1
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Vorreiter C, Robaa D, Sippl W. Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains. J Chem Inf Model 2024; 64:4553-4569. [PMID: 38771194 PMCID: PMC11167732 DOI: 10.1021/acs.jcim.4c00298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
Cosolvent molecular dynamics (MD) simulations have proven to be powerful in silico tools to predict hotspots for binding regions on protein surfaces. In the current study, the method was adapted and applied to two Tudor domain-containing proteins, namely Spindlin1 (SPIN1) and survival motor neuron protein (SMN). Tudor domains are characterized by so-called aromatic cages that recognize methylated lysine residues of protein targets. In the study, the conformational transitions from closed to open aromatic cage conformations were investigated by performing MD simulations with cosolvents using six different probe molecules. It is shown that a trajectory clustering approach in combination with volume and atomic distance tracking allows a reasonable discrimination between open and closed aromatic cage conformations and the docking of inhibitors yields very good reproducibility with crystal structures. Cosolvent MDs are suitable to capture the flexibility of aromatic cages and thus represent a promising tool for the optimization of inhibitors.
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Affiliation(s)
- Christopher Vorreiter
- Department of Medicinal Chemistry,
Institute of Pharmacy, Martin-Luther-University
of Halle-Wittenberg, 06120 Halle, Saale, Germany
| | - Dina Robaa
- Department of Medicinal Chemistry,
Institute of Pharmacy, Martin-Luther-University
of Halle-Wittenberg, 06120 Halle, Saale, Germany
| | - Wolfgang Sippl
- Department of Medicinal Chemistry,
Institute of Pharmacy, Martin-Luther-University
of Halle-Wittenberg, 06120 Halle, Saale, Germany
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2
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Xiong Y, Greschik H, Johansson C, Seifert L, Gamble V, Park KS, Fagan V, Li F, Chau I, Vedadi M, Arrowsmith CH, Brennan P, Fedorov O, Jung M, Farnie G, Liu J, Oppermann U, Schüle R, Jin J. Discovery of a Potent, Selective, and Cell-Active SPIN1 Inhibitor. J Med Chem 2024; 67:5837-5853. [PMID: 38533580 PMCID: PMC11022035 DOI: 10.1021/acs.jmedchem.4c00121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
The methyl-lysine reader protein SPIN1 plays important roles in various human diseases. However, targeting methyl-lysine reader proteins has been challenging. Very few cellularly active SPIN1 inhibitors have been developed. We previously reported that our G9a/GLP inhibitor UNC0638 weakly inhibited SPIN1. Here, we present our comprehensive structure-activity relationship study that led to the discovery of compound 11, a dual SPIN1 and G9a/GLP inhibitor, and compound 18 (MS8535), a SPIN1 selective inhibitor. We solved the cocrystal structure of SPIN1 in complex with 11, confirming that 11 occupied one of the three Tudor domains. Importantly, 18 displayed high selectivity for SPIN1 over 38 epigenetic targets, including G9a/GLP, and concentration dependently disrupted the interactions of SPIN1 and H3 in cells. Furthermore, 18 was bioavailable in mice. We also developed 19 (MS8535N), which was inactive against SPIN1, as a negative control of 18. Collectively, these compounds are useful chemical tools to study biological functions of SPIN1.
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Affiliation(s)
- Yan Xiong
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Holger Greschik
- Department of Urology and Center for Clinical Research, University Freiburg Medical Center, Freiburg 79106, Germany
| | - Catrine Johansson
- Structural Genomics Consortium, Botnar Research Center, NIHR Oxford BRU, University of Oxford, Oxford OX3 7LD, U.K
| | - Ludwig Seifert
- Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg 79104, Germany
| | - Vicki Gamble
- Structural Genomics Consortium, Botnar Research Center, NIHR Oxford BRU, University of Oxford, Oxford OX3 7LD, U.K
| | - Kwang-Su Park
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Vincent Fagan
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K.; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Irene Chau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Masoud Vedadi
- Ontario Institute for Cancer Research, 661 University Avenue, Toronto, Ontario M5G 0A3, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, 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 1L7, Canada
| | - Paul Brennan
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K.; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - Oleg Fedorov
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K.; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg 79104, Germany
- German Cancer Research Centre (DKFZ), Heidelberg 69120, Germany
- German Cancer Consortium (DKTK), Freiburg 79104, Germany
| | - Gillian Farnie
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K.; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - Jing Liu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Udo Oppermann
- Structural Genomics Consortium, Botnar Research Center, NIHR Oxford BRU, University of Oxford, Oxford OX3 7LD, U.K
- Botnar Research Centre, University of Oxford, Oxford OX3 7LD, U.K
- Oxford Translational Myeloma Centre, University of Oxford, Oxford OX3 7LD, U.K
| | - Roland Schüle
- Department of Urology and Center for Clinical Research, University Freiburg Medical Center, Freiburg 79106, Germany
- German Cancer Consortium (DKTK), Freiburg 79104, Germany
- CIBSS Centre of Biological Signalling Studies, University of Freiburg, Freiburg 79106, Germany
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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3
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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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4
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Zhao F, Deng Y, Yang F, Yan Y, Feng F, Peng B, Gao J, Bedford MT, Li H. Molecular Basis for SPINDOC-Spindlin1 Engagement and Its Role in Transcriptional Attenuation. J Mol Biol 2024; 436:168371. [PMID: 37977297 DOI: 10.1016/j.jmb.2023.168371] [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: 09/19/2023] [Revised: 11/11/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Spindlin1 is a histone reader with three Tudor-like domains and its transcriptional co-activator activity could be attenuated by SPINDOC. The first two Tudors are involved in histone methylation readout, while the function of Tudor 3 is largely unknown. Here our structural and binding studies revealed an engagement mode of SPINDOC-Spindlin1, in which a hydrophobic motif of SPINDOC, DOCpep3, stably interacts with Spindlin1 Tudor 3, and two neighboring K/R-rich motifs, DOCpep1 and DOCpep2, bind to the acidic surface of Spindlin1 Tudor 2. Although DOCpep3-Spindlin1 engagement is compatible with histone readout, an extended SPINDOC fragment containing the K/R-rich region attenuates histone or TCF4 binding by Spindlin1 due to introduced competition. This inhibitory effect is more pronounced for weaker binding targets but not for strong ones such as H3 "K4me3-K9me3" bivalent mark. Further ChIP-seq and RT-qPCR indicated that SPINDOC could promote genomic relocation of Spindlin1, thus modulate downstream gene transcription. Collectively, we revealed multivalent engagement between SPINDOC and Spindlin1, in which a hydrophobic motif acts as the primary binding site for stable SPINDOC-Spindlin1 association, while K/R-rich region modulates the target selectivity of Spindlin1 via competitive inhibition, therefore attenuating the transcriptional co-activator activity of Spindlin1.
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Affiliation(s)
- Fan Zhao
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yafang Deng
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Fen Yang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, China
| | - Yan Yan
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China
| | - Fan Feng
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Bo Peng
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Juntao Gao
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China.
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.
| | - Haitao Li
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China; SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, MOE Key Laboratory of Coal Environmental Pathogenesis and Prevention, Shanxi Medical University, Taiyuan, Shanxi Province 030001, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
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5
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Menna M, Fiorentino F, Marrocco B, Lucidi A, Tomassi S, Cilli D, Romanenghi M, Cassandri M, Pomella S, Pezzella M, Del Bufalo D, Zeya Ansari MS, Tomašević N, Mladenović M, Viviano M, Sbardella G, Rota R, Trisciuoglio D, Minucci S, Mattevi A, Rotili D, Mai A. Novel non-covalent LSD1 inhibitors endowed with anticancer effects in leukemia and solid tumor cellular models. Eur J Med Chem 2022; 237:114410. [DOI: 10.1016/j.ejmech.2022.114410] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/22/2022]
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Porzberg MRB, Moesgaard L, Johansson C, Oppermann U, Kongsted J, Mecinović J. Recognition of Dimethylarginine Analogues by Tandem Tudor Domain Protein Spindlin1. Molecules 2022; 27:983. [PMID: 35164245 PMCID: PMC8838590 DOI: 10.3390/molecules27030983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 12/20/2022] Open
Abstract
Epigenetic readout of the combinatorial posttranslational modification comprised of trimethyllysine and asymmetric dimethylarginine (H3K4me3R8me2a) takes place via biomolecular recognition of tandem Tudor-domain-containing protein Spindlin1. Through comparative thermodynamic data and molecular dynamics simulations, we sought to explore the binding scope of asymmetric dimethylarginine mimics by Spindlin1. Herein, we provide evidence that the biomolecular recognition of H3K4me2R8me2a is not significantly affected when R8me2a is replaced by dimethylarginine analogues, implying that the binding of K4me3 provides the major binding contribution. High-energy water molecules inside both aromatic cages of the ligand binding sites contribute to the reader-histone association upon displacement by histone peptide, with the K4me3 hydration site being lower in free energy due to a flip of Trp151.
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Affiliation(s)
- Miriam R. B. Porzberg
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark; (M.R.B.P.); (L.M.); (J.K.)
| | - Laust Moesgaard
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark; (M.R.B.P.); (L.M.); (J.K.)
| | - Catrine Johansson
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-Medical Research Centre, University of Oxford, Oxford OX3 7LD, UK; (C.J.); (U.O.)
| | - Udo Oppermann
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-Medical Research Centre, University of Oxford, Oxford OX3 7LD, UK; (C.J.); (U.O.)
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark; (M.R.B.P.); (L.M.); (J.K.)
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark; (M.R.B.P.); (L.M.); (J.K.)
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7
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Li D, Guo J, Jia R. Histone code reader SPIN1 is a promising target of cancer therapy. Biochimie 2021; 191:78-86. [PMID: 34492335 DOI: 10.1016/j.biochi.2021.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/07/2021] [Accepted: 09/03/2021] [Indexed: 12/19/2022]
Abstract
SPIN1 is a histone methylation reader, which can epigenetically control multiple tumorigenesis-associated signaling pathways, including the Wnt, PI3K/AKT, and RET pathways. Considerable evidence has shown that SPIN1 is overexpressed in many cancers, which can promote cell proliferation, transformation, metastasis, and chemical or radiation resistance. With the growing understanding of the SPIN1 protein structure, some inhibitors have been developed to interfere with the recognition between SPIN1 and histone H3K4me3 and H3R8me2a methylation and block the oncogenic functions of SPIN1. Therefore, SPIN1 is a potential target of cancer therapy. However, the mechanism by which SPIN1-transformed cells overcome the significant mitotic spindle defects and the factors promoting SPIN1 overexpression in cancers remain unclear. In this review, we described the current understanding of the SPIN1 protein structure and its expression, functions, and regulatory mechanisms in carcinogenesis, and discussed the challenges faced in the mechanisms of SPIN1 overexpression and oncogenic functions, and the potential application of anti-SPIN1 treatment in human cancers.
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Affiliation(s)
- Di Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jihua Guo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China; Department of Endodontics, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
| | - Rong Jia
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
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Luise C, Robaa D, Sippl W. Exploring aromatic cage flexibility of the histone methyllysine reader protein Spindlin1 and its impact on binding mode prediction: an in silico study. J Comput Aided Mol Des 2021; 35:695-706. [PMID: 34081238 PMCID: PMC8213585 DOI: 10.1007/s10822-021-00391-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/28/2021] [Indexed: 11/04/2022]
Abstract
Some of the main challenges faced in drug discovery are pocket flexibility and binding mode prediction. In this work, we explored the aromatic cage flexibility of the histone methyllysine reader protein Spindlin1 and its impact on binding mode prediction by means of in silico approaches. We first investigated the Spindlin1 aromatic cage plasticity by analyzing the available crystal structures and through molecular dynamic simulations. Then we assessed the ability of rigid docking and flexible docking to rightly reproduce the binding mode of a known ligand into Spindlin1, as an example of a reader protein displaying flexibility in the binding pocket. The ability of induced fit docking was further probed to test if the right ligand binding mode could be obtained through flexible docking regardless of the initial protein conformation. Finally, the stability of generated docking poses was verified by molecular dynamic simulations. Accurate binding mode prediction was obtained showing that the herein reported approach is a highly promising combination of in silico methods able to rightly predict the binding mode of small molecule ligands in flexible binding pockets, such as those observed in some reader proteins.
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Affiliation(s)
- Chiara Luise
- Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, Kurt-Mothes-Str.3, 06120, Halle/Saale, Germany
| | - Dina Robaa
- Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, Kurt-Mothes-Str.3, 06120, Halle/Saale, Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, Kurt-Mothes-Str.3, 06120, Halle/Saale, Germany.
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Structure-Based Design, Docking and Binding Free Energy Calculations of A366 Derivatives as Spindlin1 Inhibitors. Int J Mol Sci 2021; 22:ijms22115910. [PMID: 34072837 PMCID: PMC8199216 DOI: 10.3390/ijms22115910] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
The chromatin reader protein Spindlin1 plays an important role in epigenetic regulation, through which it has been linked to several types of malignant tumors. In the current work, we report on the development of novel analogs of the previously published lead inhibitor A366. In an effort to improve the activity and explore the structure-activity relationship (SAR), a series of 21 derivatives was synthesized, tested in vitro, and investigated by means of molecular modeling tools. Docking studies and molecular dynamics (MD) simulations were performed to analyze and rationalize the structural differences responsible for the Spindlin1 activity. The analysis of MD simulations shed light on the important interactions. Our study highlighted the main structural features that are required for Spindlin1 inhibitory activity, which include a positively charged pyrrolidine moiety embedded into the aromatic cage connected via a propyloxy linker to the 2-aminoindole core. Of the latter, the amidine group anchor the compounds into the pocket through salt bridge interactions with Asp184. Different protocols were tested to identify a fast in silico method that could help to discriminate between active and inactive compounds within the A366 series. Rescoring the docking poses with MM-GBSA calculations was successful in this regard. Because A366 is known to be a G9a inhibitor, the most active developed Spindlin1 inhibitors were also tested over G9a and GLP to verify the selectivity profile of the A366 analogs. This resulted in the discovery of diverse selective compounds, among which 1s and 1t showed Spindlin1 activity in the nanomolar range and selectivity over G9a and GLP. Finally, future design hypotheses were suggested based on our findings.
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10
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Abstract
Determining the three-dimensional structures of protein complexes is critically important to guide biological research. Structural models of complexes can be built using powerful integrative approaches that combine emerging technologies in mass spectrometry, molecular modeling, and protein docking; however, preparing enriched biochemical samples suitable for analysis remains a major challenge. Here we describe serial capture affinity purification (SCAP), which can be used for the study of protein interactions in live cells and, when combined with cross-linking mass spectrometry, contribute distance restraints for integrative structural modeling. This broadly applicable technology can be used to study any protein complex in human tissue culture cells. We demonstrate SCAP capabilities on a poorly characterized epigenetic protein complex with roles in human cancer. Streamlined characterization of protein complexes remains a challenge for the study of protein interaction networks. Here we describe serial capture affinity purification (SCAP), in which two separate proteins are tagged with either the HaloTag or the SNAP-tag, permitting a multistep affinity enrichment of specific protein complexes. The multifunctional capabilities of this protein-tagging system also permit in vivo validation of interactions using acceptor photobleaching Förster resonance energy transfer and fluorescence cross-correlation spectroscopy quantitative imaging. By coupling SCAP to cross-linking mass spectrometry, an integrative structural model of the complex of interest can be generated. We demonstrate this approach using the Spindlin1 and SPINDOC protein complex, culminating in a structural model with two SPINDOC molecules docked on one SPIN1 molecule. In this model, SPINDOC interacts with the SPIN1 interface previously shown to bind a lysine and arginine methylated sequence of histone H3. Our approach combines serial affinity purification, live cell imaging, and cross-linking mass spectrometry to build integrative structural models of protein complexes.
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11
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Reiner D, Seifert L, Deck C, Schüle R, Jung M, Stark H. Epigenetics meets GPCR: inhibition of histone H3 methyltransferase (G9a) and histamine H 3 receptor for Prader-Willi Syndrome. Sci Rep 2020; 10:13558. [PMID: 32782417 PMCID: PMC7419559 DOI: 10.1038/s41598-020-70523-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/28/2020] [Indexed: 02/08/2023] Open
Abstract
The role of epigenetic regulation is in large parts connected to cancer, but additionally, its therapeutic claim in neurological disorders has emerged. Inhibition of histone H3 lysine N-methyltransferase, especially G9a, has been recently shown to restore candidate genes from silenced parental chromosomes in the imprinting disorder Prader-Willi syndrome (PWS). In addition to this epigenetic approach, pitolisant as G-protein coupled histamine H3 receptor (H3R) antagonist has demonstrated promising therapeutic effects for Prader-Willi syndrome. To combine these pioneering principles of drug action, we aimed to identify compounds that combine both activities, guided by the pharmacophore blueprint for both targets. However, pitolisant as selective H3R inverse agonist with FDA and EMA-approval did not show the required inhibition at G9a. Pharmacological characterization of the prominent G9a inhibitor A-366, that is as well an inhibitor of the epigenetic reader protein Spindlin1, revealed its high affinity at H3R while showing subtype selectivity among subsets of the histaminergic and dopaminergic receptor families. This work moves prominent G9a ligands forward as pharmacological tools to prove for a potentially combined, symptomatic and causal, therapy in PWS by bridging the gap between drug development for G-protein coupled receptors and G9a as an epigenetic effector in a multi-targeting approach.
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Affiliation(s)
- David Reiner
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
| | - Ludwig Seifert
- Institute of Pharmaceutical Sciences, University of Freiburg, 79104, Freiburg, Germany
| | - Caroline Deck
- Institute of Pharmaceutical Sciences, University of Freiburg, 79104, Freiburg, Germany
| | - Roland Schüle
- Department of Urology, Center for Clinical Research, Medical Center, Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79106, Freiburg, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg, 79104, Freiburg, Germany
| | - Holger Stark
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany.
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12
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Fagan V, Johansson C, Gileadi C, Monteiro O, Dunford JE, Nibhani R, Philpott M, Malzahn J, Wells G, Faram R, Cribbs AP, Halidi N, Li F, Chau I, Greschik H, Velupillai S, Allali-Hassani A, Bennett J, Christott T, Giroud C, Lewis AM, Huber KVM, Athanasou N, Bountra C, Jung M, Schüle R, Vedadi M, Arrowsmith C, Xiong Y, Jin J, Fedorov O, Farnie G, Brennan PE, Oppermann U. A Chemical Probe for Tudor Domain Protein Spindlin1 to Investigate Chromatin Function. J Med Chem 2019; 62:9008-9025. [PMID: 31550156 DOI: 10.1021/acs.jmedchem.9b00562] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Modifications of histone tails, including lysine/arginine methylation, provide the basis of a "chromatin or histone code". Proteins that contain "reader" domains can bind to these modifications and form specific effector complexes, which ultimately mediate chromatin function. The spindlin1 (SPIN1) protein contains three Tudor methyllysine/arginine reader domains and was identified as a putative oncogene and transcriptional coactivator. Here we report a SPIN1 chemical probe inhibitor with low nanomolar in vitro activity, exquisite selectivity on a panel of methyl reader and writer proteins, and with submicromolar cellular activity. X-ray crystallography showed that this Tudor domain chemical probe simultaneously engages Tudor domains 1 and 2 via a bidentate binding mode. Small molecule inhibition and siRNA knockdown of SPIN1, as well as chemoproteomic studies, identified genes which are transcriptionally regulated by SPIN1 in squamous cell carcinoma and suggest that SPIN1 may have a role in cancer related inflammation and/or cancer metastasis.
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Affiliation(s)
- Vincent Fagan
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Catrine Johansson
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Carina Gileadi
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Octovia Monteiro
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - James E Dunford
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Reshma Nibhani
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Martin Philpott
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Jessica Malzahn
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Graham Wells
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Ruth Faram
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Adam P Cribbs
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Nadia Halidi
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Fengling Li
- Structural Genomics Consortium , University of Toronto , 101 College Street , Toronto , Ontario M5G 1L7 , Canada
| | - Irene Chau
- Structural Genomics Consortium , University of Toronto , 101 College Street , Toronto , Ontario M5G 1L7 , Canada
| | - Holger Greschik
- Department of Urology, Center for Clinical Research, Medical Center, Signalling Research Centres BIOSS and CIBSS , University of Freiburg , D-79106 Freiburg , Germany
| | - Srikannathasan Velupillai
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
| | - Abdellah Allali-Hassani
- Structural Genomics Consortium , University of Toronto , 101 College Street , Toronto , Ontario M5G 1L7 , Canada
| | - James Bennett
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Thomas Christott
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Charline Giroud
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Andrew M Lewis
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Kilian V M Huber
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Nick Athanasou
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Chas Bountra
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
| | - Manfred Jung
- FRIAS-Freiburg Institute of Advanced Studies , University of Freiburg , 79104 Freiburg , Germany
- Institute of Pharmaceutical Sciences , University of Freiburg , Albertstraße 25 , 79104 Freiburg , Germany
| | - Roland Schüle
- Department of Urology, Center for Clinical Research, Medical Center, Signalling Research Centres BIOSS and CIBSS , University of Freiburg , D-79106 Freiburg , Germany
| | - Masoud Vedadi
- Structural Genomics Consortium , University of Toronto , 101 College Street , Toronto , Ontario M5G 1L7 , Canada
| | - Cheryl Arrowsmith
- Structural Genomics Consortium , University of Toronto , 101 College Street , Toronto , Ontario M5G 1L7 , Canada
| | - Yan Xiong
- 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 , New York 10029 , United States
| | - 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 , New York 10029 , United States
| | - Oleg Fedorov
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Gillian Farnie
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Paul E Brennan
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
- Alzheimer's Research UK Oxford Drug Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Udo Oppermann
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
- FRIAS-Freiburg Institute of Advanced Studies , University of Freiburg , 79104 Freiburg , Germany
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13
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Richa K, Karmaker R, Longkumer N, Das V, Bhuyan PJ, Pal M, Sinha UB. Synthesis, In Vitro Evaluation, Molecular Docking and DFT Studies of Some Phenyl Isothiocyanates as Anticancer Agents. Anticancer Agents Med Chem 2019; 19:2211-2222. [PMID: 31566135 DOI: 10.2174/1871520619666190930122137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 06/11/2019] [Accepted: 06/30/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Isothiocyanates (ITCs) are small molecules that are important in synthetic organic chemistry, but their actual importance lies in their potential as anti-carcinogens. Through this piece of work, an effort was made to assess the anti-cancer activity of some simple ITCs which can be synthesized through easy greener pathways. METHODS Cell proliferation assay was performed on ovarian cancer cells (PA-1) and non-tumorigenic ovarian epithelial cells (IOSE-364). Furthermore, qRT-PCR for transcript expression levels of Spindlin1 and caspases in ovarian cancer cells and cell cycle analysis was performed. In silico studies were incorporated to understand the mode of ligand-protein interaction, ADME/Toxicity and drug-likeliness parameters. Density functional theory studies have been also been employed on the ITCs to assess their efficiency in anticancer activity. RESULTS An inexpensive, environmentally benign pathway has been developed for synthesizing a series of ITCs. Among the synthesized ITCs, NC6 showed better cytotoxic effects as compared to its counterparts. Novel findings revealed that NC6 had 5-folds lower transcript expression levels of Spindlin1 and induced caspases 3 and 7 expressions assessed by qRT-PCR in ovarian cancer cells. Furthermore, flow cytometry assay showed the cell cycle arrest at G1/S phase of cell cycle. The molecular docking studies revealed favorable binding affinities and the physiochemical parameters were predicted to be compatible with drug-likeliness. CONCLUSION The results demonstrated the possibility that small isothiocyanate molecules which can be synthesized by a simple green methodology, can pose as promising candidates for their application as anticancer agents.
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Affiliation(s)
- Kikoleho Richa
- Department of Chemistry, Nagaland University, Lumami-798627, Nagaland, India.,Bioinformatics Facility Centre, Nagaland University, Lumami-798627, Nagaland, India
| | - Rituparna Karmaker
- Department of Chemistry, Nagaland University, Lumami-798627, Nagaland, India
| | - Naruti Longkumer
- Department of Chemistry, Nagaland University, Lumami-798627, Nagaland, India
| | - Vishal Das
- Biological Sciences and Technology Division, Biotechnology Group, CSIR-North East Institute of Science and Technology (NEIST), Academy of Scientific and Innovative Research, Jorhat, Assam-785006, India
| | - Pulak J Bhuyan
- Chemical Sciences and Technology Division, CSIR- North East Institute of Science and Technology (NEIST), Jorhat, Assam-785006, India
| | - Mintu Pal
- Biological Sciences and Technology Division, Biotechnology Group, CSIR-North East Institute of Science and Technology (NEIST), Academy of Scientific and Innovative Research, Jorhat, Assam-785006, India
| | - Upasana B Sinha
- Department of Chemistry, Nagaland University, Lumami-798627, Nagaland, India
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14
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Targeting epigenetic modifications in cancer therapy: erasing the roadmap to cancer. Nat Med 2019; 25:403-418. [PMID: 30842676 DOI: 10.1038/s41591-019-0376-8] [Citation(s) in RCA: 251] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 01/25/2019] [Indexed: 12/31/2022]
Abstract
Epigenetic dysregulation is a common feature of most cancers, often occurring directly through alteration of epigenetic machinery. Over the last several years, a new generation of drugs directed at epigenetic modulators have entered clinical development, and results from these trials are now being disclosed. Unlike first-generation epigenetic therapies, these new agents are selective, and many are targeted to proteins which are mutated or translocated in cancer. This review will provide a summary of the epigenetic modulatory agents currently in clinical development and discuss the opportunities and challenges in their development. As these drugs advance in the clinic, drug discovery has continued with a focus on both novel and existing epigenetic targets. We will provide an overview of these efforts and the strategies being employed.
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15
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Daskalakis M, Brocks D, Sheng YH, Islam MS, Ressnerova A, Assenov Y, Milde T, Oehme I, Witt O, Goyal A, Kühn A, Hartmann M, Weichenhan D, Jung M, Plass C. Reactivation of endogenous retroviral elements via treatment with DNMT- and HDAC-inhibitors. Cell Cycle 2018; 17:811-822. [PMID: 29633898 DOI: 10.1080/15384101.2018.1442623] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Inhibitors of DNA methyltransferases (DNMTis) or histone deacetylases (HDACis) are epigenetic drugs which are investigated since decades. Several have been approved and are applied in the treatment of hematopoietic and lymphatic malignancies, although their mode of action has not been fully understood. Two recent findings improved mechanistic insights: i) activation of human endogenous retroviral elements (HERVs) with concomitant synthesis of double-stranded RNAs (dsRNAs), and ii) massive activation of promoters from long terminal repeats (LTRs) which originated from past HERV invasions. These dsRNAs activate an antiviral response pathway followed by apoptosis. LTR promoter activation leads to synthesis of non-annotated transcripts potentially encoding novel or cryptic proteins. Here, we discuss the current knowledge of the molecular effects exerted by epigenetic drugs with a focus on DNMTis and HDACis. We highlight the role in LTR activation and provide novel data from both in vitro and in vivo epigenetic drug treatment.
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Affiliation(s)
- Michael Daskalakis
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany.,f German Cancer Research Consortium (DKTK) , Heidelberg , Germany
| | - David Brocks
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Yi-Hua Sheng
- b School of Pharmacy, College of Medicine , National Taiwan University , Taipei , Taiwan
| | - Md Saiful Islam
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Alzbeta Ressnerova
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Yassen Assenov
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Till Milde
- c Translational Program, Hopp Children's Cancer Center at NCT Heidelberg (KiTZ) , Germany.,d CCU Pediatric Oncology , German Cancer Research Center (DKFZ) , Heidelberg , Germany.,e Department of Pediatric Oncology, Hematology and Immunology , University Hospital, and Clinical Cooperation Unit Pediatric Oncology, DKFZ , Heidelberg , Germany.,f German Cancer Research Consortium (DKTK) , Heidelberg , Germany
| | - Ina Oehme
- c Translational Program, Hopp Children's Cancer Center at NCT Heidelberg (KiTZ) , Germany.,d CCU Pediatric Oncology , German Cancer Research Center (DKFZ) , Heidelberg , Germany.,e Department of Pediatric Oncology, Hematology and Immunology , University Hospital, and Clinical Cooperation Unit Pediatric Oncology, DKFZ , Heidelberg , Germany.,f German Cancer Research Consortium (DKTK) , Heidelberg , Germany
| | - Olaf Witt
- c Translational Program, Hopp Children's Cancer Center at NCT Heidelberg (KiTZ) , Germany.,d CCU Pediatric Oncology , German Cancer Research Center (DKFZ) , Heidelberg , Germany.,e Department of Pediatric Oncology, Hematology and Immunology , University Hospital, and Clinical Cooperation Unit Pediatric Oncology, DKFZ , Heidelberg , Germany.,f German Cancer Research Consortium (DKTK) , Heidelberg , Germany
| | - Ashish Goyal
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Alexander Kühn
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Mark Hartmann
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany.,g Regulation of Cellular Differentiation Group , German Cancer Research Center , Heidelberg , Germany
| | - Dieter Weichenhan
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Manfred Jung
- h Institute of Pharmaceutical Sciences, University of Freiburg , Germany
| | - Christoph Plass
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany.,f German Cancer Research Consortium (DKTK) , Heidelberg , Germany
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16
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Hauser AT, Robaa D, Jung M. Epigenetic small molecule modulators of histone and DNA methylation. Curr Opin Chem Biol 2018; 45:73-85. [PMID: 29579619 DOI: 10.1016/j.cbpa.2018.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/05/2018] [Accepted: 03/07/2018] [Indexed: 12/14/2022]
Abstract
DNA and histone methylation belong to the key regulatory components in the epigenetic machinery, and dysregulations of these processes have been associated with various human diseases. Small molecule modulators of these epigenetic targets are highly valuable both as chemical probes to study the biological roles of the target proteins, and as potential therapeutics. Indeed, recent years have seen the discovery of chemical modulators of several epigenetic targets, some of which are already marketed drugs or undergoing clinical trials. In this review, we will focus on small molecule modulators of DNA and histone methylation.
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Affiliation(s)
- Alexander-Thomas Hauser
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg im Breisgau, Germany
| | - Dina Robaa
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Wolfgang-Langenbeck-Straße 4, 06120 Halle (Saale), Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg im Breisgau, Germany.
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17
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Lu W, Zhang R, Jiang H, Zhang H, Luo C. Computer-Aided Drug Design in Epigenetics. Front Chem 2018; 6:57. [PMID: 29594101 PMCID: PMC5857607 DOI: 10.3389/fchem.2018.00057] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 02/23/2018] [Indexed: 12/31/2022] Open
Abstract
Epigenetic dysfunction has been widely implicated in several diseases especially cancers thus highlights the therapeutic potential for chemical interventions in this field. With rapid development of computational methodologies and high-performance computational resources, computer-aided drug design has emerged as a promising strategy to speed up epigenetic drug discovery. Herein, we make a brief overview of major computational methods reported in the literature including druggability prediction, virtual screening, homology modeling, scaffold hopping, pharmacophore modeling, molecular dynamics simulations, quantum chemistry calculation, and 3D quantitative structure activity relationship that have been successfully applied in the design and discovery of epi-drugs and epi-probes. Finally, we discuss about major limitations of current virtual drug design strategies in epigenetics drug discovery and future directions in this field.
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Affiliation(s)
- Wenchao Lu
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Rukang Zhang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Hao Jiang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Huimin Zhang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Cheng Luo
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
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18
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Maity P, Kundu D, Ghosh T, Ranu BC. Copper catalyzed cyanation through CC bond cleavage of gem-aryl dibromide followed by second cyanation of iodoarene by a released CN unit. Org Chem Front 2018. [DOI: 10.1039/c8qo00108a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new approach for the synthesis of aryl cyanides through CC cleavage of styrenyl gem-dibromide has been achieved.
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Affiliation(s)
- Pintu Maity
- Department of Organic Chemistry
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - Debasish Kundu
- Department of Organic Chemistry
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - Tubai Ghosh
- Department of Organic Chemistry
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - Brindaban C. Ranu
- Department of Organic Chemistry
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
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19
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Luise C, Robaa D. Application of Virtual Screening Approaches for the Identification of Small Molecule Inhibitors of the Methyllysine Reader Protein Spindlin1. Methods Mol Biol 2018; 1824:347-370. [PMID: 30039418 DOI: 10.1007/978-1-4939-8630-9_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Computer-based approaches represent a powerful tool which helps to identify and optimize lead structures in the process of drug discovery. Computer-aided drug design techniques (CADD) encompass a large variety of methods which are subdivided into structure-based (SBDD) and ligand-based drug design (LBDD) methods. Several approaches have been successfully used over the last three decades in different fields. Indeed also in the field of epigenetics, virtual screening (VS) studies and structure-based approaches have been applied to identify novel chemical modulators of epigenetic targets as well as to predict the binding mode of active ligands and to study the protein dynamics.In this chapter, an iterative VS approach using both SBDD and LBDD methods, which was successful in identifying Spindlin1 inhibitors, will be described. All protocol steps, starting from structure-based pharmacophore modeling, protein and database preparation along with docking and similarity search, will be explained in details.
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Affiliation(s)
- Chiara Luise
- Department of Pharmaceutical Chemistry, Martin-Luther University of Halle-Wittenberg, Halle/Saale, Germany
| | - Dina Robaa
- Department of Pharmaceutical Chemistry, Martin-Luther University of Halle-Wittenberg, Halle/Saale, Germany.
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20
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Barnash KD, Lamb KN, James LI, Frye SV. Peptide Technologies in the Development of Chemical Tools for Chromatin-Associated Machinery. Drug Dev Res 2017. [DOI: 10.1002/ddr.21398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kimberly D. Barnash
- 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 North Carolina 27599
| | - 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 North Carolina 27599
| | - 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 North Carolina 27599
| | - Stephen V. Frye
- 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 North Carolina 27599
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21
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Bae N, Viviano M, Su X, Lv J, Cheng D, Sagum C, Castellano S, Bai X, Johnson C, Khalil MI, Shen J, Chen K, Li H, Sbardella G, Bedford MT. Developing Spindlin1 small-molecule inhibitors by using protein microarrays. Nat Chem Biol 2017; 13:750-756. [PMID: 28504676 PMCID: PMC5831360 DOI: 10.1038/nchembio.2377] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 02/15/2017] [Indexed: 12/19/2022]
Abstract
The discovery of inhibitors of methyl- and acetyl-binding domains has provided evidence for the 'druggability' of epigenetic effector molecules. The small-molecule probe UNC1215 prevents methyl-dependent protein-protein interactions by engaging the aromatic cage of MBT domains and, with lower affinity, Tudor domains. Using a library of tagged UNC1215 analogs, we screened a protein-domain microarray of human methyllysine effector molecules to rapidly detect compounds with new binding profiles with either increased or decreased specificity. Using this approach, we identified a compound (EML405) that acquired a novel interaction with the Tudor-domain-containing protein Spindlin1 (SPIN1). Structural studies facilitated the rational synthesis of SPIN1 inhibitors with increased selectivity (EML631-633), which engage SPIN1 in cells, block its ability to 'read' H3K4me3 marks and inhibit its transcriptional-coactivator activity. Protein microarrays can thus be used as a platform to 'target-hop' and identify small molecules that bind and compete with domain-motif interactions.
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Affiliation(s)
- Narkhyun Bae
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Monica Viviano
- Dipartimento di Farmacia, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano (SA), Italy
| | - Xiaonan Su
- Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, 100084, P.R. China
| | - Jie Lv
- Center for Regenerative Medicine, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA & Department of Cardiothoracic Surgery, Weill Cornell Medical College, Cornell University
| | - Donghang Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Cari Sagum
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Sabrina Castellano
- Dipartimento di Farmacia, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano (SA), Italy
- Dipartimento di Medicina e Chirurgia, Università degli Studi di Salerno, Via Salvador Allende, I-84081 Baronissi (SA), Italy
| | - Xue Bai
- Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, 100084, P.R. China
| | - Claire Johnson
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Mahmoud Ibrahim Khalil
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
- Molecular Biology Unit, Department of Zoology, Faculty of Science, Alexandria University, Egypt
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Kaifu Chen
- Center for Regenerative Medicine, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA & Department of Cardiothoracic Surgery, Weill Cornell Medical College, Cornell University
| | - Haitao Li
- Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, 100084, P.R. China
| | - Gianluca Sbardella
- Dipartimento di Farmacia, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano (SA), Italy
| | - Mark T. Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
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22
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Shanle EK, Shinsky SA, Bridgers JB, Bae N, Sagum C, Krajewski K, Rothbart SB, Bedford MT, Strahl BD. Histone peptide microarray screen of chromo and Tudor domains defines new histone lysine methylation interactions. Epigenetics Chromatin 2017; 10:12. [PMID: 28293301 PMCID: PMC5348760 DOI: 10.1186/s13072-017-0117-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/01/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Histone posttranslational modifications (PTMs) function to regulate chromatin structure and function in part through the recruitment of effector proteins that harbor specialized "reader" domains. Despite efforts to elucidate reader domain-PTM interactions, the influence of neighboring PTMs and the target specificity of many reader domains is still unclear. The aim of this study was to use a high-throughput histone peptide microarray platform to interrogate 83 known and putative histone reader domains from the chromo and Tudor domain families to identify their interactions and characterize the influence of neighboring PTMs on these interactions. RESULTS Nearly a quarter of the chromo and Tudor domains screened showed interactions with histone PTMs by peptide microarray, revealing known and several novel methyllysine interactions. Specifically, we found that the CBX/HP1 chromodomains that recognize H3K9me also recognize H3K23me2/3-a poorly understood histone PTM. We also observed that, in addition to their interaction with H3K4me3, Tudor domains of the Spindlin family also recognized H4K20me3-a previously uncharacterized interaction. Several Tudor domains also showed novel interactions with H3K4me as well. CONCLUSIONS These results provide an important resource for the epigenetics and chromatin community on the interactions of many human chromo and Tudor domains. They also provide the basis for additional studies into the functional significance of the novel interactions that were discovered.
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Affiliation(s)
- Erin K Shanle
- Department of Biological and Environmental Sciences, Longwood University, Farmville, VA 23909 USA
| | - Stephen A Shinsky
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, NC 27599 USA.,Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC 27599 USA.,Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA USA
| | - Joseph B Bridgers
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, NC 27599 USA
| | - Narkhyun Bae
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957 USA
| | - Cari Sagum
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957 USA
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, NC 27599 USA
| | - Scott B Rothbart
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503 USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957 USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, NC 27599 USA.,Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC 27599 USA
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23
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Hau M, Zenk F, Ganesan A, Iovino N, Jung M. Cellular analysis of the action of epigenetic drugs and probes. Epigenetics 2017; 12:308-322. [PMID: 28071961 DOI: 10.1080/15592294.2016.1274472] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Small molecule drugs and probes are important tools in drug discovery, pharmacology, and cell biology. This is of course also true for epigenetic inhibitors. Important examples for the use of established epigenetic inhibitors are the study of the mechanistic role of a certain target in a cellular setting or the modulation of a certain phenotype in an approach that aims toward therapeutic application. Alternatively, cellular testing may aim at the validation of a new epigenetic inhibitor in drug discovery approaches. Cellular and eventually animal models provide powerful tools for these different approaches but certain caveats have to be recognized and taken into account. This involves both the selectivity of the pharmacological tool as well as the specificity and the robustness of the cellular system. In this article, we present an overview of different methods that are used to profile and screen for epigenetic agents and comment on their limitations. We describe not only diverse successful case studies of screening approaches using different assay formats, but also some problematic cases, critically discussing selected applications of these systems.
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Affiliation(s)
- Mirjam Hau
- a University of Freiburg, Institute for Pharmaceutical Sciences , Freiburg , Germany
| | - Fides Zenk
- b Max Planck Institute of Immunobiology and Epigenetics , Freiburg , Germany
| | - A Ganesan
- c School of Pharmacy, University of East Anglia , Norwich NR4 7TJ , United Kingdom.,d Freiburg Institute of Advanced Studies (FRIAS), University of Freiburg , Freiburg , Germany
| | - Nicola Iovino
- b Max Planck Institute of Immunobiology and Epigenetics , Freiburg , Germany
| | - Manfred Jung
- a University of Freiburg, Institute for Pharmaceutical Sciences , Freiburg , Germany.,d Freiburg Institute of Advanced Studies (FRIAS), University of Freiburg , Freiburg , Germany
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