LLY-507, a cell-active, potent, and selective inhibitor of protein-lysine methyltransferase SMYD2

Nguyen, Hannah; Allali-Hassani, Abdellah; Antonysamy, Stephen; Chang, Shawn; Chen, Lisa Hong; Curtis, Carmen; Emtage, Spencer; Fan, Li; Gheyi, Tarun; Li, Fengling; Liu, Shichong; Martin, Joseph R.; Mendel, David; Olsen, Jonathan B.; Pelletier, Laura; Shatseva, Tatiana; Wu, Song; Zhang, Feiyu Fred; Arrowsmith, Cheryl H.; Brown, Peter J.; Campbell, Robert M.; Garcia, Benjamin A.; Barsyte-Lovejoy, Dalia; Mader, Mary; Vedadi, Masoud

doi:10.1074/jbc.m114.626861

Title: LLY-507, a cell-active, potent, and selective inhibitor of protein-lysine methyltransferase SMYD2

Journal Article · Mon Mar 30 00:00:00 EDT 2015 · Journal of Biological Chemistry

DOI:https://doi.org/10.1074/jbc.m114.626861· OSTI ID:1347984

Nguyen, Hannah ^[1]; Allali-Hassani, Abdellah ^[2]; Antonysamy, Stephen ^[1]; Chang, Shawn ^[1]; Chen, Lisa Hong ^[1]; Curtis, Carmen ^[1]; Emtage, Spencer ^[1]; Fan, Li ^[1]; Gheyi, Tarun ^[1]; Li, Fengling ^[2]; Liu, Shichong ^[3]; Martin, Joseph R. ^[1]; Mendel, David ^[1]; Olsen, Jonathan B. ^[1]; Pelletier, Laura ^[1]; Shatseva, Tatiana ^[2]; Wu, Song ^[1]; Zhang, Feiyu Fred ^[1]; Arrowsmith, Cheryl H. ^[4]; Brown, Peter J. ^[2] more »

Eli Lily and Co., Indianapolis, IN (United States)
Univ. of Toronto, Toronto, ON (Canada)
Univ. of Pennsylvania, Philadelphia, PA (United States)
Univ. of Toronto, Toronto, ON (Canada); Univ. of Toronto and Princess Margaret Cancer Centre, Toronto, ON (Canada)

SMYD2 is a lysine methyltransferase that catalyzes the monomethylation of several protein substrates including p53. SMYD2 is overexpressed in a significant percentage of esophageal squamous primary carcinomas, and that overexpression correlates with poor patient survival. However, the mechanism(s) by which SMYD2 promotes oncogenesis is not understood. A small molecule probe for SMYD2 would allow for the pharmacological dissection of this biology. In this report, we disclose LLY-507, a cell-active, potent small molecule inhibitor of SMYD2. LLY-507 is >100-fold selective for SMYD2 over a broad range of methyltransferase and non-methyltransferase targets. A 1.63-Å resolution crystal structure of SMYD2 in complex with LLY-507 shows the inhibitor binding in the substrate peptide binding pocket. LLY-507 is active in cells as measured by reduction of SMYD2-induced monomethylation of p53 Lys(370) at submicromolar concentrations. We used LLY-507 to further test other potential roles of SMYD2. Mass spectrometry-based proteomics showed that cellular global histone methylation levels were not significantly affected by SMYD2 inhibition with LLY-507, and subcellular fractionation studies indicate that SMYD2 is primarily cytoplasmic, suggesting that SMYD2 targets a very small subset of histones at specific chromatin loci and/or non-histone substrates. Breast and liver cancers were identified through in silico data mining as tumor types that display amplification and/or overexpression of SMYD2. LLY-507 inhibited the proliferation of several esophageal, liver, and breast cancer cell lines in a dose-dependent manner. As a result, these findings suggest that LLY-507 serves as a valuable chemical probe to aid in the dissection of SMYD2 function in cancer and other biological processes.

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Research Organization:: UChicago, LLC., Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1347984

Journal Information:: Journal of Biological Chemistry, Vol. 290, Issue 22; ISSN 0021-9258

Publisher:: American Society for Biochemistry and Molecular BiologyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 88 works

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References (38)

RB1 Methylation by SMYD2 Enhances Cell Cycle Progression through an Increase of RB1 Phosphorylation Cho, Hyun-Soo; Hayami, Shinya; Toyokawa, Gouji Neoplasia, Vol. 14, Issue 6 https://doi.org/10.1593/neo.12656	journal	June 2012
SmyD1, a histone methyltransferase, is required for myofibril organization and muscle contraction in zebrafish embryos Tan, X.; Rotllant, J.; Li, H. Proceedings of the National Academy of Sciences, Vol. 103, Issue 8 https://doi.org/10.1073/pnas.0509503103	journal	February 2006
Chromatin proteins and modifications as drug targets Helin, Kristian; Dhanak, Dashyant Nature, Vol. 502, Issue 7472 https://doi.org/10.1038/nature12751	journal	October 2013
The Histone Methyltransferase SMYD2 Methylates PARP1 and Promotes Poly(ADP-ribosyl)ation Activity in Cancer Cells Piao, Lianhua; Kang, Daechun; Suzuki, Takehiro Neoplasia, Vol. 16, Issue 3 https://doi.org/10.1016/j.neo.2014.03.002	journal	March 2014
Crystal Structures of Histone and p53 Methyltransferase SmyD2 Reveal a Conformational Flexibility of the Autoinhibitory C-Terminal Domain Jiang, Yuanyuan; Sirinupong, Nualpun; Brunzelle, Joseph PLoS ONE, Vol. 6, Issue 6 https://doi.org/10.1371/journal.pone.0021640	journal	June 2011
Biochemical Characterization of Human SET and MYND Domain-Containing Protein 2 Methyltransferase Wu, Jiaquan; Cheung, Tony; Grande, Christie Biochemistry, Vol. 50, Issue 29 https://doi.org/10.1021/bi200725p	journal	July 2011
Proteomic analyses of the SMYD family interactomes identify HSP90 as a novel target for SMYD2 Abu-Farha, Mohamed; Lanouette, Sylvain; Elisma, Fred Journal of Molecular Cell Biology, Vol. 3, Issue 5 https://doi.org/10.1093/jmcb/mjr025	journal	October 2011
SMYD3 encodes a histone methyltransferase involved in the proliferation of cancer cells Hamamoto, Ryuji; Furukawa, Yoichi; Morita, Masashi Nature Cell Biology, Vol. 6, Issue 8 https://doi.org/10.1038/ncb1151	journal	July 2004
Control of Proinflammatory Gene Programs by Regulated Trimethylation and Demethylation of Histone H4K20 Stender, Joshua D.; Pascual, Gabriel; Liu, Wen Molecular Cell, Vol. 48, Issue 1 https://doi.org/10.1016/j.molcel.2012.07.020	journal	October 2012
The CCP4 suite programs for protein crystallography Acta Crystallographica Section D Biological Crystallography, Vol. 50, Issue 5, p. 760-763 https://doi.org/10.1107/S0907444994003112	journal	September 1994
Gene expression profiling in hepatocellular carcinoma: upregulation of genes in amplified chromosome regions Skawran, Britta; Steinemann, Doris; Weigmann, Anja Modern Pathology, Vol. 21, Issue 5 https://doi.org/10.1038/modpathol.3800998	journal	February 2008
The methyltransferase SMYD3 mediates the recruitment of transcriptional cofactors at the myostatin and c-Met genes and regulates skeletal muscle atrophy Proserpio, V.; Fittipaldi, R.; Ryall, J. G. Genes & Development, Vol. 27, Issue 11 https://doi.org/10.1101/gad.217240.113	journal	June 2013
The Tale of Two Domains: Proteomics and Genomics Analysis of SMYD2, A New Histone Methyltransferase Abu-Farha, Mohamed; Lambert, Jean-Philippe; Al-Madhoun, Ashraf S. Molecular & Cellular Proteomics, Vol. 7, Issue 3 https://doi.org/10.1074/mcp.M700271-MCP200	journal	December 2007
Repression of p53 activity by Smyd2-mediated methylation Huang, Jing; Perez-Burgos, Laura; Placek, Brandon J. Nature, Vol. 444, Issue 7119 https://doi.org/10.1038/nature05287	journal	November 2006
Smyd2 controls cytoplasmic lysine methylation of Hsp90 and myofilament organization Donlin, L. T.; Andresen, C.; Just, S. Genes & Development, Vol. 26, Issue 2 https://doi.org/10.1101/gad.177758.111	journal	January 2012
The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1. Cerami, Ethan; Gao, Jianjiong; Dogrusoz, Ugur Cancer Discovery, Vol. 2, Issue 5 https://doi.org/10.1158/2159-8290.CD-12-0095	journal	May 2012
Structural Insights into Estrogen Receptor α Methylation by Histone Methyltransferase SMYD2, a Cellular Event Implicated in Estrogen Signaling Regulation Jiang, Yuanyuan; Trescott, Laura; Holcomb, Joshua Journal of Molecular Biology, Vol. 426, Issue 20 https://doi.org/10.1016/j.jmb.2014.02.019	journal	October 2014
Structure of human lysine methyltransferase Smyd2 reveals insights into the substrate divergence in Smyd proteins Xu, Shutong; Zhong, Chen; Zhang, Tianlong Journal of Molecular Cell Biology, Vol. 3, Issue 5 https://doi.org/10.1093/jmcb/mjr015	journal	July 2011
Structural Basis of Substrate Methylation and Inhibition of SMYD2 Ferguson, Andrew D.; Larsen, Nicholas A.; Howard, Tina Structure, Vol. 19, Issue 9 https://doi.org/10.1016/j.str.2011.06.011	journal	September 2011
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity Barretina, Jordi; Caponigro, Giordano; Stransky, Nicolas Nature, Vol. 483, Issue 7391 https://doi.org/10.1038/nature11003	journal	March 2012
Small changes in expression affect predisposition to tumorigenesis Yan, Hai; Dobbie, Zuzana; Gruber, Stephen B. Nature Genetics, Vol. 30, Issue 1 https://doi.org/10.1038/ng799	journal	December 2001
SMYD2 is highly expressed in pediatric acute lymphoblastic leukemia and constitutes a bad prognostic factor Sakamoto, Luis Henrique Toshihiro; Andrade, Rosangela Vieira de; Felipe, Maria Sueli Soares Leukemia Research, Vol. 38, Issue 4 https://doi.org/10.1016/j.leukres.2014.01.013	journal	April 2014
Regulation of estrogen receptor by histone methyltransferase SMYD2-mediated protein methylation Zhang, X.; Tanaka, K.; Yan, J. Proceedings of the National Academy of Sciences, Vol. 110, Issue 43 https://doi.org/10.1073/pnas.1307959110	journal	October 2013
Methylation of the Retinoblastoma Tumor Suppressor by SMYD2 Saddic, Louis A.; West, Lisandra E.; Aslanian, Aaron Journal of Biological Chemistry, Vol. 285, Issue 48 https://doi.org/10.1074/jbc.M110.137612	journal	September 2010
Overexpression of SMYD2 relates to tumor cell proliferation and malignant outcome of esophageal squamous cell carcinoma Komatsu, Shuhei; Imoto, Issei; Tsuda, Hitoshi Carcinogenesis, Vol. 30, Issue 7 https://doi.org/10.1093/carcin/bgp116	journal	May 2009
The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability Niesen, Frank H.; Berglund, Helena; Vedadi, Masoud Nature Protocols, Vol. 2, Issue 9 https://doi.org/10.1038/nprot.2007.321	journal	September 2007
Smyd3 regulates cancer cell phenotypes and catalyzes histone H4 lysine 5 methylation Van Aller, Glenn S.; Reynoird, Nicolas; Barbash, Olena Epigenetics, Vol. 7, Issue 4 https://doi.org/10.4161/epi.19506	journal	April 2012
SMYD3 links lysine methylation of MAP3K2 to Ras-driven cancer Mazur, Pawel K.; Reynoird, Nicolas; Khatri, Purvesh Nature, Vol. 510, Issue 7504 https://doi.org/10.1038/nature13320	journal	May 2014
Cardiac Deletion of Smyd2 Is Dispensable for Mouse Heart Development Diehl, Florian; Brown, Mark A.; van Amerongen, Machteld J. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009748	journal	March 2010
Epigenetic protein families: a new frontier for drug discovery Arrowsmith, Cheryl H.; Bountra, Chas; Fish, Paul V. Nature Reviews Drug Discovery, Vol. 11, Issue 5 https://doi.org/10.1038/nrd3674	journal	April 2012
Bop encodes a muscle-restricted protein containing MYND and SET domains and is essential for cardiac differentiation and morphogenesis Gottlieb, Paul D.; Pierce, Stephanie A.; Sims, Robert J. Nature Genetics, Vol. 31, Issue 1 https://doi.org/10.1038/ng866	journal	April 2002
A genomic and epigenomic atlas of prostate cancer in Asian populations Li, Jing; Xu, Chuanliang; Lee, Hyung Joo Nature, Vol. 580, Issue 7801 https://doi.org/10.1038/s41586-020-2135-x	journal	March 2020
OncoOmics approaches to reveal essential genes in breast cancer: a panoramic view from pathogenesis to precision medicine López-Cortés, Andrés; Paz-y-Miño, César; Guerrero, Santiago Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-62279-2	journal	March 2020
Cancer epigenetics drug discovery and development: the challenge of hitting the mark Campbell, Robert M.; Tummino, Peter J. Journal of Clinical Investigation, Vol. 124, Issue 3 https://doi.org/10.1172/jci75448	journal	March 2014
Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity Barretina, Jordi; Caponigro, Giordano; Stransky, Nicolas Nature, Vol. 565, Issue 7738 https://doi.org/10.1038/s41586-018-0722-x	journal	December 2018
Structure of Human SMYD2 Protein Reveals the Basis of p53 Tumor Suppressor Methylation Wang, Li; Li, Ling; Zhang, Hailong Journal of Biological Chemistry, Vol. 286, Issue 44 https://doi.org/10.1074/jbc.m111.262410	journal	August 2011
Identification of Smyd4 as a Potential Tumor Suppressor Gene Involved in Breast Cancer Development Hu, Liping; Zhu, Yiwei Tony; Qi, Chao Cancer Research, Vol. 69, Issue 9 https://doi.org/10.1158/0008-5472.can-08-4097	journal	April 2009
Cancer epigenetics drug discovery and development: the challenge of hitting the mark Campbell, Robert M.; Tummino, Peter J. Journal of Clinical Investigation, Vol. 124, Issue 1 https://doi.org/10.1172/jci71605	journal	January 2014

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Bisphenol A and Phthalates Modulate Peritoneal Macrophage Function in Female Mice Involving SYMD2-H3K36 Dimethylation Li, Quanxi; Lawrence, Catherine R.; Nowak, Romana A. Endocrinology, Vol. 159, Issue 5 https://doi.org/10.1210/en.2017-03000	journal	March 2018
Identification of a peptide inhibitor for the histone methyltransferase WHSC1 Morrison, Michael J.; Boriack-Sjodin, P. Ann; Swinger, Kerren K. PLOS ONE, Vol. 13, Issue 5 https://doi.org/10.1371/journal.pone.0197082	journal	May 2018
Marked for death: targeting epigenetic changes in cancer Pfister, Sophia Xiao; Ashworth, Alan Nature Reviews Drug Discovery, Vol. 16, Issue 4 https://doi.org/10.1038/nrd.2016.256	journal	March 2017
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Dysregulation of histone methyltransferases in breast cancer - Opportunities for new targeted therapies? Michalak, Ewa M.; Visvader, Jane E. Molecular Oncology, Vol. 10, Issue 10 https://doi.org/10.1016/j.molonc.2016.09.003	journal	September 2016
Dysregulation of protein methyltransferases in human cancer: An emerging target class for anticancer therapy Hamamoto, Ryuji; Nakamura, Yusuke Cancer Science, Vol. 107, Issue 4 https://doi.org/10.1111/cas.12884	journal	February 2016
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59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
SMYD2
cancer biology
chemical probe
crystal structure
enzyme inhibitor
epigenetics
methyltransferase
protein methylation

Title: LLY-507, a cell-active, potent, and selective inhibitor of protein-lysine methyltransferase SMYD2

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