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Vital T, Wali A, Butler KV, Xiong Y, Foster JP, Marcel SS, McFadden AW, Nguyen VU, Bailey BM, Lamb KN, James LI, Frye SV, Mosely AL, Jin J, Pattenden SG, Davis IJ. MS0621, a novel small-molecule modulator of Ewing sarcoma chromatin accessibility, interacts with an RNA-associated macromolecular complex and influences RNA splicing. Front Oncol 2023; 13:1099550. [PMID: 36793594 PMCID: PMC9924231 DOI: 10.3389/fonc.2023.1099550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/11/2023] [Indexed: 01/31/2023] Open
Abstract
Ewing sarcoma is a cancer of children and young adults characterized by the critical translocation-associated fusion oncoprotein EWSR1::FLI1. EWSR1::FLI1 targets characteristic genetic loci where it mediates aberrant chromatin and the establishment of de novo enhancers. Ewing sarcoma thus provides a model to interrogate mechanisms underlying chromatin dysregulation in tumorigenesis. Previously, we developed a high-throughput chromatin-based screening platform based on the de novo enhancers and demonstrated its utility in identifying small molecules capable of altering chromatin accessibility. Here, we report the identification of MS0621, a molecule with previously uncharacterized mechanism of action, as a small molecule modulator of chromatin state at sites of aberrant chromatin accessibility at EWSR1::FLI1-bound loci. MS0621 suppresses cellular proliferation of Ewing sarcoma cell lines by cell cycle arrest. Proteomic studies demonstrate that MS0621 associates with EWSR1::FLI1, RNA binding and splicing proteins, as well as chromatin regulatory proteins. Surprisingly, interactions with chromatin and many RNA-binding proteins, including EWSR1::FLI1 and its known interactors, were RNA-independent. Our findings suggest that MS0621 affects EWSR1::FLI1-mediated chromatin activity by interacting with and altering the activity of RNA splicing machinery and chromatin modulating factors. Genetic modulation of these proteins similarly inhibits proliferation and alters chromatin in Ewing sarcoma cells. The use of an oncogene-associated chromatin signature as a target allows for a direct approach to screen for unrecognized modulators of epigenetic machinery and provides a framework for using chromatin-based assays for future therapeutic discovery efforts.
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Affiliation(s)
- Tamara Vital
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Aminah Wali
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kyle V. Butler
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Yan Xiong
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Joseph P. Foster
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Shelsa S. Marcel
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Andrew W. McFadden
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Valerie U. Nguyen
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Benton M. Bailey
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kelsey N. Lamb
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lindsey I. James
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Stephen V. Frye
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Amber L. Mosely
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Samantha G. Pattenden
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ian J. Davis
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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2
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Chiarella AM, Butler KV, Gryder BE, Lu D, Wang TA, Yu X, Pomella S, Khan J, Jin J, Hathaway NA. Dose-dependent activation of gene expression is achieved using CRISPR and small molecules that recruit endogenous chromatin machinery. Nat Biotechnol 2020; 38:50-55. [PMID: 31712774 PMCID: PMC6954327 DOI: 10.1038/s41587-019-0296-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/24/2019] [Indexed: 01/10/2023]
Abstract
Gene expression can be activated or suppressed using CRISPR--Cas9 systems. However, tools that enable dose-dependent activation of gene expression without the use of exogenous transcription regulatory proteins are lacking. Here we describe chemical epigenetic modifiers (CEMs) designed to activate the expression of target genes by recruiting components of the endogenous chromatin-activating machinery, eliminating the need for exogenous transcriptional activators. The system has two parts: catalytically inactive Cas9 (dCas9) in complex with FK506-binding protein (FKBP) and a CEM consisting of FK506 linked to a molecule that interacts with cellular epigenetic machinery. We show that CEMs upregulate gene expression at target endogenous loci up to 20-fold or more depending on the gene. We also demonstrate dose-dependent control of transcriptional activation, function across multiple diverse genes, reversibility of CEM activity and specificity of our best-in-class CEM across the genome.
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Affiliation(s)
- Anna M Chiarella
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Kyle V Butler
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Berkley E Gryder
- Oncogenomics Section, Genetics Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Dongbo Lu
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Tiffany A Wang
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Silvia Pomella
- Oncogenomics Section, Genetics Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA
- Department of Pediatric Hematology and Oncology, Bambino Gesu' Children's Hospital, Rome, Italy
| | - Javed Khan
- Oncogenomics Section, Genetics Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Nathaniel A Hathaway
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA.
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MacDonald IA, Butler KV, Herring LE, Clinkscales SE, Yelagandula R, Stecher K, Bell O, Graves LM, Jin J, Hathaway NA. Pathway-Based High-Throughput Chemical Screen Identifies Compounds That Decouple Heterochromatin Transformations. SLAS Discov 2019; 24:802-816. [PMID: 31145866 DOI: 10.1177/2472555219849838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Heterochromatin protein 1 (HP1) facilitates the formation of repressive heterochromatin domains by recruiting histone lysine methyltransferase enzymes to chromatin, resulting in increased levels of histone H3K9me3. To identify chemical inhibitors of the HP1-heterochromatin gene repression pathway, we combined a cell-based assay that utilized chemical-mediated recruitment of HP1 to an endogenous active gene with high-throughput flow cytometry. Here we characterized small molecule inhibitors that block HP1-mediated heterochromatin formation. Our lead compounds demonstrated dose-dependent inhibition of HP1-stimulated gene repression and were validated in an orthogonal cell-based system. One lead inhibitor was improved by a change in stereochemistry, resulting in compound 2, which was further used to decouple the inverse relationship between H3K9 and H3K4 methylation states. We identified molecular components that bound compound 2, either directly or indirectly, by chemical affinity purification with a biotin-tagged derivative, followed by quantitative proteomic techniques. In summary, our pathway-based chemical screening approach resulted in the discovery of new inhibitors of HP1-mediated heterochromatin formation while identifying exciting new molecular interactions in the pathway to explore in the future. This modular platform can be expanded to test a wide range of chromatin modification pathways yielding inhibitors that are cell permeable and function in a physiologically relevant setting.
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Affiliation(s)
- Ian A MacDonald
- 1 The Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kyle V Butler
- 2 Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura E Herring
- 3 Department of Pharmacology, UNC Michael Hooker Proteomics Core Facility, University of North Carolina, Chapel Hill, NC, USA
| | - Sarah E Clinkscales
- 1 The Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ramesh Yelagandula
- 4 Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Karin Stecher
- 4 Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Oliver Bell
- 4 Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria.,5 Department of Biochemistry and Molecular Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Lee M Graves
- 3 Department of Pharmacology, UNC Michael Hooker Proteomics Core Facility, University of North Carolina, Chapel Hill, NC, USA
| | - Jian Jin
- 2 Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nathaniel A Hathaway
- 1 The Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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4
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Chiarella AM, Wang TA, Butler KV, Jin J, Hathaway NA. Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers. J Vis Exp 2018. [PMID: 30295665 DOI: 10.3791/58222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Regulation of chromatin compaction is an important process that governs gene expression in higher eukaryotes. Although chromatin compaction and gene expression regulation are commonly disrupted in many diseases, a locus-specific, endogenous, and reversible method to study and control these mechanisms of action has been lacking. To address this issue, we have developed and characterized novel gene-regulating bifunctional molecules. One component of the bifunctional molecule binds to a DNA-protein anchor so that it will be recruited to an allele-specific locus. The other component engages endogenous cellular chromatin-modifying machinery, recruiting these proteins to a gene of interest. These small molecules, called chemical epigenetic modifiers (CEMs), are capable of controlling gene expression and the chromatin environment in a dose-dependent and reversible manner. Here, we detail a CEM approach and its application to decrease gene expression and histone tail acetylation at a Green Fluorescent Protein (GFP) reporter located at the Oct4 locus in mouse embryonic stem cells (mESCs). We characterize the lead CEM (CEM23) using fluorescent microscopy, flow cytometry, and chromatin immunoprecipitation (ChIP), followed by a quantitative polymerase chain reaction (qPCR). While the power of this system is demonstrated at the Oct4 locus, conceptually, the CEM technology is modular and can be applied in other cell types and at other genomic loci.
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Affiliation(s)
- Anna M Chiarella
- Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Curriculum in Genetics and Molecular Biology, University of North Carolina
| | - Tiffany A Wang
- College of Arts and Sciences, Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina
| | - Kyle V Butler
- Chemical Biology and Drug Discovery, Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai
| | - Jian Jin
- Chemical Biology and Drug Discovery, Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai
| | - Nathaniel A Hathaway
- Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, University of North Carolina;
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5
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Chiarella AM, Butler KV, Jin J, Hathaway NA. Abstract LB-342: Targeted gene control with bifunctional molecules to harness endogenous chromatin-modifying activity. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-lb-342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Epigenetic pathways are commonly found disrupted in many human diseases including cancer, yet much remains unknown about the mechanisms by which dysregulation of chromatin regulatory pathways leads to disease pathology. To investigate and control these complex interactions in live cells, we developed a novel system that will unveil the underlying mechanisms of proteins responsible for modulating chromatin states using a gene-specific manipulation strategy. To explore how dynamic changes in acetylation levels impact chromatin structure we generated an endogenous reporter system at the murine Oct4 locus with a Gal4 DNA binding array upstream of an EGFP reporter allele. In our system, a FKBP protein fused to a Gal4 DNA-binding-domain serves as a protein anchor to the DNA binding array. Next, we synthesized novel cell-permeable, bifunctional molecules that include FK506 (which binds to FKBP) linked to a component that selectively binds to a histone tail chromatin-modifying enzyme. We characterized the effects of the Chemical Epigenetic Modifiers (CEM)s using flow cytometry, high-content microscopy and chromatin immunoprecipitation. We show that our lead repressive CEM can repress GFP expression by 50%. Next, we have made our system more modular by creating a deactivated Cas9 (dCas9)-FKBP fusion protein. The FKBP portion allows us to recruit our CEMs to any region of the genome to which we design a guide RNA. To study the addition of histone acetylation we utilized our new activating, HAT-binding CEMs and designed our dCas9-FKBP to target low-expression reporters. Our lead activating CEM increases expression over 20-fold. We are now using our activating CEM system to target tumor suppressor genes in hard to treat cancers. To show proof-of-principle, we have targeted the tumor suppressor p53 in a colon cancer cell line. We hypothesize that our activating CEM platform will activate the repressed P53 allele leading to slower tumor cell proliferation and apoptosis. This work represents a novel therapeutic strategy that is capable of modulating gene expression in a reversible and dose-dependent manner.
Citation Format: Anna M. Chiarella, Kyle V. Butler, Jian Jin, Nathaniel A. Hathaway. Targeted gene control with bifunctional molecules to harness endogenous chromatin-modifying activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-342.
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Affiliation(s)
| | | | - Jian Jin
- 2Icahn School of Medicine at Mount Sinai, New York, NY
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6
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Butler KV, Chiarella AM, Jin J, Hathaway NA. Targeted Gene Repression Using Novel Bifunctional Molecules to Harness Endogenous Histone Deacetylation Activity. ACS Synth Biol 2018; 7:38-45. [PMID: 29073761 DOI: 10.1021/acssynbio.7b00295] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Epigenome editing is a powerful method for life science research and could give rise to new therapies for diseases initiated or maintained by epigenetic dysregulation, including several types of cancers and autoimmune disorders. In addition, much is still unknown about the mechanisms by which histone-modifying proteins work in concert to properly regulate gene expression. To investigate and manipulate complex epigenetic interactions in live cells, we have developed a small molecule platform for specifically inducing gene repression and histone deacetylation at a reporter gene. We synthesized bifunctional ligands, or chemical epigenetic modifiers (CEMs), that contain two functional groups: a FK506 derivative capable of binding to a FKBP-Gal4 fusion transcription factor, and a histone deacetylase (HDAC) inhibitor that recruits HDAC-containing corepressor complexes. In our reporter cell line, which contains a GFP reporter allele upstream of a Gal4 DNA binding array in the murine Oct4 locus, our lead CEM repressed GFP expression by 50%. We also show that CEM recruitment of deacetylation activity causes marked deacetylation along our target loci. This system allowed us to detail the direct results of deacetylation to chromatin and measure the resulting gene expression in a chemically dependent and reversible manner. The CEMs system provides new insights into epigenetic gene regulation and has the potential to control disease-relevant gene regulation. The CEMs are derived from FDA-approved epigenetic modulator drugs, and use their pharmacology in a gene-specific way that avoids the toxicities and off-target effects caused by whole-cell application of these drugs.
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Affiliation(s)
- Kyle V. Butler
- Center
for Chemical Biology and Drug Discovery, Departments of Pharmacological
Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Anna M. Chiarella
- Division
of Chemical Biology and Medicinal Chemistry, Center for Integrative
Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina 27599, United States
| | - Jian Jin
- Center
for Chemical Biology and Drug Discovery, Departments of Pharmacological
Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Nathaniel A. Hathaway
- Division
of Chemical Biology and Medicinal Chemistry, Center for Integrative
Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina 27599, United States
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7
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Abstract
![]()
Small molecule tool compounds have
enabled profound advances in
life science research. These chemicals are potent, cell active, and
selective, and, thus, are suitable for interrogating biological processes.
For these chemicals to be useful they must be correctly characterized
and researchers must be aware of them. We mined the ChEMBL bioactivity
database to identify high quality tool compounds in an unbiased way.
We identified 407 best-in-class compounds for 278 protein targets,
and these are reported in an annotated data set. Additionally, we
developed informatics functions and a web application for data visualization
and automated pharmacological hypothesis generation. These functions
were used to predict inhibitors of the Chromobox Protein Homologue
5 (CBX5) mediated gene repression pathway that currently lacks appropriate
inhibitors. The predictions were subsequently validated by a highly
specific cell based assay, revealing new chemical modulators of CBX5-mediated
heterochromatin formation. This data set and associated functions
will help researchers make the best use of these valuable compounds.
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Affiliation(s)
- Kyle V Butler
- Center for Chemical Biology and Drug Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Ian A MacDonald
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy , Chapel Hill, North Carolina 27599, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Nathaniel A Hathaway
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy , Chapel Hill, North Carolina 27599, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Jian Jin
- Center for Chemical Biology and Drug Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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8
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Abstract
Biased ligands (also known as functionally selective ligands) of G protein-coupled receptors are valuable tools for dissecting the roles of G protein-dependent and independent signaling pathways in health and disease. Biased ligands have also been increasingly pursued by the biomedical community as promising therapeutics with improved efficacy and reduced side effects compared with unbiased ligands. We previously discovered first-in-class β-arrestin-biased agonists of dopamine D2 receptor (D2R) by extensively exploring multiple regions of aripiprazole, a balanced D2R agonist. In our continuing efforts to identify biased agonists of D2R, we unexpectedly discovered a G protein-biased agonist of D2R, compound 1, which is the first G protein-biased D2R agonist from the aripiprazole scaffold. We designed and synthesized novel analogues to explore two regions of 1 and conducted structure-functional selectivity relationship (SFSR) studies. Here we report the discovery of 1, findings from our SFSR studies, and characterization of novel G protein-biased D2R agonists.
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Affiliation(s)
- Xin Chen
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, New York 10029, USA
| | - John D. McCorvy
- Department of Pharmacology and National Institute of Mental Health Psychoactive Drug Screening Program, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Matthew G. Fischer
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, New York 10029, USA
| | - Kyle V. Butler
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, New York 10029, USA
| | - Yudao Shen
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, New York 10029, USA
| | - Bryan L. Roth
- Department of Pharmacology and National Institute of Mental Health Psychoactive Drug Screening Program, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jian Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, New York 10029, USA
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9
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Butler KV, Ma A, Yu W, Li F, Tempel W, Babault N, Pittella-Silva F, Shao J, Wang J, Luo M, Vedadi M, Brown PJ, Arrowsmith CH, Jin J. Structure-Based Design of a Covalent Inhibitor of the SET Domain-Containing Protein 8 (SETD8) Lysine Methyltransferase. J Med Chem 2016; 59:9881-9889. [PMID: 27804297 DOI: 10.1021/acs.jmedchem.6b01244] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Selective inhibitors of protein lysine methyltransferases, including SET domain-containing protein 8 (SETD8), are highly desired, as only a fraction of these enzymes are associated with high-quality inhibitors. From our previously discovered SETD8 inhibitor, we developed a more potent analog and solved a cocrystal structure, which is the first crystal structure of SETD8 in complex with a small-molecule inhibitor. This cocrystal structure allowed the design of a covalent inhibitor of SETD8 (MS453), which specifically modifies a cysteine residue near the inhibitor binding site, has an IC50 value of 804 nM, reacts with SETD8 with near-quantitative yield, and is selective for SETD8 against 28 other methyltransferases. We also solved the crystal structure of the covalent inhibitor in complex with SETD8. This work provides atomic-level perspective on the inhibition of SETD8 by small molecules and will help identify high-quality chemical probes of SETD8.
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Affiliation(s)
- Kyle V Butler
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Anqi Ma
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Wenyu Yu
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | - Nicolas Babault
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Fabio Pittella-Silva
- Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
| | - Jason Shao
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Junyi Wang
- Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
| | - Minkui Luo
- Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Jian Jin
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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10
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Butler KV, Bohn K, Hrycyna CA, Jin J. Non-Substrate Based, Small Molecule Inhibitors of the Human Isoprenylcysteine Carboxyl Methyltransferase. Medchemcomm 2016; 7:1016-1021. [PMID: 27547295 DOI: 10.1039/c6md00130k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Activating mutations of human K-Ras proteins are among the most common oncogenic mutations, present in approximately 30% of all human cancers. Posttranslational modifications to K-Ras guide it to the plasma membrane and disruption of this localization inhibits the growth of Ras-driven cancers. The human isoprenylcysteine carboxyl methyltransferase (hIcmt) enzyme catalyzes the final α-carboxyl methylesterification of the C-terminal farnesyl cysteine of K-Ras, which is necessary for its proper localization. Thus, hIcmt inhibition is a regarded as a promising cancer therapy. A high quality inhibitor of hIcmt with in vivo activity would advance hIcmt research and drug development. Herein, Wwe report the results of a screen for small molecule hIcmt inhibitors in a library of molecules that were not hIcmt substrate analogs. The lead compound identified by this screen (1) was modified to remove chemical liabilities and to increase potency. The most potent resulting compound (5) inhibited hIcmt in vitro with low micromolar potency (IC50 = 1.5 ± 0.2 μM) and was kinetically characterized as a competitive inhibitor for prenylated substrates and a non-competitive inhibitor for the cofactor and methyl donor S-adenosylmethionine (SAM). These inhibitors offer important structure activity relationships for the future development of hIcmt inhibitors with in vivo activity.
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Affiliation(s)
- Kyle V Butler
- Departments of Structural and Chemical Biology, Oncological Sciences, and Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Kelsey Bohn
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Christine A Hrycyna
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Jian Jin
- Departments of Structural and Chemical Biology, Oncological Sciences, and Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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11
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Eram MS, Shen Y, Szewczyk MM, Wu H, Senisterra G, Li F, Butler KV, Kaniskan HÜ, Speed BA, dela Seña C, Dong A, Zeng H, Schapira M, Brown PJ, Arrowsmith CH, Barsyte-Lovejoy D, Liu J, Vedadi M, Jin J. A Potent, Selective, and Cell-Active Inhibitor of Human Type I Protein Arginine Methyltransferases. ACS Chem Biol 2016; 11:772-781. [PMID: 26598975 DOI: 10.1021/acschembio.5b00839] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein arginine methyltransferases (PRMTs) play a crucial role in a variety of biological processes. Overexpression of PRMTs has been implicated in various human diseases including cancer. Consequently, selective small-molecule inhibitors of PRMTs have been pursued by both academia and the pharmaceutical industry as chemical tools for testing biological and therapeutic hypotheses. PRMTs are divided into three categories: type I PRMTs which catalyze mono- and asymmetric dimethylation of arginine residues, type II PRMTs which catalyze mono- and symmetric dimethylation of arginine residues, and type III PRMT which catalyzes only monomethylation of arginine residues. Here, we report the discovery of a potent, selective, and cell-active inhibitor of human type I PRMTs, MS023, and characterization of this inhibitor in a battery of biochemical, biophysical, and cellular assays. MS023 displayed high potency for type I PRMTs including PRMT1, -3, -4, -6, and -8 but was completely inactive against type II and type III PRMTs, protein lysine methyltransferases and DNA methyltransferases. A crystal structure of PRMT6 in complex with MS023 revealed that MS023 binds the substrate binding site. MS023 potently decreased cellular levels of histone arginine asymmetric dimethylation. It also reduced global levels of arginine asymmetric dimethylation and concurrently increased levels of arginine monomethylation and symmetric dimethylation in cells. We also developed MS094, a close analog of MS023, which was inactive in biochemical and cellular assays, as a negative control for chemical biology studies. MS023 and MS094 are useful chemical tools for investigating the role of type I PRMTs in health and disease.
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Affiliation(s)
- Mohammad S. Eram
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Yudao Shen
- Departments
of Structural and Chemical Biology, Oncological Sciences, and Pharmacology
and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Magdalena M. Szewczyk
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Hong Wu
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Guillermo Senisterra
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Fengling Li
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Kyle V. Butler
- Departments
of Structural and Chemical Biology, Oncological Sciences, and Pharmacology
and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - H. Ümit Kaniskan
- Departments
of Structural and Chemical Biology, Oncological Sciences, and Pharmacology
and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Brandon A. Speed
- Departments
of Structural and Chemical Biology, Oncological Sciences, and Pharmacology
and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Carlo dela Seña
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Aiping Dong
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Hong Zeng
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Matthieu Schapira
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Department
of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Peter J. Brown
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Cheryl H. Arrowsmith
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Princess
Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Dalia Barsyte-Lovejoy
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Jing Liu
- Departments
of Structural and Chemical Biology, Oncological Sciences, and Pharmacology
and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Masoud Vedadi
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Department
of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jian Jin
- Departments
of Structural and Chemical Biology, Oncological Sciences, and Pharmacology
and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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12
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Ma A, Yu W, Li F, Bleich RM, Herold JM, Butler KV, Norris JL, Korboukh V, Tripathy A, Janzen WP, Arrowsmith CH, Frye SV, Vedadi M, Brown PJ, Jin J. Discovery of a selective, substrate-competitive inhibitor of the lysine methyltransferase SETD8. J Med Chem 2014; 57:6822-33. [PMID: 25032507 PMCID: PMC4136711 DOI: 10.1021/jm500871s] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The lysine methyltransferase SETD8 is the only known methyltransferase that catalyzes monomethylation of histone H4 lysine 20 (H4K20). Monomethylation of H4K20 has been implicated in regulating diverse biological processes including the DNA damage response. In addition to H4K20, SETD8 monomethylates non-histone substrates including proliferating cell nuclear antigen (PCNA) and promotes carcinogenesis by deregulating PCNA expression. However, selective inhibitors of SETD8 are scarce. The only known selective inhibitor of SETD8 to date is nahuoic acid A, a marine natural product, which is competitive with the cofactor. Here, we report the discovery of the first substrate-competitive inhibitor of SETD8, UNC0379 (1). This small-molecule inhibitor is active in multiple biochemical assays. Its affinity to SETD8 was confirmed by ITC (isothermal titration calorimetry) and SPR (surface plasmon resonance) studies. Importantly, compound 1 is selective for SETD8 over 15 other methyltransferases. We also describe structure-activity relationships (SAR) of this series.
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Affiliation(s)
- Anqi Ma
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, ‡Department of Pharmacology, School of Medicine, §Lineberger Comprehensive Cancer Center, and ∥Department of Biochemistry and Biophysics, UNC Macromolecular Interactions Facility, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
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13
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Abstract
SETD8 (also known as SET8, PR-SET7, or KMT5A (lysine methyltransferase 5A)) is the only known lysine methyltransferase that catalyzes monomethylation of histone H4 lysine 20 (H4K20). In addition to H4K20, SETD8 monomethylates non-histone substrates such as the tumor suppressor p53 and proliferating cell nuclear antigen (PCNA). Because of its role in regulating diverse biological processes, SETD8 has been pursued as a potential therapeutic target. We recently reported the first substrate-competitive SETD8 inhibitor, UNC0379 (1), which is selective for SETD8 over 15 other methyltransferases. We characterized this inhibitor in a battery of biochemical and biophysical assays. Here we describe our comprehensive structure-activity relationship (SAR) studies of this chemical series. In addition to 2- and 4-substituents, we extensively explored 6- and 7-substituents of the quinazoline scaffold. These SAR studies led to the discovery of several new compounds, which displayed similar potencies as compound 1, and interesting SAR trends.
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Affiliation(s)
- Anqi Ma
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, United States
| | - Wenyu Yu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Yan Xiong
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, United States
| | - Kyle V Butler
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, United States
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Jian Jin
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, United States ; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, United States ; Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, United States
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14
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Kalin JH, Butler KV, Akimova T, Hancock WW, Kozikowski AP. Second-generation histone deacetylase 6 inhibitors enhance the immunosuppressive effects of Foxp3+ T-regulatory cells. J Med Chem 2012; 55:639-51. [PMID: 22165909 DOI: 10.1021/jm200773h] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Second-generation Tubastatin A analogues were synthesized and evaluated for their ability to inhibit selectively histone deacetylase 6 (HDAC6). Substitutions to the carboline cap group were well-tolerated with substitution at the 2-position of both β- and γ-carbolines being optimal for HDAC6 activity and selectivity. Some compounds in this series were determined to have subnanomolar activity at HDAC6 with more than 7000 fold selectivity for HDAC6 versus HDAC1. Selected compounds were then evaluated for their ability to augment the immunosuppressive effect of Foxp3+ regulatory T cells. All compounds tested were found to enhance the ability of regulatory T cells to inhibit the mitotic division of effector T cells both in vitro and in vivo, suggesting that further investigation into the use of these compounds for the treatment of autoimmune disorders is warranted.
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Affiliation(s)
- Jay H Kalin
- Drug Discovery Program, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
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15
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Butler KV, Kalin J, Brochier C, Vistoli G, Langley B, Kozikowski AP. Rational design and simple chemistry yield a superior, neuroprotective HDAC6 inhibitor, tubastatin A. J Am Chem Soc 2010; 132:10842-6. [PMID: 20614936 DOI: 10.1021/ja102758v] [Citation(s) in RCA: 564] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Structure-based drug design combined with homology modeling techniques were used to develop potent inhibitors of HDAC6 that display superior selectivity for the HDAC6 isozyme compared to other inhibitors. These inhibitors can be assembled in a few synthetic steps, and thus are readily scaled up for in vivo studies. An optimized compound from this series, designated Tubastatin A, was tested in primary cortical neuron cultures in which it was found to induce elevated levels of acetylated alpha-tubulin, but not histone, consistent with its HDAC6 selectivity. Tubastatin A also conferred dose-dependent protection in primary cortical neuron cultures against glutathione depletion-induced oxidative stress. Importantly, when given alone at all concentrations tested, this hydroxamate-containing HDAC6-selective compound displayed no neuronal toxicity, thus, forecasting the potential application of this agent and its analogues to neurodegenerative conditions.
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Affiliation(s)
- Kyle V Butler
- Drug Discovery Program, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 South Wood, Chicago, Illinois 60612, USA
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16
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Tang H, Wang XS, Huang XP, Roth BL, Butler KV, Kozikowski AP, Jung M, Tropsha A. Novel Inhibitors of Human Histone Deacetylase (HDAC) Identified by QSAR Modeling of Known Inhibitors, Virtual Screening, and Experimental Validation. J Chem Inf Model 2009; 49:461-76. [DOI: 10.1021/ci800366f] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hao Tang
- Laboratory for Molecular Modeling, and Carolina Exploratory Center for Cheminformatics Research, Division of Medicinal Chemistry and Natural Products, School of Pharmacy, Biophysics Training Program, Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 833 South Wood Street, Chicago, Illinois 60612, and Department of Radiation Medicine, Georgetown University Medical
| | - Xiang S. Wang
- Laboratory for Molecular Modeling, and Carolina Exploratory Center for Cheminformatics Research, Division of Medicinal Chemistry and Natural Products, School of Pharmacy, Biophysics Training Program, Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 833 South Wood Street, Chicago, Illinois 60612, and Department of Radiation Medicine, Georgetown University Medical
| | - Xi-Ping Huang
- Laboratory for Molecular Modeling, and Carolina Exploratory Center for Cheminformatics Research, Division of Medicinal Chemistry and Natural Products, School of Pharmacy, Biophysics Training Program, Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 833 South Wood Street, Chicago, Illinois 60612, and Department of Radiation Medicine, Georgetown University Medical
| | - Bryan L. Roth
- Laboratory for Molecular Modeling, and Carolina Exploratory Center for Cheminformatics Research, Division of Medicinal Chemistry and Natural Products, School of Pharmacy, Biophysics Training Program, Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 833 South Wood Street, Chicago, Illinois 60612, and Department of Radiation Medicine, Georgetown University Medical
| | - Kyle V. Butler
- Laboratory for Molecular Modeling, and Carolina Exploratory Center for Cheminformatics Research, Division of Medicinal Chemistry and Natural Products, School of Pharmacy, Biophysics Training Program, Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 833 South Wood Street, Chicago, Illinois 60612, and Department of Radiation Medicine, Georgetown University Medical
| | - Alan P. Kozikowski
- Laboratory for Molecular Modeling, and Carolina Exploratory Center for Cheminformatics Research, Division of Medicinal Chemistry and Natural Products, School of Pharmacy, Biophysics Training Program, Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 833 South Wood Street, Chicago, Illinois 60612, and Department of Radiation Medicine, Georgetown University Medical
| | - Mira Jung
- Laboratory for Molecular Modeling, and Carolina Exploratory Center for Cheminformatics Research, Division of Medicinal Chemistry and Natural Products, School of Pharmacy, Biophysics Training Program, Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 833 South Wood Street, Chicago, Illinois 60612, and Department of Radiation Medicine, Georgetown University Medical
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, and Carolina Exploratory Center for Cheminformatics Research, Division of Medicinal Chemistry and Natural Products, School of Pharmacy, Biophysics Training Program, Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 833 South Wood Street, Chicago, Illinois 60612, and Department of Radiation Medicine, Georgetown University Medical
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