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Huang X, Chen Y, Xiao Q, Shang X, Liu Y. Chemical inhibitors targeting histone methylation readers. Pharmacol Ther 2024; 256:108614. [PMID: 38401773 DOI: 10.1016/j.pharmthera.2024.108614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/01/2024] [Accepted: 02/15/2024] [Indexed: 02/26/2024]
Abstract
Histone methylation reader domains are protein modules that recognize specific histone methylation marks, such as methylated or unmethylated lysine or arginine residues on histones. These reader proteins play crucial roles in the epigenetic regulation of gene expression, chromatin structure, and DNA damage repair. Dysregulation of these proteins has been linked to various diseases, including cancer, neurodegenerative diseases, and developmental disorders. Therefore, targeting these proteins with chemical inhibitors has emerged as an attractive approach for therapeutic intervention, and significant progress has been made in this area. In this review, we will summarize the development of inhibitors targeting histone methylation readers, including MBT domains, chromodomains, Tudor domains, PWWP domains, PHD fingers, and WD40 repeat domains. For each domain, we will briefly discuss its identification and biological/biochemical functions, and then focus on the discovery of inhibitors tailored to target this domain, summarizing the property and potential application of most inhibitors. We will also discuss the structural basis for the potency and selectivity of these inhibitors, which will aid in further lead generation and optimization. Finally, we will also address the challenges and strategies involved in the development of these inhibitors. It should facilitate the rational design and development of novel chemical scaffolds and new targeting strategies for histone methylation reader domains with the help of this body of data.
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Affiliation(s)
- Xiaolei Huang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Yichang Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Qin Xiao
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Xinci Shang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Yanli Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China.
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Enders L, Siklos M, Borggräfe J, Gaussmann S, Koren A, Malik M, Tomek T, Schuster M, Reiniš J, Hahn E, Rukavina A, Reicher A, Casteels T, Bock C, Winter GE, Hannich JT, Sattler M, Kubicek S. Pharmacological perturbation of the phase-separating protein SMNDC1. Nat Commun 2023; 14:4504. [PMID: 37587144 PMCID: PMC10432564 DOI: 10.1038/s41467-023-40124-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 07/13/2023] [Indexed: 08/18/2023] Open
Abstract
SMNDC1 is a Tudor domain protein that recognizes di-methylated arginines and controls gene expression as an essential splicing factor. Here, we study the specific contributions of the SMNDC1 Tudor domain to protein-protein interactions, subcellular localization, and molecular function. To perturb the protein function in cells, we develop small molecule inhibitors targeting the dimethylarginine binding pocket of the SMNDC1 Tudor domain. We find that SMNDC1 localizes to phase-separated membraneless organelles that partially overlap with nuclear speckles. This condensation behavior is driven by the unstructured C-terminal region of SMNDC1, depends on RNA interaction and can be recapitulated in vitro. Inhibitors of the protein's Tudor domain drastically alter protein-protein interactions and subcellular localization, causing splicing changes for SMNDC1-dependent genes. These compounds will enable further pharmacological studies on the role of SMNDC1 in the regulation of nuclear condensates, gene regulation and cell identity.
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Affiliation(s)
- Lennart Enders
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Marton Siklos
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Jan Borggräfe
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, München, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Garching, 85748, München, Germany
| | - Stefan Gaussmann
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, München, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Garching, 85748, München, Germany
| | - Anna Koren
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Monika Malik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Tatjana Tomek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Jiří Reiniš
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Elisa Hahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Andrea Rukavina
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Andreas Reicher
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Tamara Casteels
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
- Sloan Kettering Institute, 1275 York Avenue, New York, NY, 10065, USA
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
- Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Währinger Straße 25a, 1090, Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - J Thomas Hannich
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Michael Sattler
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, München, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Garching, 85748, München, Germany
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria.
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Ortiz G, Kutateladze TG, Fujimori DG. Chemical tools targeting readers of lysine methylation. Curr Opin Chem Biol 2023; 74:102286. [PMID: 36948085 PMCID: PMC10264141 DOI: 10.1016/j.cbpa.2023.102286] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 02/01/2023] [Accepted: 02/20/2023] [Indexed: 03/22/2023]
Abstract
Reader domains that recognize methylated lysine and arginine residues on histones play a role in the recruitment, stabilization, and regulation of chromatin regulatory proteins. Targeting reader proteins with small molecule and peptidomimetic inhibitors has enabled the elucidation of the structure and function of specific domains and uncovered their role in diseases. Recent progress towards chemical probes that target readers of lysine methylation, including the Royal family and plant homeodomains (PHD), is discussed here. We highlight recently developed covalent cyclic peptide inhibitors of a plant homeodomain. Additionally, inhibitors targeting previously untargeted Tudor domains and chromodomains are discussed.
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Affiliation(s)
- Gloria Ortiz
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco, CA 94158, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
| | - Danica Galonic Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco San Francisco, CA 94158, USA.
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Van Holsbeeck K, Elsocht M, Ballet S. Propargylamine Amino Acids as Constrained Nε-Substituted Lysine Mimetics. Org Lett 2023; 25:130-133. [PMID: 36546856 DOI: 10.1021/acs.orglett.2c03931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Herein, alkylated propargylamines are reported as constrained lysine mimetics and constructed in a single step using a copper(I)-catalyzed A3-coupling reaction. Using multiple secondary amines, the reaction allowed the generation of a structurally diverse set of N-Fmoc protected amino acid derivatives. In addition, the A3-reaction was applied on solid phase via the assembly of short model tripeptides. Moreover, the internal alkyne moiety allowed further functionalization toward novel 1,4,5-trisubstituted 1,2,3-triazole-based amino acids.
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Affiliation(s)
- Kevin Van Holsbeeck
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
| | - Mathias Elsocht
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. ACS Chem Biol 2022; 17:2673-2678. [PMID: 36268572 DOI: 10.1021/acschembio.2c00661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. ACS Pharmacol Transl Sci 2022; 5:829-834. [PMID: 36268124 PMCID: PMC9578134 DOI: 10.1021/acsptsci.2c00169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Indexed: 11/28/2022]
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. ACS Infect Dis 2022; 8:1975-1980. [PMID: 36073808 DOI: 10.1021/acsinfecdis.2c00434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. ACS Med Chem Lett 2022; 13:1524-1529. [PMID: 36262399 PMCID: PMC9575161 DOI: 10.1021/acsmedchemlett.2c00393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Indexed: 11/30/2022] Open
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. J Med Chem 2022; 65:11894-11899. [PMID: 36073827 DOI: 10.1021/acs.jmedchem.2c01386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. ACS Chem Neurosci 2022. [PMID: 36067366 DOI: 10.1021/acschemneuro.2c00501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Kean KM, Baril SA, Lamb KN, Dishman SN, Treacy JW, Houk KN, Brustad EM, James LI, Waters ML. Systematic Variation of Both the Aromatic Cage and Dialkyllysine via GCE-SAR Reveal Mechanistic Insights in CBX5 Reader Protein Binding. J Med Chem 2022; 65:2646-2655. [PMID: 35014255 PMCID: PMC9048841 DOI: 10.1021/acs.jmedchem.1c02049] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Development of inhibitors for histone methyllysine reader proteins is an active area of research due to the importance of reader protein-methyllysine interactions in transcriptional regulation and disease. Optimized peptide-based chemical probes targeting methyllysine readers favor larger alkyllysine residues in place of methyllysine. However, the mechanism by which these larger substituents drive tighter binding is not well understood. This study describes the development of a two-pronged approach combining genetic code expansion (GCE) and structure-activity relationships (SAR) through systematic variation of both the aromatic binding pocket in the protein and the alkyllysine residues in the peptide to probe inhibitor recognition in the CBX5 chromodomain. We demonstrate a novel change in driving force for larger alkyllysines, which weaken cation-π interactions but increases dispersion forces, resulting in tighter binding. This GCE-SAR approach establishes discrete energetic contributions to binding from both ligand and protein, providing a powerful tool to gain mechanistic understanding of SAR trends.
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Affiliation(s)
- Kelsey M. Kean
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Stefanie A. Baril
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - 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 27599 USA
| | - Sarah N. Dishman
- 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 27599 USA
| | - Joseph W. Treacy
- Department of Chemistry and Biochemistry, Box 951569, University of California, Los Angeles, CA 90095 USA
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry, Box 951569, University of California, Los Angeles, CA 90095 USA
| | - Eric M. Brustad
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Lindsey I. James
- 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 27599 USA
| | - Marcey L. Waters
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA,Corresponding Author: Marcey L. Waters – Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States;
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