title: LLY-507, a Cell-active, Potent, and Selective Inhibitor of Protein-lysine Methyltransferase SMYD2.
abstract: 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. 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.
authors.affiliation: From the Departments of Oncology Discovery, Structural Biology, Tailored Therapeutics, and Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285, nguyen_anh-quan_hannah@lilly.com.
authors.forename: Hannah
authors.initials: H
authors.lastname: Nguyen
authors.affiliation: Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower, 7th floor, Toronto, Ontario M5G 1L7, Canada.
authors.forename: Abdellah
authors.initials: A
authors.lastname: Allali-Hassani
authors.affiliation: From the Departments of Oncology Discovery, Structural Biology, Tailored Therapeutics, and Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285.
authors.forename: Stephen
authors.initials: S
authors.lastname: Antonysamy
authors.affiliation: From the Departments of Oncology Discovery, Structural Biology, Tailored Therapeutics, and Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285.
authors.forename: Shawn
authors.initials: S
authors.lastname: Chang
authors.affiliation: From the Departments of Oncology Discovery, Structural Biology, Tailored Therapeutics, and Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285.
authors.forename: Lisa Hong
authors.initials: LH
authors.lastname: Chen
authors.affiliation: From the Departments of Oncology Discovery, Structural Biology, Tailored Therapeutics, and Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285.
authors.forename: Carmen
authors.initials: C
authors.lastname: Curtis
authors.affiliation: From the Departments of Oncology Discovery, Structural Biology, Tailored Therapeutics, and Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285.
authors.forename: Spencer
authors.initials: S
authors.lastname: Emtage
authors.affiliation: From the Departments of Oncology Discovery, Structural Biology, Tailored Therapeutics, and Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285.
authors.forename: Li
authors.initials: L
authors.lastname: Fan
authors.affiliation: From the Departments of Oncology Discovery, Structural Biology, Tailored Therapeutics, and Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285.
authors.forename: Tarun
authors.initials: T
authors.lastname: Gheyi
authors.affiliation: Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower, 7th floor, Toronto, Ontario M5G 1L7, Canada.
authors.forename: Fengling
authors.initials: F
authors.lastname: Li
authors.affiliation: Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104.
authors.forename: Shichong
authors.initials: S
authors.lastname: Liu
authors.affiliation: From the Departments of Oncology Discovery, Structural Biology, Tailored Therapeutics, and Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285.
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Martin
authors.affiliation: From the Departments of Oncology Discovery, Structural Biology, Tailored Therapeutics, and Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285.
authors.forename: David
authors.initials: D
authors.lastname: Mendel
authors.affiliation: From the Departments of Oncology Discovery, Structural Biology, Tailored Therapeutics, and Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285.
authors.forename: Jonathan B
authors.initials: JB
authors.lastname: Olsen
authors.affiliation: From the Departments of Oncology Discovery, Structural Biology, Tailored Therapeutics, and Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285.
authors.forename: Laura
authors.initials: L
authors.lastname: Pelletier
authors.affiliation: Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower, 7th floor, Toronto, Ontario M5G 1L7, Canada.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Shatseva
authors.affiliation: From the Departments of Oncology Discovery, Structural Biology, Tailored Therapeutics, and Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285.
authors.forename: Song
authors.initials: S
authors.lastname: Wu
authors.affiliation: From the Departments of Oncology Discovery, Structural Biology, Tailored Therapeutics, and Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285.
authors.forename: Feiyu Fred
authors.initials: FF
authors.lastname: Zhang
authors.affiliation: Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower, 7th floor, Toronto, Ontario M5G 1L7, Canada, Department of Medical Biophysics, University of Toronto and Princess Margaret Cancer Centre, 101 College Street, MaRS South Tower, Suite 707, Toronto, Ontario M5G 1L7, Canada, and.
authors.forename: Cheryl H
authors.initials: CH
authors.lastname: Arrowsmith
authors.affiliation: Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower, 7th floor, Toronto, Ontario M5G 1L7, Canada.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Brown
authors.affiliation: From the Departments of Oncology Discovery, Structural Biology, Tailored Therapeutics, and Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Campbell
authors.affiliation: Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104.
authors.forename: Benjamin A
authors.initials: BA
authors.lastname: Garcia
authors.affiliation: Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower, 7th floor, Toronto, Ontario M5G 1L7, Canada.
authors.forename: Dalia
authors.initials: D
authors.lastname: Barsyte-Lovejoy
authors.affiliation: From the Departments of Oncology Discovery, Structural Biology, Tailored Therapeutics, and Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285.
authors.forename: Mary
authors.initials: M
authors.lastname: Mader
authors.affiliation: Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower, 7th floor, Toronto, Ontario M5G 1L7, Canada.
authors.forename: Masoud
authors.initials: M
authors.lastname: Vedadi
mesh_terms: D000970:Antineoplastic Agents / Q000737:chemistry*; D001549:Benzamides / Q000737:chemistry*; D045744:Cell Line, Tumor; D049109:Cell Proliferation; D002843:Chromatin / Q000737:chemistry; D019295:Computational Biology; D003460:Crystallization; D018360:Crystallography, X-Ray; D004305:Dose-Response Relationship, Drug; D004354:Drug Screening Assays, Antitumor; D004791:Enzyme Inhibitors / Q000737:chemistry*; D044127:Epigenesis, Genetic; D011495:Histone-Lysine N-Methyltransferase / Q000037:antagonists & inhibitors*; D006657:Histones / Q000737:chemistry; D006801:Humans; D013058:Mass Spectrometry; D009369:Neoplasms / Q000188:drug therapy / Q000201:enzymology*; D010455:Peptides / Q000737:chemistry; D011489:Protein Denaturation; D040901:Proteomics; D011759:Pyrrolidines / Q000737:chemistry*; D016159:Tumor Suppressor Protein p53 / Q000378:metabolism
chemical_list: D000970:Antineoplastic Agents; D001549:Benzamides; D002843:Chromatin; D004791:Enzyme Inhibitors; D006657:Histones; C000600304:LLY-507; D010455:Peptides; D011759:Pyrrolidines; C495901:TP53 protein, human; D016159:Tumor Suppressor Protein p53; D011495:Histone-Lysine N-Methyltransferase; C512569:SMYD2 protein, human
keywords: SMYD2; cancer biology; chemical probe; crystal structure; enzyme inhibitor; epigenetics; methyltransferase; protein methylation
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