhibitor and the covalent inhibitors with activated phenolic esters. For the representative p-NO2, p-F, p-H, and p-OCH3 phenolic esters, the Gibbs free energy profiles of alternative mechanistic paths through either Asp782 or Asp911 demonstrate the modulatory role of active site aspartate residues. The most plausible path alters depending on the electron-withdrawing/donating nature of the p-substituted phenolate leaving group. Inhibitors with sufficiently strong electron-withdrawing group prefer direct dissociation of the leaving group from the tetrahedral zwitterion intermediate, while the ones with electron-donating group favor the formation of a neutral tetrahedral intermediate prior to the dissociation. The relative Gibbs free energy barriers of p-NO2 < p-F < p-H < p-OCH3 substituted phenyl esters display the same qualitative trend as the experimentally measured kinact/KI values. Our results provide in depth insight into the mechanism, which can pave the way for optimizing the inhibitor efficiency.
Collapse
Affiliation(s)
- Volkan Fındık
- LPCT, UMR 7019, University of Lorraine, CNRS, 54000, Nancy, France.,Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722, Istanbul, Turkey
| | | | - Öykü Sinek
- Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722, Istanbul, Turkey
| | - Safiye Sağ Erdem
- Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722, Istanbul, Turkey
| | | |
Collapse
|
4
|
Idigo NJ, Voigt P. Detection and Quantification of Histone Methyltransferase Activity In Vitro. Methods Mol Biol 2022; 2529:43-61. [PMID: 35733009 DOI: 10.1007/978-1-0716-2481-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Histone methyltransferases (HMTs) catalyze the methylation of lysine and arginine residues in histone as well as nonhistone substrates. In vitro histone methyltransferase assays have been instrumental in identifying HMTs, and they continue to be invaluable tools for the study of these important enzymes, revealing novel substrates and modes of regulation.Here we describe a universal protocol to examine HMT activity in vitro that can be adapted to a range of HMTs, substrates, and experimental objectives. We provide protocols for the detection of activity based on incorporation of 3H-labeled methyl groups from S-adenosylmethionine (SAM), methylation-specific antibodies, and quantification of the reaction product S-adenosylhomocysteine (SAH).
Collapse
Affiliation(s)
- Nwamaka J Idigo
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Philipp Voigt
- Epigenetics Programme, Babraham Institute, Cambridge, UK.
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
5
|
Exploration of the Activation Mechanism of the Epigenetic Regulator MLL3: A QM/MM Study. Biomolecules 2021; 11:biom11071051. [PMID: 34356675 PMCID: PMC8301819 DOI: 10.3390/biom11071051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/07/2021] [Accepted: 07/10/2021] [Indexed: 11/17/2022] Open
Abstract
The mixed lineage leukemia 3 or MLL3 is the enzyme in charge of the writing of an epigenetic mark through the methylation of lysine 4 from the N-terminal domain of histone 3 and its deregulation has been related to several cancer lines. An interesting feature of this enzyme comes from its regulation mechanism, which involves its binding to an activating dimer before it can be catalytically functional. Once the trimer is formed, the reaction mechanism proceeds through the deprotonation of the lysine followed by the methyl-transfer reaction. Here we present a detailed exploration of the activation mechanism through a QM/MM approach focusing on both steps of the reaction, aiming to provide new insights into the deprotonation process and the role of the catalytic machinery in the methyl-transfer reaction. Our finding suggests that the source of the activation mechanism comes from conformational restriction mediated by the formation of a network of salt-bridges between MLL3 and one of the activating subunits, which restricts and stabilizes the positioning of several residues relevant for the catalysis. New insights into the deprotonation mechanism of lysine are provided, identifying a valine residue as crucial in the positioning of the water molecule in charge of the process. Finally, a tyrosine residue was found to assist the methyl transfer from SAM to the target lysine.
Collapse
|
6
|
Wang H, Lan Y, Bai P, Chen Z, Luo S, Xu Y, Fiedler S, Striar R, Wang C. Radiosynthesis of [11C]EI1 for imaging EZH2 using positron emission tomography. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02633-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
7
|
Zhou Y, Du DH, Wang J, Cai XQ, Deng AX, Nosjean O, Boutin JA, Renard P, Yang DH, Luo C, Wang MW. Identification of catalytic and non-catalytic activity inhibitors against PRC2-EZH2 complex through multiple high-throughput screening campaigns. Chem Biol Drug Des 2020; 96:1024-1051. [PMID: 32394628 DOI: 10.1111/cbdd.13702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/21/2020] [Accepted: 04/26/2020] [Indexed: 12/19/2022]
Abstract
Enhancer of zeste homolog 2 (EZH2) is the catalytic subunit of the polycomb repressive complex 2 (PRC2) along with embryonic ectoderm development (EED) and suppressor of zeste 12 (SUZ12), which implements transcriptional repression mainly by depositing trimethylation marks at lysine 27 of histone H3 (H3K27me3). Its catalytic activity is closely correlated with the stability of PRC2, and somatic activating mutation of EZH2 Y641F within the catalytic SET domain drives tumor aggressiveness, drug resistance, and poor prognosis. Here, we report two high-throughput screening (HTS) campaigns targeting EZH2 Y641F and EZH2-EED interaction, respectively. For the EZH2 Y641F mutant, the HTS campaign involved a library of 250,000 compounds using a homogenous time-resolved fluorescence (HTRF) assay and identified 162 hits, while 60,160 compounds were screened against EZH2-EED interaction with a fluorescence polarization (FP) assay resulting in 97 hits. Among the 162 EZH2 Y641F inhibitors, 38 also suppressed EZH2-EED interaction and 80 showed inhibitory effects on the wide-type (WT) EZH2. Meanwhile, 10 of the 97 EZH2-EED interaction inhibitors were active against WT EZH2. These hit compounds provide useful tools for the development of novel PRC2-EZH2 inhibitors targeting its catalytic and non-catalytic activities.
Collapse
Affiliation(s)
- Yan Zhou
- The National Center for Drug Screening and The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Dao-Hai Du
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jia Wang
- The National Center for Drug Screening and The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Xiao-Qing Cai
- The National Center for Drug Screening and The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Alicia X Deng
- The National Center for Drug Screening and The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, China
| | | | | | | | - De-Hua Yang
- The National Center for Drug Screening and The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Cheng Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Ming-Wei Wang
- The National Center for Drug Screening and The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, China.,School of Basic Medical Sciences, Fudan University, Shanghai, China
| |
Collapse
|
8
|
Genna V, Marcia M, De Vivo M. A Transient and Flexible Cation-π Interaction Promotes Hydrolysis of Nucleic Acids in DNA and RNA Nucleases. J Am Chem Soc 2019; 141:10770-10776. [PMID: 31251587 DOI: 10.1021/jacs.9b03663] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Metal-dependent DNA and RNA nucleases are enzymes that cleave nucleic acids with great efficiency and precision. These enzyme-mediated hydrolytic reactions are fundamental for the replication, repair, and storage of genetic information within the cell. Here, extensive classical and quantum-based free-energy molecular simulations show that a cation-π interaction is transiently formed in situ at the metal core of Bacteriophage-λ Exonuclease (Exo-λ), during catalysis. This noncovalent interaction (Lys131-Tyr154) triggers nucleophile activation for nucleotide excision. Then, our simulations also show the oscillatory dynamics and swinging of the newly formed cation-π dyad, whose conformational change may favor proton release from the cationic Lys131 to the bulk solution, thus restoring the precatalytic protonation state in Exo-λ. Altogether, we report on the novel mechanistic character of cation-π interactions for catalysis. Structural and bioinformatic analyses support that flexible orientation and transient formation of mobile cation-π interactions may represent a common catalytic strategy to promote nucleic acid hydrolysis in DNA and RNA nucleases.
Collapse
Affiliation(s)
- Vito Genna
- Laboratory of Molecular Modeling and Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 , Genoa , Italy
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble , 71 Avenue des Martyrs , Grenoble 38042 , France
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 , Genoa , Italy
| |
Collapse
|
9
|
Singh PK. Histone methyl transferases: A class of epigenetic opportunities to counter uncontrolled cell proliferation. Eur J Med Chem 2019; 166:351-368. [PMID: 30735901 DOI: 10.1016/j.ejmech.2019.01.069] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 01/03/2019] [Accepted: 01/28/2019] [Indexed: 02/06/2023]
Abstract
With each newly disclosed resistance mechanism, management of cancer with previously established targets have become a "failure" oriented approach. Molecular targets such as kinases did initially provide a ray of hope against cancer but with decades of struggle between novel therapeutic agents and more sophisticated resistance mechanisms, they seem to have saturated as anti-cancer targets. Now, with more exhaustive molecular recognition techniques and approaches, epigenetic targets have accessed the centre stage as anti-cancer targets. Accordingly, several classes of epigenetic enzymes are being studied for this role and histone methyltransferases form one such class. They include a class of epigenetic enzymes which transfer methyl group from histone proteins and maintain genetic homeostasis. In cancer, several reports have deduced upregulation of different members of this family according to the tumor environment, establishing them as one of the novel anti-cancer targets. This compilation provides an updated information on several members of histone methyltransferases family as epigenetic targets for developing novel anti-cancer agents.
Collapse
Affiliation(s)
- Pankaj Kumar Singh
- Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India.
| |
Collapse
|
10
|
Abstract
Epigenetic targets are exciting new avenues for cancer drug discovery. Zhang and colleagues have designed the open-source EZH2 inhibitor JQEZ5 and shown antitumor efficacy in vitro and in vivo in preclinical studies in murine and human lung adenocarcinoma models expressing high levels of EZH2. Cancer Discov; 6(9); 949-52. ©2016 AACRSee related article by Zhang and colleagues, p. 1006.
Collapse
Affiliation(s)
- Arthur E Frankel
- Department of Internal Medicine and Simmons Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Xin Liu
- Cecil H. and Ida Green Center for Reproductive Biologic Sciences and Division of Basic Sciences, Department of Obstetrics and Gynecology and Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - John D Minna
- Department of Internal Medicine and Simmons Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas. Hamon Center for Therapeutic Oncology Research and Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, Texas.
| |
Collapse
|
11
|
Aier I, Varadwaj PK, Raj U. Structural insights into conformational stability of both wild-type and mutant EZH2 receptor. Sci Rep 2016; 6:34984. [PMID: 27713574 PMCID: PMC5054529 DOI: 10.1038/srep34984] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/14/2016] [Indexed: 12/22/2022] Open
Abstract
Polycomb group (PcG) proteins have been observed to maintain the pattern of histone by methylation of the histone tail responsible for the gene expression in various cellular processes, of which enhancer of zeste homolog 2 (EZH2) acts as tumor suppressor. Overexpression of EZH2 results in hyper activation found in a variety of cancer. Point mutation on two important residues were induced and the results were compared between the wild type and mutant EZH2. The mutation of Y641 and A677 present in the active region of the protein alters the interaction of the top ranked compound with the newly modeled binding groove of the SET domain, giving a GLIDE score of -12.26 kcal/mol, better than that of the wild type at -11.664 kcal/mol. In depth analysis were carried out for understanding the underlying molecular mechanism using techniques viz. molecular dynamics, principal component analysis, residue interaction network and free energy landscape analysis, which showed that the mutated residues changed the overall conformation of the system along with the residue-residue interaction network. The insight from this study could be of great relevance while designing new compounds for EZH2 enzyme inhibition and the effect of mutation on the overall binding mechanism of the system.
Collapse
Affiliation(s)
- Imlimaong Aier
- Department of Bioinformatics, Indian Institute of Information Technology Allahabad, Uttar Pradesh, India
| | - Pritish Kumar Varadwaj
- Department of Bioinformatics, Indian Institute of Information Technology Allahabad, Uttar Pradesh, India
| | - Utkarsh Raj
- Department of Bioinformatics, Indian Institute of Information Technology Allahabad, Uttar Pradesh, India
| |
Collapse
|
12
|
Structure-Based Design of a Novel SMYD3 Inhibitor that Bridges the SAM-and MEKK2-Binding Pockets. Structure 2016; 24:774-781. [PMID: 27066749 DOI: 10.1016/j.str.2016.03.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 02/14/2016] [Accepted: 03/10/2016] [Indexed: 01/28/2023]
Abstract
SMYD3 is a lysine methyltransferase overexpressed in colorectal, breast, prostate, and hepatocellular tumors, and has been implicated as an oncogene in human malignancies. Methylation of MEKK2 by SMYD3 is important for regulation of the MEK/ERK pathway, suggesting the possibility of selectively targeting SMYD3 in RAS-driven cancers. Structural and kinetic characterization of SMYD3 was undertaken leading to a co-crystal structure of SMYD3 with a MEKK2-peptide substrate bound, and the observation that SMYD3 follows a partially processive mechanism. These insights allowed for the design of GSK2807, a potent and selective, SAM-competitive inhibitor of SMYD3 (Ki = 14 nM). A high-resolution crystal structure reveals that GSK2807 bridges the gap between the SAM-binding pocket and the substrate lysine tunnel of SMYD3. Taken together, our data demonstrate that small-molecule inhibitors of SMYD3 can be designed to prevent methylation of MEKK2 and these could have potential use as anticancer therapeutics.
Collapse
|
13
|
Mavrakis KJ, McDonald ER, Schlabach MR, Billy E, Hoffman GR, deWeck A, Ruddy DA, Venkatesan K, Yu J, McAllister G, Stump M, deBeaumont R, Ho S, Yue Y, Liu Y, Yan-Neale Y, Yang G, Lin F, Yin H, Gao H, Kipp DR, Zhao S, McNamara JT, Sprague ER, Zheng B, Lin Y, Cho YS, Gu J, Crawford K, Ciccone D, Vitari AC, Lai A, Capka V, Hurov K, Porter JA, Tallarico J, Mickanin C, Lees E, Pagliarini R, Keen N, Schmelzle T, Hofmann F, Stegmeier F, Sellers WR. Disordered methionine metabolism in MTAP/CDKN2A-deleted cancers leads to dependence on PRMT5. Science 2016; 351:1208-13. [PMID: 26912361 DOI: 10.1126/science.aad5944] [Citation(s) in RCA: 315] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/01/2016] [Indexed: 12/13/2022]
Abstract
5-Methylthioadenosine phosphorylase (MTAP) is a key enzyme in the methionine salvage pathway. The MTAP gene is frequently deleted in human cancers because of its chromosomal proximity to the tumor suppressor gene CDKN2A. By interrogating data from a large-scale short hairpin RNA-mediated screen across 390 cancer cell line models, we found that the viability of MTAP-deficient cancer cells is impaired by depletion of the protein arginine methyltransferase PRMT5. MTAP-deleted cells accumulate the metabolite methylthioadenosine (MTA), which we found to inhibit PRMT5 methyltransferase activity. Deletion of MTAP in MTAP-proficient cells rendered them sensitive to PRMT5 depletion. Conversely, reconstitution of MTAP in an MTAP-deficient cell line rescued PRMT5 dependence. Thus, MTA accumulation in MTAP-deleted cancers creates a hypomorphic PRMT5 state that is selectively sensitized toward further PRMT5 inhibition. Inhibitors of PRMT5 that leverage this dysregulated metabolic state merit further investigation as a potential therapy for MTAP/CDKN2A-deleted tumors.
Collapse
Affiliation(s)
| | - E Robert McDonald
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | | | - Eric Billy
- Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Gregory R Hoffman
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Antoine deWeck
- Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - David A Ruddy
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | | | - Jianjun Yu
- Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Gregg McAllister
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Mark Stump
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | | | - Samuel Ho
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Yingzi Yue
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Yue Liu
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Yan Yan-Neale
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Guizhi Yang
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Fallon Lin
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Hong Yin
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Hui Gao
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - D Randal Kipp
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Songping Zhao
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Joshua T McNamara
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | | | - Bing Zheng
- Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Ying Lin
- China Novartis Institutes for Biomedical Research, Shanghai 201203, China
| | - Young Shin Cho
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Justin Gu
- China Novartis Institutes for Biomedical Research, Shanghai 201203, China
| | - Kenneth Crawford
- Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - David Ciccone
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Alberto C Vitari
- Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Albert Lai
- Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Vladimir Capka
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Kristen Hurov
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Jeffery A Porter
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - John Tallarico
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Craig Mickanin
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Emma Lees
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | | | - Nicholas Keen
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Tobias Schmelzle
- Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Francesco Hofmann
- Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Frank Stegmeier
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA.
| | - William R Sellers
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA.
| |
Collapse
|
14
|
Poulin MB, Schneck JL, Matico RE, McDevitt PJ, Huddleston MJ, Hou W, Johnson NW, Thrall SH, Meek TD, Schramm VL. Transition state for the NSD2-catalyzed methylation of histone H3 lysine 36. Proc Natl Acad Sci U S A 2016; 113:1197-201. [PMID: 26787850 PMCID: PMC4747696 DOI: 10.1073/pnas.1521036113] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nuclear receptor SET domain containing protein 2 (NSD2) catalyzes the methylation of histone H3 lysine 36 (H3K36). It is a determinant in Wolf-Hirschhorn syndrome and is overexpressed in human multiple myeloma. Despite the relevance of NSD2 to cancer, there are no potent, selective inhibitors of this enzyme reported. Here, a combination of kinetic isotope effect measurements and quantum chemical modeling was used to provide subangstrom details of the transition state structure for NSD2 enzymatic activity. Kinetic isotope effects were measured for the methylation of isolated HeLa cell nucleosomes by NSD2. NSD2 preferentially catalyzes the dimethylation of H3K36 along with a reduced preference for H3K36 monomethylation. Primary Me-(14)C and (36)S and secondary Me-(3)H3, Me-(2)H3, 5'-(14)C, and 5'-(3)H2 kinetic isotope effects were measured for the methylation of H3K36 using specifically labeled S-adenosyl-l-methionine. The intrinsic kinetic isotope effects were used as boundary constraints for quantum mechanical calculations for the NSD2 transition state. The experimental and calculated kinetic isotope effects are consistent with an SN2 chemical mechanism with methyl transfer as the first irreversible chemical step in the reaction mechanism. The transition state is a late, asymmetric nucleophilic displacement with bond separation from the leaving group at (2.53 Å) and bond making to the attacking nucleophile (2.10 Å) advanced at the transition state. The transition state structure can be represented in a molecular electrostatic potential map to guide the design of inhibitors that mimic the transition state geometry and charge.
Collapse
Affiliation(s)
- Myles B Poulin
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461
| | - Jessica L Schneck
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Rosalie E Matico
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Patrick J McDevitt
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Michael J Huddleston
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Wangfang Hou
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Neil W Johnson
- Cancer Epigenetics Discovery Performance Unit, GlaxoSmithKline, Collegeville, PA 19426
| | - Sara H Thrall
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Thomas D Meek
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461;
| |
Collapse
|
15
|
DesJarlais R, Tummino PJ. Role of Histone-Modifying Enzymes and Their Complexes in Regulation of Chromatin Biology. Biochemistry 2016; 55:1584-99. [DOI: 10.1021/acs.biochem.5b01210] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Renee DesJarlais
- Lead Discovery, Janssen Research & Development, Spring House, Pennsylvania 19477, United States
| | - Peter J. Tummino
- Lead Discovery, Janssen Research & Development, Spring House, Pennsylvania 19477, United States
| |
Collapse
|
16
|
Gibaja V, Shen F, Harari J, Korn J, Ruddy D, Saenz-Vash V, Zhai H, Rejtar T, Paris CG, Yu Z, Lira M, King D, Qi W, Keen N, Hassan AQ, Chan HM. Development of secondary mutations in wild-type and mutant EZH2 alleles cooperates to confer resistance to EZH2 inhibitors. Oncogene 2015; 35:558-66. [PMID: 25893294 PMCID: PMC4744243 DOI: 10.1038/onc.2015.114] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 02/27/2015] [Accepted: 03/06/2015] [Indexed: 12/22/2022]
Abstract
The histone methyltransferase Enhancer of Zeste Homolog 2 (EZH2) is frequently dysregulated in cancers, and gain-of-function (GOF) EZH2 mutations have been identified in non-Hodgkin lymphomas. Small-molecule inhibitors against EZH2 demonstrated anti-tumor activity in EZH2-mutated lymphomas and entered clinical trials. Here, we developed models of acquired resistance to EZH2 inhibitor EI1 with EZH2-mutated lymphoma cells. Resistance was generated by secondary mutations in both wild-type (WT) and GOF Y641N EZH2 alleles. These EZH2 mutants retained the substrate specificity of their predecessor complexes but became refractory to biochemical inhibition by EZH2 inhibitors. Resistant cells were able to maintain a high level of H3K27Me3 in the presence of inhibitors. Interestingly, mutation of EZH2 WT alone generated an intermediate resistance phenotype, which is consistent with a previously proposed model of cooperation between EZH2 WT and Y641N mutants to promote tumorigenesis. In addition, the findings presented here have implications for the clinical translation of EZH2 inhibitors and underscore the need to develop novel EZH2 inhibitors to target potential resistance emerging in clinical settings.
Collapse
Affiliation(s)
- V Gibaja
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - F Shen
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - J Harari
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - J Korn
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - D Ruddy
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - V Saenz-Vash
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - H Zhai
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - T Rejtar
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - C G Paris
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Z Yu
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - M Lira
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - D King
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - W Qi
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - N Keen
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - A Q Hassan
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - H M Chan
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| |
Collapse
|
17
|
Hart-Smith G, Chia SZ, Low JKK, McKay MJ, Molloy MP, Wilkins MR. Stoichiometry of Saccharomyces cerevisiae Lysine Methylation: Insights into Non-histone Protein Lysine Methyltransferase Activity. J Proteome Res 2014; 13:1744-56. [DOI: 10.1021/pr401251k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Gene Hart-Smith
- NSW
Systems Biology Initiative, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Samantha Z. Chia
- NSW
Systems Biology Initiative, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Jason K. K. Low
- NSW
Systems Biology Initiative, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Matthew J. McKay
- Australian
Proteome Analysis Facility, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Mark P. Molloy
- Australian
Proteome Analysis Facility, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Marc R. Wilkins
- NSW
Systems Biology Initiative, University of New South Wales, Sydney, New South Wales 2052, Australia
| |
Collapse
|