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Nishigaya Y, Takase S, Sumiya T, Sato T, Niwa H, Sato S, Nakata A, Matsuoka S, Maemoto Y, Hashimoto N, Namie R, Honma T, Umehara T, Shirouzu M, Koyama H, Yoshida M, Ito A, Shirai F. Structure-based development of novel substrate-type G9a inhibitors as epigenetic modulators for sickle cell disease treatment. Bioorg Med Chem Lett 2024; 110:129856. [PMID: 38914346 DOI: 10.1016/j.bmcl.2024.129856] [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: 04/24/2024] [Revised: 06/14/2024] [Accepted: 06/19/2024] [Indexed: 06/26/2024]
Abstract
The discovery and development of structurally distinct lysine methyltransferase G9a inhibitors have been the subject of intense research in epigenetics. Structure-based optimization was conducted, starting with the previously reported seed compound 7a and lead to the identification of a highly potent G9a inhibitor, compound 7i (IC50 = 0.024 μM). X-ray crystallography for the ligand-protein interaction and kinetics study, along with surface plasmon resonance (SPR) analysis, revealed that compound 7i interacts with G9a in a unique binding mode. In addition, compound 7i caused attenuation of cellular H3K9me2 levels and induction of γ-globin mRNA expression in HUDEP-2 cells in a dose-dependent manner.
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Affiliation(s)
- Yosuke Nishigaya
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi 329-0114, Japan.
| | - Shohei Takase
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Tatsunobu Sumiya
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Tomohiro Sato
- Drug Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hideaki Niwa
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shin Sato
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Akiko Nakata
- Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Seiji Matsuoka
- Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuki Maemoto
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Noriaki Hashimoto
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Ryosuke Namie
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Teruki Honma
- Drug Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Takashi Umehara
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Mikako Shirouzu
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroo Koyama
- Drug Discovery Chemistry Platform Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Minoru Yoshida
- Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Office of University Professor, the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akihiro Ito
- Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Fumiyuki Shirai
- Drug Discovery Chemistry Platform Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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Yang C, Li B, Feng Z, Li H, Yang H, Yang Z, Liu L, Shi Q, Wang H, Chen ZZ, Huang X, Wang J, Wang Y. Discovery of a Highly Potent Lysine Methyltransferases G9a/NSD2 Dual Inhibitor to Treat Solid Tumors. J Med Chem 2024. [PMID: 39008565 DOI: 10.1021/acs.jmedchem.4c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Both G9a and NSD2 have been recognized as promising therapeutic targets for cancer treatment. However, G9a inhibitors only showed moderate inhibitory activity against solid tumors and NSD2 inhibitors were limited to the treatment of hematological malignancies. Inspired by the advantages of dual-target inhibitors that show great potential in enhancing efficiency, we developed a series of highly potent G9a/NSD2 dual inhibitors to treat solid tumors. The candidate 16 demonstrated much enhanced antiproliferative activity compared to the selective G9a inhibitor 3 and NSD2 inhibitor 15. In addition, it exhibited superior potency in inhibiting colony formation, inducing cell apoptosis, and blocking cancer cell metastasis. Furthermore, it effectively inhibited the catalytic functions of both G9a and NSD2 in cells and exhibited significant antitumor efficacy in the PANC-1 xenograft model with good safety. Therefore, compound 16 as a highly potent G9a/NSD2 dual inhibitor presents an attractive anticancer drug candidate for the treatment of solid tumors.
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Affiliation(s)
- Chunju Yang
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Bang Li
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Zongbo Feng
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Huaxuan Li
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Hong Yang
- Lingang Laboratory, Shanghai 200031, P. R. China
| | - Zhenjiao Yang
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Li Liu
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Qiongyu Shi
- Lingang Laboratory, Shanghai 200031, P. R. China
| | - Hong Wang
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
- State Key Laboratory of Anti-Infective Drug Development, Guangzhou 510006, China
| | - Zhong-Zhu Chen
- College of Pharmacy, National & Local Joint Engineering Research Center of Targeted and Innovative Therapeutics, Chongqing University of Arts and Sciences, Chongqing 402160, China
| | - Xun Huang
- Lingang Laboratory, Shanghai 200031, P. R. China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Junjian Wang
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
- State Key Laboratory of Anti-Infective Drug Development, Guangzhou 510006, China
| | - Yuanxiang Wang
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
- State Key Laboratory of Anti-Infective Drug Development, Guangzhou 510006, China
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3
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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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4
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Odeyemi I, Douglas TA, Igie NF, Hargrove JA, Hamilton G, Bradley BB, Thai C, Le B, Unjia M, Wicherts D, Ferneyhough Z, Pillai A, Koirala S, Hagge LM, Polara H, Trievel RC, Fick RJ, Stelling AL. An optimized purification protocol for enzymatically synthesized S-adenosyl-L-methionine (SAM) for applications in solution state infrared spectroscopic studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 309:123816. [PMID: 38198991 DOI: 10.1016/j.saa.2023.123816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/07/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024]
Abstract
S-adenosyl-L-methionine (SAM) is an abundant biomolecule used by methyltransferases to regulate a wide range of essential cellular processes such as gene expression, cell signaling, protein functions, and metabolism. Despite considerable effort, there remain many specificity challenges associated with designing small molecule inhibitors for methyltransferases, most of which exhibit off-target effects. Interestingly, NMR evidence suggests that SAM undergoes conformeric exchange between several states when free in solution. Infrared spectroscopy can detect different conformers of molecules if present in appreciable populations. When SAM is noncovalently bound within enzyme active sites, the nature and the number of different conformations of the molecule are likely to be altered from when it is free in solution. If there are unique structures or different numbers of conformers between different methyltransferase active sites, solution-state information may provide promising structural leads to increase inhibitor specificity for a particular methyltransferase. Toward this goal, frequencies measured in SAM's infrared spectra must be assigned to the motions of specific atoms via isotope incorporation at discrete positions. The incorporation of isotopes into SAM's structure can be accomplished via an established enzymatic synthesis using isotopically labeled precursors. However, published protocols produced an intense and highly variable IR signal which overlapped with many of the signals from SAM rendering comparison between isotopes challenging. We observed this intense absorption to be from co-purifying salts and the SAM counterion, producing a strong, broad signal at 1100 cm-1. Here, we report a revised SAM purification protocol that mitigates the contaminating salts and present the first IR spectra of isotopically labeled CD3-SAM. These results provide a foundation for isotopic labeling experiments of SAM that will define which atoms participate in individual molecular vibrations, as a means to detect specific molecular conformations.
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Affiliation(s)
- Isaiah Odeyemi
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Teri A Douglas
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Nosakhare F Igie
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - James A Hargrove
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Grace Hamilton
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Brianna B Bradley
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Cathy Thai
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Brendan Le
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Maitri Unjia
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Dylan Wicherts
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Zackery Ferneyhough
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Anjali Pillai
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Shailendra Koirala
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Laurel M Hagge
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Himanshu Polara
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Raymond C Trievel
- University of Michigan, 1150 W. Medical Center Dr., Ann Arbor, 48109, MI, USA
| | - Robert J Fick
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Allison L Stelling
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA.
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5
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Yan J, Li KX, Yu L, Yuan HY, Zhao ZM, Lin J, Wang CS. PRMT1 Integrates Immune Microenvironment and Fatty Acid Metabolism Response in Progression of Hepatocellular Carcinoma. J Hepatocell Carcinoma 2024; 11:15-27. [PMID: 38213310 PMCID: PMC10778267 DOI: 10.2147/jhc.s443130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/20/2023] [Indexed: 01/13/2024] Open
Abstract
Background Protein arginine methyltransferase (PRMT) family members have important roles in cancer processes. However, its functions in the regulation of cancer immunotherapy of hepatocellular carcinoma (HCC) are incompletely understood. This study aimed to investigate the roles of PRMT1 in HCC. Methods Single-cell RNA sequencing (scRNA-seq) and clinicopathological data were obtained and used to explore the diagnostic and prognostic value, cellular functions and roles in immune microenvironment regulation of PRMT1 in HCC. The functions of PRMT1 were explored using Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO), as well as gene set enrichment analysis (GSEA). TIMER and CIBERSORT were used to analyze the relationships between PRMT1 expression and immune cell infiltration. The STRING database was used to construct a protein-protein interaction (PPI) network. Results PRMT1 was aberrantly expressed in HCC, which high expression was associated with tumor progression, worse overall survival (OS) and disease-free survival (DFS) of patients with HCC. PRMT1 was also associated with immune cell infiltration. Moreover, it was specifically expressed in immune cells, including exhausted CD8 T cells, B cells, and mono/macro cells in patients with immunotherapy. The expression of immune checkpoints was significantly increased in the high-PRMT1 expression groups of HCC patients. Regarding biological mechanisms, cell viability, migration and invasion, and the expression of genes related to fatty acid metabolism were suppressed in PRMT1 knockdown HCC cells. Moreover, genes co-expressed with PRMT1 were involved in the fatty acid metabolic process and enriched in fatty and drug-induced liver disease. Conclusion Taken together, these results indicate that PRMT1 might exert its oncogenic effects via immune microenvironment regulation and fatty acid metabolism in HCC. Our finding will provide a foundation for further studies and indicate a potential clinical therapeutic target for liver cancer.
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Affiliation(s)
- Jia Yan
- School of Basic Medicine, Inner Mongolia Medical University, Hohhot, Inner Mongolia, People’s Republic of China
- College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia, People’s Republic of China
- Medical Experimental Center of Basic Medical School, Inner Mongolia Medical University, Hohhot, Inner Mongolia, People’s Republic of China
| | - Ke xin Li
- College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia, People’s Republic of China
| | - Lei Yu
- College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia, People’s Republic of China
| | - Heng ye Yuan
- College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia, People’s Republic of China
| | - Zhi min Zhao
- College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia, People’s Republic of China
| | - Jing Lin
- College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia, People’s Republic of China
- Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, People’s Republic of China
| | - Chang Shan Wang
- College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia, People’s Republic of China
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6
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Wang S, Klein SO, Urban S, Staudt M, Barthes NPF, Willmann D, Bacher J, Sum M, Bauer H, Peng L, Rennar GA, Gratzke C, Schüle KM, Zhang L, Einsle O, Greschik H, MacLeod C, Thomson CG, Jung M, Metzger E, Schüle R. Structure-guided design of a selective inhibitor of the methyltransferase KMT9 with cellular activity. Nat Commun 2024; 15:43. [PMID: 38167811 PMCID: PMC10762027 DOI: 10.1038/s41467-023-44243-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
Inhibition of epigenetic regulators by small molecules is an attractive strategy for cancer treatment. Recently, we characterised the role of lysine methyltransferase 9 (KMT9) in prostate, lung, and colon cancer. Our observation that the enzymatic activity was required for tumour cell proliferation identified KMT9 as a potential therapeutic target. Here, we report the development of a potent and selective KMT9 inhibitor (compound 4, KMI169) with cellular activity through structure-based drug design. KMI169 functions as a bi-substrate inhibitor targeting the SAM and substrate binding pockets of KMT9 and exhibits high potency, selectivity, and cellular target engagement. KMT9 inhibition selectively downregulates target genes involved in cell cycle regulation and impairs proliferation of tumours cells including castration- and enzalutamide-resistant prostate cancer cells. KMI169 represents a valuable tool to probe cellular KMT9 functions and paves the way for the development of clinical candidate inhibitors as therapeutic options to treat malignancies such as therapy-resistant prostate cancer.
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Affiliation(s)
- Sheng Wang
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Sebastian O Klein
- CIBSS Centre of Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Sylvia Urban
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Maximilian Staudt
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Nicolas P F Barthes
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Dominica Willmann
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Johannes Bacher
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Manuela Sum
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Helena Bauer
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Ling Peng
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Georg A Rennar
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Christian Gratzke
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Katrin M Schüle
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Holger Greschik
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Calum MacLeod
- Drug Discovery, Pharmaron UK Ltd, Hoddesdon, United Kingdom
| | | | - Manfred Jung
- CIBSS Centre of Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Deutsches Konsortium für Translationale Krebsforschung, Standort Freiburg, Freiburg, Germany
| | - Eric Metzger
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
- Deutsches Konsortium für Translationale Krebsforschung, Standort Freiburg, Freiburg, Germany.
| | - Roland Schüle
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
- CIBSS Centre of Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
- Deutsches Konsortium für Translationale Krebsforschung, Standort Freiburg, Freiburg, Germany.
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7
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Cao MT, Feng Y, Zheng YG. Protein arginine methyltransferase 6 is a novel substrate of protein arginine methyltransferase 1. World J Biol Chem 2023; 14:84-98. [PMID: 37901302 PMCID: PMC10600687 DOI: 10.4331/wjbc.v14.i5.84] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/08/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Post-translational modifications play key roles in various biological processes. Protein arginine methyltransferases (PRMTs) transfer the methyl group to specific arginine residues. Both PRMT1 and PRMT6 have emerges as crucial factors in the development and progression of multiple cancer types. We posit that PRMT1 and PRMT6 might interplay directly or in-directly in multiple ways accounting for shared disease phenotypes. AIM To investigate the mechanism of the interaction between PRMT1 and PRMT6. METHODS Gel electrophoresis autoradiography was performed to test the methyltranferase activity of PRMTs and characterize the kinetics parameters of PRMTs. Liquid chromatography-tandem mass spectrometryanalysis was performed to detect the PRMT6 methylation sites. RESULTS In this study we investigated the interaction between PRMT1 and PRMT6, and PRMT6 was shown to be a novel substrate of PRMT1. We identified specific arginine residues of PRMT6 that are methylated by PRMT1, with R106 being the major methylation site. Combined biochemical and cellular data showed that PRMT1 downregulates the enzymatic activity of PRMT6 in histone H3 methylation. CONCLUSION PRMT6 is methylated by PRMT1 and R106 is a major methylation site induced by PRMT1. PRMT1 methylation suppresses the activity of PRMT6.
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Affiliation(s)
- Meng-Tong Cao
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, United States
| | - You Feng
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, United States
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, United States
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8
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Velez J, Kaniskan HÜ, Jin J. Recent advances in developing degraders & inhibitors of lysine methyltransferases. Curr Opin Chem Biol 2023; 76:102356. [PMID: 37379717 PMCID: PMC10527319 DOI: 10.1016/j.cbpa.2023.102356] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/29/2023] [Accepted: 06/01/2023] [Indexed: 06/30/2023]
Abstract
Over the last several decades, there has been continued interest in developing novel therapeutic approaches targeting protein lysine methyltransferases (PKMTs). Along with PKMT inhibitors, targeted protein degradation (TPD) has emerged as a promising strategy to attenuate aberrant PKMT activity. Particularly, proteolysis targeting chimeras (PROTACs) effectively eliminate PKMTs of interest, suppressing all enzymatic and non-enzymatic functions. PROTACs and other TPD approaches add new depth to PKMT research and novel therapeutics discovery. This review focuses on recent advances in PKMT degrader and inhibitor development over the last several years.
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Affiliation(s)
- Julia Velez
- 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, NY 10029, United States
| | - H Ümit Kaniskan
- 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, NY 10029, United States.
| | - 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, NY 10029, United States.
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9
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Zheng J, Li B, Wu Y, Wu X, Wang Y. Targeting Arginine Methyltransferase PRMT5 for Cancer Therapy: Updated Progress and Novel Strategies. J Med Chem 2023. [PMID: 37366223 DOI: 10.1021/acs.jmedchem.3c00250] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
As a predominant type II protein arginine methyltransferase, PRMT5 plays critical roles in various normal cellular processes by catalyzing the mono- and symmetrical dimethylation of a wide range of histone and nonhistone substrates. Clinical studies have revealed that high expression of PRMT5 is observed in different solid tumors and hematological malignancies and is closely associated with cancer initiation and progression. Accordingly, PRMT5 is becoming a promising anticancer target and has received great attention in both the pharmaceutical industry and the academic community. In this Perspective, we comprehensively summarize recent advances in the development of first-generation PRMT5 enzymatic inhibitors and highlight novel strategies targeting PRMT5 in the past 5 years. We also discuss the challenges and opportunities of PRMT5 inhibition, with the aim of shedding light on future PRMT5 drug discovery.
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Affiliation(s)
- Jiahong Zheng
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Bang Li
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yingqi Wu
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Xiaoshuang Wu
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yuanxiang Wang
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
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10
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Feng Z, Yang C, Zhang Y, Li H, Fang W, Wang J, Nie Y, Wang CY, Liu Z, Jiang Z, Wang J, Wang Y. Structure-Based Design and Characterization of the Highly Potent and Selective Covalent Inhibitors Targeting the Lysine Methyltransferases G9a/GLP. J Med Chem 2023. [PMID: 37268593 DOI: 10.1021/acs.jmedchem.3c00411] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protein lysine methyltransferases G9a and GLP, which catalyze mono- and di-methylation of histone H3K9 and nonhistone proteins, play important roles in diverse cellular processes. Overexpression or dysregulation of G9a and GLP has been identified in various types of cancer. Here, we report the discovery of a highly potent and selective covalent inhibitor 27 of G9a/GLP via the structure-based drug design approach following structure-activity relationship exploration and cellular potency optimization. Mass spectrometry assays and washout experiments confirmed its covalent inhibition mechanism. Compound 27 displayed improved potency in inhibiting the proliferation and colony formation of PANC-1 and MDA-MB-231 cell lines and exhibited enhanced potency in reducing the levels of H3K9me2 in cells compared to noncovalent inhibitor 26. In vivo, 27 showed significant antitumor efficacy in the PANC-1 xenograft model with good safety. These results clearly indicate that 27 is a highly potent and selective covalent inhibitor of G9a/GLP.
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Affiliation(s)
- Zongbo Feng
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
- School of Pharmacy, Guilin Medical University, Zhiyuan Road, Lingui District, Guilin 541199, China
| | - Chunju Yang
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yi Zhang
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Huaxuan Li
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
- School of Medicine and Pharmacy, Institute of Evolution & Marine Biodiversity, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Wei Fang
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Junhua Wang
- The Department of Biliary-Pancreatic Surgery, The First People's Hospital of Foshan, Foshan 528000, China
| | - Yichu Nie
- Clinical Research Institute, The First People's Hospital of Foshan, Foshan 528000, China
| | - Chang-Yun Wang
- School of Medicine and Pharmacy, Institute of Evolution & Marine Biodiversity, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Zhiqing Liu
- School of Medicine and Pharmacy, Institute of Evolution & Marine Biodiversity, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Zhimin Jiang
- School of Pharmacy, Guilin Medical University, Zhiyuan Road, Lingui District, Guilin 541199, China
| | - Junjian Wang
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yuanxiang Wang
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
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11
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Nishigaya Y, Takase S, Sumiya T, Kikuzato K, Sato T, Niwa H, Sato S, Nakata A, Sonoda T, Hashimoto N, Namie R, Honma T, Umehara T, Shirouzu M, Koyama H, Yoshida M, Ito A, Shirai F. Discovery of Novel Substrate-Competitive Lysine Methyltransferase G9a Inhibitors as Anticancer Agents. J Med Chem 2023; 66:4059-4085. [PMID: 36882960 DOI: 10.1021/acs.jmedchem.2c02059] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Identification of structurally novel inhibitors of lysine methyltransferase G9a has been a subject of intense research in cancer epigenetics. Starting with the high-throughput screening (HTS) hit rac-10a obtained from the chemical library of the University of Tokyo Drug Discovery Initiative, the structure-activity relationship of the unique substrate-competitive inhibitors was established with the help of X-ray crystallography and fragment molecular orbital (FMO) calculations for the ligand-protein interaction. Further optimization of the in vitro characteristics and drug metabolism and pharmacokinetics (DMPK) properties led to the identification of 26j (RK-701), which is a structurally distinct potent inhibitor of G9a/GLP (IC50 = 27/53 nM). Compound 26j exhibited remarkable selectivity against other related methyltransferases, dose-dependent attenuation of cellular H3K9me2 levels, and tumor growth inhibition in MOLT-4 cells in vitro. Moreover, compound 26j showed inhibition of tumor initiation and growth in a carcinogen-induced hepatocellular carcinoma (HCC) in vivo mouse model without overt acute toxicity.
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Affiliation(s)
- Yosuke Nishigaya
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Shohei Takase
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Tatsunobu Sumiya
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | | | | | | | | | | | | | - Noriaki Hashimoto
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Ryosuke Namie
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | | | | | | | | | - Minoru Yoshida
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akihiro Ito
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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12
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Bioactive Compounds as Inhibitors of Inflammation, Oxidative Stress and Metabolic Dysfunctions via Regulation of Cellular Redox Balance and Histone Acetylation State. Foods 2023; 12:foods12050925. [PMID: 36900446 PMCID: PMC10000917 DOI: 10.3390/foods12050925] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
Bioactive compounds (BCs) are known to exhibit antioxidant, anti-inflammatory, and anti-cancer properties by regulating the cellular redox balance and histone acetylation state. BCs can control chronic oxidative states caused by dietary stress, i.e., alcohol, high-fat, or high-glycemic diet, and adjust the redox balance to recover physiological conditions. Unique functions of BCs to scavenge reactive oxygen species (ROS) can resolve the redox imbalance due to the excessive generation of ROS. The ability of BCs to regulate the histone acetylation state contributes to the activation of transcription factors involved in immunity and metabolism against dietary stress. The protective properties of BCs are mainly ascribed to the roles of sirtuin 1 (SIRT1) and nuclear factor erythroid 2-related factor 2 (NRF2). As a histone deacetylase (HDAC), SIRT1 modulates the cellular redox balance and histone acetylation state by mediating ROS generation, regulating nicotinamide adenine dinucleotide (NAD+)/NADH ratio, and activating NRF2 in metabolic progression. In this study, the unique functions of BCs against diet-induced inflammation, oxidative stress, and metabolic dysfunction have been considered by focusing on the cellular redox balance and histone acetylation state. This work may provide evidence for the development of effective therapeutic agents from BCs.
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13
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Park KS, Xiong Y, Yim H, Velez J, Babault N, Kumar P, Liu J, Jin J. Discovery of the First-in-Class G9a/GLP Covalent Inhibitors. J Med Chem 2022; 65:10506-10522. [PMID: 35763668 DOI: 10.1021/acs.jmedchem.2c00652] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The highly homologous protein lysine methyltransferases G9a and GLP, which catalyze mono- and dimethylation of histone H3 lysine 9 (H3K9), have been implicated in various human diseases. To investigate functions of G9a and GLP in human diseases, we and others reported several noncovalent reversible small-molecule inhibitors of G9a and GLP. Here, we report the discovery of the first-in-class G9a/GLP covalent irreversible inhibitors, 1 and 8 (MS8511), by targeting a cysteine residue at the substrate binding site. We characterized these covalent inhibitors in enzymatic, mass spectrometry based and cellular assays and using X-ray crystallography. Compared to the noncovalent G9a/GLP inhibitor UNC0642, covalent inhibitor 8 displayed improved potency in enzymatic and cellular assays. Interestingly, compound 8 also displayed potential kinetic preference for covalently modifying G9a over GLP. Collectively, compound 8 could be a useful chemical tool for studying the functional roles of G9a and GLP by covalently modifying and inhibiting these methyltransferases.
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Affiliation(s)
- 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
| | - 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
| | - Hyerin Yim
- 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
| | - Julia Velez
- 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
| | - Nicolas Babault
- 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
| | - Prashasti Kumar
- 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
| | - 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
| | - 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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14
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Randazzo P, Sinisi R, Gornati D, Bertuolo S, Bencheva L, De Matteo M, Nibbio M, Monteagudo E, Turcano L, Bianconi V, Peruzzi G, Summa V, Bresciani A, Mozzetta C, Di Fabio R. Identification and in vitro characterization of a new series of potent and highly selective G9a inhibitors as novel anti-fibroadipogenic agents. Bioorg Med Chem Lett 2022; 72:128858. [PMID: 35718104 DOI: 10.1016/j.bmcl.2022.128858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 11/20/2022]
Abstract
A new series of in vitro potent and highly selective histone methyl transferase enzyme G9a inhibitors was obtained. In particular, compound 2a, one the most potent G9a inhibitor identified, was endowed with >130-fold selectivity over GLP and excellent ligand efficiency. Therefore, it may represent a valuable tool compound to validate the role of highly selective G9a inhibitors in different pathological conditions. When 2a was characterized in vitro in cellular models of skeletal muscle differentiation, a relevant increase of myofibers' size and reduction of the fibroadipogenic infiltration were observed, further confirming the therapeutic potential of selective G9a inhibitors for the treatment of Duchenne muscle dystrophy.
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Affiliation(s)
| | | | | | | | | | | | - Martina Nibbio
- IRBM Science Park, Via Pontina Km 30.600, 00070 Pomezia, Italy
| | - Edith Monteagudo
- CHDI Foundation, 6080 Center Drive, Suite 700, CA 90045, Los Angeles
| | - Lorenzo Turcano
- IRBM Science Park, Via Pontina Km 30.600, 00070 Pomezia, Italy
| | - Valeria Bianconi
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy c/o, Department of Biology and Biotechnology "C. Darwin", Sapienza University, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Giovanna Peruzzi
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), V.le Regina, Elena 291, 00161 Rome, Italy
| | - Vincenzo Summa
- University of Naples Federico II, Vial Domenico Montesano 49, 80131, Naples, Italy
| | - Alberto Bresciani
- Exscientia LTD, The Schrödinger Building Oxford Science Park, Oxford OX4 4GE, UK
| | - Chiara Mozzetta
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy c/o, Department of Biology and Biotechnology "C. Darwin", Sapienza University, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Romano Di Fabio
- Promidis, Via Olgettina 60, 20132 Milano, Italy; IRBM Science Park, Via Pontina Km 30.600, 00070 Pomezia, Italy.
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15
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Brown T, Cao M, Zheng YG. Synthesis and Activity of Triazole-Adenosine Analogs as Protein Arginine Methyltransferase 5 Inhibitors. Molecules 2022; 27:3779. [PMID: 35744905 PMCID: PMC9228412 DOI: 10.3390/molecules27123779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 11/17/2022] Open
Abstract
Protein arginine methyltransferase 5 (PRMT5) is an attractive molecular target in anticancer drug discovery due to its extensive involvement in transcriptional control, RNA processing, and other cellular pathways that are causally related to tumor initiation and progression. In recent years, various compounds have been screened or designed to target either the substrate- or cofactor-binding site of PRMT5. To expand the diversity of chemotypes for inhibitory binding to PRMT5 and other AdoMet-dependent methyltransferases, in this work, we designed a series of triazole-containing adenosine analogs aimed at targeting the cofactor-binding site of PRMT5. Triazole rings have commonly been utilized in drug discovery due to their ease of synthesis and functionalization as bioisosteres of amide bonds. Herein, we utilized the electronic properties of the triazole ring as a novel way to specifically target the cofactor-binding site of PRMT5. A total of about 30 compounds were synthesized using the modular alkyne-azide cycloaddition reaction. Biochemical tests showed that these compounds exhibited inhibitory activity of PRMT5 at varying degrees and several showed single micromolar potency, with clear selectivity for PRMT5 over PRMT1. Docking-based structural analysis showed that the triazole ring plays a key role in binding to the characteristic residue Phe327 in the active pocket of PRMT5, explaining the compounds' selectivity for this type-II enzyme. Overall, this work provides new structure-activity relationship information on the design of AdoMet analogs for selective inhibition of PRMT5. Further structural optimization work will further improve the potency of the top leads.
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Affiliation(s)
| | | | - Y. George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA; (T.B.); (M.C.)
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16
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Rong D, Zhou K, Fang W, Yang H, Zhang Y, Shi Q, Huang Y, Li J, Dong H, Li L, Ding J, Huang X, Wang Y. Structure-Aided Design, Synthesis, and Biological Evaluation of Potent and Selective Non-Nucleoside Inhibitors Targeting Protein Arginine Methyltransferase 5. J Med Chem 2022; 65:7854-7875. [PMID: 35612488 DOI: 10.1021/acs.jmedchem.2c00398] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
PRMT5 is a major type II protein arginine methyltransferase and plays important roles in diverse cellular processes. Overexpression of PRMT5 is implicated in various types of cancer. Many efforts have been made to develop potent and selective PRMT5 inhibitors, the most potent of which is usually derived from nucleoside structures. Here, we designed a novel series of non-nucleoside PRMT5 inhibitors through the structure-aided drug design approach. SAR exploration and metabolic stability optimization led to the discovery of compound 41 as a potent PRMT5 inhibitor with good selectivity. Additionally, compound 41 exerted antiproliferative effects against A375 cells by inducing apoptosis and potently inhibited the methyltransferase activity of PRMT5 in cells. Moreover, it showed attractive pharmacokinetic properties and markedly suppressed the tumor growth in an A375 tumor xenograft model. These results clearly indicate that 41 is a highly potent and selective non-nucleoside PRMT5 inhibitor.
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Affiliation(s)
- Deqin Rong
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Kaixin Zhou
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.,Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China.,University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing 100049, P. R. China
| | - Wei Fang
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Hong Yang
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Yi Zhang
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Qiongyu Shi
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Yuting Huang
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China.,University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing 100049, P. R. China
| | - Jiayi Li
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China.,University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing 100049, P. R. China.,Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, P. R. China
| | - Hui Dong
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Lanlan Li
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Jian Ding
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.,Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China.,University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing 100049, P. R. China.,Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, P. R. China
| | - Xun Huang
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China.,University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing 100049, P. R. China.,Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, P. R. China.,Lingang Laboratory, Shanghai 200031, China
| | - Yuanxiang Wang
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
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17
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Iannelli G, Milite C, Marechal N, Cura V, Bonnefond L, Troffer-Charlier N, Feoli A, Rescigno D, Wang Y, Cipriano A, Viviano M, Bedford MT, Cavarelli J, Castellano S, Sbardella G. Turning Nonselective Inhibitors of Type I Protein Arginine Methyltransferases into Potent and Selective Inhibitors of Protein Arginine Methyltransferase 4 through a Deconstruction-Reconstruction and Fragment-Growing Approach. J Med Chem 2022; 65:11574-11606. [PMID: 35482954 PMCID: PMC9469100 DOI: 10.1021/acs.jmedchem.2c00252] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Protein arginine
methyltransferases (PRMTs) are important therapeutic
targets, playing a crucial role in the regulation of many cellular
processes and being linked to many diseases. Yet, there is still much
to be understood regarding their functions and the biological pathways
in which they are involved, as well as on the structural requirements
that could drive the development of selective modulators of PRMT activity.
Here we report a deconstruction–reconstruction approach that,
starting from a series of type I PRMT inhibitors previously identified
by us, allowed for the identification of potent and selective inhibitors
of PRMT4, which regardless of the low cell permeability show an evident
reduction of arginine methylation levels in MCF7 cells and a marked
reduction of proliferation. We also report crystal structures with
various PRMTs supporting the observed specificity and selectivity.
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Affiliation(s)
| | | | - Nils Marechal
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France
| | - Vincent Cura
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France
| | - Luc Bonnefond
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France
| | - Nathalie Troffer-Charlier
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France
| | | | | | - Yalong Wang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | | | | | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Jean Cavarelli
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France
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18
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Pei H, Guo W, Peng Y, Xiong H, Chen Y. Targeting key proteins involved in transcriptional regulation for cancer therapy: Current strategies and future prospective. Med Res Rev 2022; 42:1607-1660. [PMID: 35312190 DOI: 10.1002/med.21886] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/10/2022] [Accepted: 02/22/2022] [Indexed: 12/14/2022]
Abstract
The key proteins involved in transcriptional regulation play convergent roles in cellular homeostasis, and their dysfunction mediates aberrant gene expressions that underline the hallmarks of tumorigenesis. As tumor progression is dependent on such abnormal regulation of transcription, it is important to discover novel chemical entities as antitumor drugs that target key tumor-associated proteins involved in transcriptional regulation. Despite most key proteins (especially transcription factors) involved in transcriptional regulation are historically recognized as undruggable targets, multiple targeting approaches at diverse levels of transcriptional regulation, such as epigenetic intervention, inhibition of DNA-binding of transcriptional factors, and inhibition of the protein-protein interactions (PPIs), have been established in preclinically or clinically studies. In addition, several new approaches have recently been described, such as targeting proteasomal degradation and eliciting synthetic lethality. This review will emphasize on accentuating these developing therapeutic approaches and provide a thorough conspectus of the drug development to target key proteins involved in transcriptional regulation and their impact on future oncotherapy.
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Affiliation(s)
- Haixiang Pei
- Institute for Advanced Study, Shenzhen University and Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, China.,Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Weikai Guo
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China.,Joint National Laboratory for Antibody Drug Engineering, School of Basic Medical Science, Henan University, Kaifeng, China
| | - Yangrui Peng
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Hai Xiong
- Institute for Advanced Study, Shenzhen University and Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, China
| | - Yihua Chen
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
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19
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Sui J, Qiao W, Xiang X, Luo Y. Epigenetic Changes in Mycobacterium tuberculosis and its Host Provide Potential Targets or Biomarkers for Drug Discovery and Clinical Diagnosis. Pharmacol Res 2022; 179:106195. [DOI: 10.1016/j.phrs.2022.106195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/14/2022] [Accepted: 03/25/2022] [Indexed: 11/26/2022]
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20
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Nickoloff JA, Sharma N, Taylor L, Allen SJ, Lee SH, Hromas R. Metnase and EEPD1: DNA Repair Functions and Potential Targets in Cancer Therapy. Front Oncol 2022; 12:808757. [PMID: 35155245 PMCID: PMC8831698 DOI: 10.3389/fonc.2022.808757] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/12/2022] [Indexed: 12/30/2022] Open
Abstract
Cells respond to DNA damage by activating signaling and DNA repair systems, described as the DNA damage response (DDR). Clarifying DDR pathways and their dysregulation in cancer are important for understanding cancer etiology, how cancer cells exploit the DDR to survive endogenous and treatment-related stress, and to identify DDR targets as therapeutic targets. Cancer is often treated with genotoxic chemicals and/or ionizing radiation. These agents are cytotoxic because they induce DNA double-strand breaks (DSBs) directly, or indirectly by inducing replication stress which causes replication fork collapse to DSBs. EEPD1 and Metnase are structure-specific nucleases, and Metnase is also a protein methyl transferase that methylates histone H3 and itself. EEPD1 and Metnase promote repair of frank, two-ended DSBs, and both promote the timely and accurate restart of replication forks that have collapsed to single-ended DSBs. In addition to its roles in HR, Metnase also promotes DSB repair by classical non-homologous recombination, and chromosome decatenation mediated by TopoIIα. Although mutations in Metnase and EEPD1 are not common in cancer, both proteins are frequently overexpressed, which may help tumor cells manage oncogenic stress or confer resistance to therapeutics. Here we focus on Metnase and EEPD1 DNA repair pathways, and discuss opportunities for targeting these pathways to enhance cancer therapy.
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Affiliation(s)
- Jac A Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | - Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | - Lynn Taylor
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | - Sage J Allen
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | - Suk-Hee Lee
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Robert Hromas
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, United States
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21
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Talukdar A, Mukherjee A, Bhattacharya D. Fascinating Transformation of SAM-Competitive Protein Methyltransferase Inhibitors from Nucleoside Analogues to Non-Nucleoside Analogues. J Med Chem 2022; 65:1662-1684. [PMID: 35014841 DOI: 10.1021/acs.jmedchem.1c01208] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The abnormal expression of protein methyltransferase (PMT) has been linked with many diseases such as diabetes, neurological disorders, and cancer. S-Adenyl-l-methionine (SAM) is a universal methyl donor and gets converted to S-adenyl-l-homocysteine (SAH), an endogenous competitive inhibitor of SAM. Initially developed SAM/SAH mimetic nucleoside analogues were pan methyltransferase inhibitors. The gradual understanding achieved through ligand-receptor interaction paved the way for various rational approaches of drug design leading to potent and selective nucleoside inhibitors. The present perspective is based on the systematic evolution of selective SAM-competitive heterocyclic non-nucleoside inhibitors from nucleoside inhibitors. This fascinating transition has resolved several issues inherent to nucleoside analogues such as poor pharmacokinetics leading to poor in vivo efficacy. The perspective has brought together various concepts and strategies of drug design that contributed to this rational transition. We firmly believe that the strategies described herein will serve as a template for the future development of drugs in general.
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Affiliation(s)
- Arindam Talukdar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, WB, India.,Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Ayan Mukherjee
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, WB, India.,Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Debomita Bhattacharya
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, WB, India
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22
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Dhorma LP, Teli MK, Nangunuri BG, Venkanna A, Ragam R, Maturi A, Mirzaei A, Vo DK, Maeng HJ, Kim MH. Positioning of an unprecedented 1,5-oxaza spiroquinone scaffold into SMYD2 inhibitors in epigenetic space. Eur J Med Chem 2022; 227:113880. [PMID: 34656041 DOI: 10.1016/j.ejmech.2021.113880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 09/04/2021] [Accepted: 09/28/2021] [Indexed: 11/26/2022]
Abstract
Lysine methyltransferases are important regulators of epigenetic signaling and are emerging as a novel drug target for drug discovery. This work demonstrates the positioning of novel 1,5-oxaza spiroquinone scaffold into selective SET and MYND domain-containing proteins 2 methyltransferases inhibitors. Selectivity of the scaffold was identified by epigenetic target screening followed by SAR study for the scaffold. The optimization was performed iteratively by two-step optimization consisting of iterative synthesis and computational studies (docking, metadynamics simulations). Computational binding studies guided the important interactions of the spiro[5.5]undeca scaffold in pocket 1 and Lysine channel and suggested extension of tail length for the improvement of potency (IC50: up to 399 nM). The effective performance of cell proliferation assay for chosen compounds (IC50: up to 11.9 nM) led to further evaluation in xenograft assay. The potent compound 24 demonstrated desirable in vivo efficacy with growth inhibition rate of 77.7% (4 fold decrease of tumor weight and 3 fold decrease of tumor volume). Moreover, mirosomal assay and pharmacokinetic profile suggested further developability of this scaffold through the identification of major metabolites (dealkylation at silyl group, reversible hydration product, the absence of toxic quinone fragments) and enough exposure of the testing compound 24 in plasma. Such spiro[5.5]undeca framework or ring system was neither been reported nor suggested as a modulator of methyltransferases. The chemo-centric target positioning and structural novelty can lead to potential pharmacological benefit.
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Affiliation(s)
- Lama Prema Dhorma
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, South Korea
| | - Mahesh K Teli
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, South Korea
| | - Bhargav Gupta Nangunuri
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, South Korea
| | - Arramshetti Venkanna
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, South Korea
| | - Rao Ragam
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, South Korea
| | - Arunkranthi Maturi
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, South Korea
| | - Anvar Mirzaei
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, South Korea
| | - Dang-Khoa Vo
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, South Korea
| | - Han-Joo Maeng
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, South Korea
| | - Mi-Hyun Kim
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, South Korea.
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23
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Guillade L, Mora P, Villar P, Alvarez R, R de Lera A. Total synthesis of nahuoic acid A via a putative biogenetic intramolecular Diels-Alder (IMDA) reaction. Chem Sci 2021; 12:15157-15169. [PMID: 34909158 PMCID: PMC8612404 DOI: 10.1039/d1sc04524e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/26/2021] [Indexed: 11/21/2022] Open
Abstract
Inspired by the biogenetic proposal of an intramolecular Diels–Alder (IMDA) cycloaddition, the total synthesis of natural product nahuoic acid A, a cofactor-competitive inhibitor of the epigenetic enzyme lysine methyl transferase SETD8, has been carried out. A non-conjugated pentaenal precursor was synthesized with high levels of stereoselectivity at seven stereogenic centers and with the appropriate control of double bond geometries. Although the IMDA reaction of the non-conjugated pentaenal using Me2AlCl for catalysis at −40 °C selectively afforded the trans-fused diastereomer corresponding to the Re-endo mode of cycloaddition, under thermal reaction conditions it gave rise to a mixture of diastereomers, that preferentially formed through the exo mode, including the cis-fused angularly-methylated octahydronaphthalene diastereomer precursor of nahuoic acid A. The natural product could be obtained upon oxidation and overall deprotection of the hydroxyl groups present in the Si-exo IMDA diastereomer. The total synthesis of natural product nahuoic acid A, a cofactor-competitive inhibitor of the epigenetic enzyme lysine methyl transferase SETD8, has been carried out based on the biogenetic proposal of an intramolecular Diels–Alder (IMDA) cycloaddition.![]()
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Affiliation(s)
- Lucía Guillade
- Departamento de Química Orgánica, Facultade de Química, CINBIO, IIS Galicia Sur, Universidade de Vigo 36310 Vigo Spain
| | - Paula Mora
- Departamento de Química Orgánica, Facultade de Química, CINBIO, IIS Galicia Sur, Universidade de Vigo 36310 Vigo Spain
| | - Pedro Villar
- Departamento de Química Orgánica, Facultade de Química, CINBIO, IIS Galicia Sur, Universidade de Vigo 36310 Vigo Spain
| | - Rosana Alvarez
- Departamento de Química Orgánica, Facultade de Química, CINBIO, IIS Galicia Sur, Universidade de Vigo 36310 Vigo Spain
| | - Angel R de Lera
- Departamento de Química Orgánica, Facultade de Química, CINBIO, IIS Galicia Sur, Universidade de Vigo 36310 Vigo Spain
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24
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Trager MH, Sah B, Chen Z, Liu L. Control of Breast Cancer Pathogenesis by Histone Methylation and the Hairless Histone Demethylase. Endocrinology 2021; 162:6259332. [PMID: 33928351 PMCID: PMC8237996 DOI: 10.1210/endocr/bqab088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Indexed: 12/19/2022]
Abstract
Breast cancer is a highly heterogeneous disease, encompassing many subtypes that have distinct origins, behaviors, and prognoses. Although traditionally seen as a genetic disease, breast cancer is now also known to involve epigenetic abnormalities. Epigenetic regulators, such as DNA methyltransferases and histone-modifying enzymes, play essential roles in gene regulation and cancer development. Dysregulation of epigenetic regulator activity has been causally linked with breast cancer pathogenesis. Hairless (HR) encodes a 130-kDa transcription factor that is essential for development and tissue homeostasis. Its role in transcription regulation is partly mediated by its interaction with multiple nuclear receptors, including thyroid hormone receptor, retinoic acid receptor-related orphan receptors, and vitamin D receptor. HR has been studied primarily in epidermal development and homeostasis. Hr-mutant mice are highly susceptible to ultraviolet- or carcinogen-induced skin tumors. Besides its putative tumor suppressor function in skin, loss of HR function has also been implicated in increased leukemia susceptibility and promotes the growth of melanoma and brain cancer cells. HR has also been demonstrated to function as a histone H3 lysine 9 demethylase. Recent genomics studies have identified HR mutations in a variety of human cancers, including breast cancer. The anticancer function and mechanism of action by HR in mammary tissue remains to be investigated. Here, we review the emerging role of HR, its histone demethylase activity and histone methylation in breast cancer development, and potential for epigenetic therapy.
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Affiliation(s)
- Megan H Trager
- Columbia University Vagelos College of Physicians and Surgeons, New York, New York 10032, USA
| | - Bindeshwar Sah
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, USA
| | - Zhongming Chen
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55912, USA
| | - Liang Liu
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55912, USA
- Correspondence: Liang Liu, PhD, The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA.
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25
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Berdasco M, Esteller M. Towards a druggable epitranscriptome: Compounds that target RNA modifications in cancer. Br J Pharmacol 2021; 179:2868-2889. [PMID: 34185879 DOI: 10.1111/bph.15604] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 05/27/2021] [Accepted: 06/10/2021] [Indexed: 10/21/2022] Open
Abstract
Epitranscriptomics is an exciting emerging area that studies biochemical modifications of RNA. The field has been opened up by the technical efforts of the last decade to characterize and quantify RNA modifications, and this has led to a map of post-transcriptional RNA marks in normal cell fate and development. However, the scientific interest has been fuelled by the discovery of aberrant epitranscriptomes associated with human diseases, mainly cancer. The challenge is now to see whether epitrancriptomics offers mechanisms that can be effectively targeted by low MW compounds and are thus druggable. In this review, we will describe the principal RNA modifications (with a focus on mRNA), summarize the latest scientific evidence of their dysregulation in cancer and provide an overview of the state-of-the-art drug discovery to target the epitranscriptome. Finally, we will discuss the principal challenges in the field of chemical biology and drug development to increase the potential of targeted-RNA for clinical benefit.
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Affiliation(s)
- María Berdasco
- Epigenetic Therapies Group, Experimental and Clinical Hematology Program (PHEC), Josep Carreras Leukaemia Research Institute, Barcelona, Spain.,Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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26
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Zhang Y, Rong D, Li B, Wang Y. Targeting Epigenetic Regulators with Covalent Small-Molecule Inhibitors. J Med Chem 2021; 64:7900-7925. [PMID: 33599482 DOI: 10.1021/acs.jmedchem.0c02055] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epigenetic regulation of gene expression plays a critical role in various physiological processes, and epigenetic dysregulation is implicated in a number of diseases, prominently including cancer. Epigenetic regulators have been validated as potential therapeutic targets, and significant progress has been made in the discovery and development of epigenetic-based inhibitors. However, successful epigenetic drug discovery is still facing challenges, including moderate selectivity, limited efficacy, and acquired drug resistance. Inspired by the advantages of covalent small-molecule inhibitors, targeted covalent inhibition has attracted increasing interest in epigenetic drug discovery. In this review, we comprehensively summarize the structure-based design and characterization of covalent inhibitors targeting epigenetic writers, readers, and erasers and highlight their potential benefits in enhancing selectivity across the enzyme family and improving in vivo efficacy. We also discuss the challenges and opportunities of covalent small-molecule inhibitors and hope to shed light on future epigenetic drug discovery.
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Affiliation(s)
- Yi Zhang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Deqin Rong
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Bingbing Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yuanxiang Wang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
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27
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Strepkos D, Markouli M, Klonou A, Papavassiliou AG, Piperi C. Histone Methyltransferase SETDB1: A Common Denominator of Tumorigenesis with Therapeutic Potential. Cancer Res 2021; 81:525-534. [PMID: 33115801 DOI: 10.1158/0008-5472.can-20-2906] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/06/2020] [Accepted: 10/23/2020] [Indexed: 11/16/2022]
Abstract
Epigenetic regulation of gene expression has been ultimately linked to cancer development, with posttranslational histone modifications representing attractive targets for disease monitoring and therapy. Emerging data have demonstrated histone lysine (K) methylation by methyltransferase SETDB1 as a common denominator of gene regulation in several cancer types. SETDB1 reversibly catalyzes the di- and trimethylation of histone 3 (H3) K9 in euchromatic regions of chromosomes, inhibiting gene transcription within these regions and promoting a switch from euchromatic to heterochromatic states. Recent studies have implicated aberrant SETDB1 activity in the development of various types of cancers, including brain, head and neck, lung, breast, gastrointestinal, ovarian, endometrial and prostate cancer, mesothelioma, melanoma, leukemias, and osteosarcoma. Although its role has not been fully elucidated in every case, most data point toward a pro-oncogenic potential of SETDB1 via the downregulation of critical tumor-suppressive genes. Less commonly, however, SETDB1 can also acquire a tumor-suppressive role, depending on cancer type and stage. Here we provide an updated overview of the cellular and molecular effects underlying SETDB1 activity in cancer development and progression along with current targeting strategies in different cancer types, with promising effects either as a standalone therapy or in conjunction with other therapeutic agents.
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Affiliation(s)
- Dimitrios Strepkos
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Mariam Markouli
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Alexia Klonou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
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28
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Bhat KP, Ümit Kaniskan H, Jin J, Gozani O. Epigenetics and beyond: targeting writers of protein lysine methylation to treat disease. Nat Rev Drug Discov 2021; 20:265-286. [PMID: 33469207 DOI: 10.1038/s41573-020-00108-x] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2020] [Indexed: 02/07/2023]
Abstract
Protein lysine methylation is a crucial post-translational modification that regulates the functions of both histone and non-histone proteins. Deregulation of the enzymes or 'writers' of protein lysine methylation, lysine methyltransferases (KMTs), is implicated in the cause of many diseases, including cancer, mental health disorders and developmental disorders. Over the past decade, significant advances have been made in developing drugs to target KMTs that are involved in histone methylation and epigenetic regulation. The first of these inhibitors, tazemetostat, was recently approved for the treatment of epithelioid sarcoma and follicular lymphoma, and several more are in clinical and preclinical evaluation. Beyond chromatin, the many KMTs that regulate protein synthesis and other fundamental biological processes are emerging as promising new targets for drug development to treat diverse diseases.
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Affiliation(s)
- Kamakoti P Bhat
- Department of Biology, Stanford University, Stanford, CA, USA
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA, USA.
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29
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Noberini R, Robusti G, Bonaldi T. Mass spectrometry-based characterization of histones in clinical samples: applications, progresses, and challenges. FEBS J 2021; 289:1191-1213. [PMID: 33415821 PMCID: PMC9291046 DOI: 10.1111/febs.15707] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/24/2020] [Accepted: 01/06/2021] [Indexed: 12/12/2022]
Abstract
In the last 15 years, increasing evidence linking epigenetics to various aspects of cancer biology has prompted the investigation of histone post-translational modifications (PTMs) and histone variants in the context of clinical samples. The studies performed so far demonstrated the potential of this type of investigations for the discovery of both potential epigenetic biomarkers for patient stratification and novel epigenetic mechanisms potentially targetable for cancer therapy. Although traditionally the analysis of histones in clinical samples was performed through antibody-based methods, mass spectrometry (MS) has emerged as a more powerful tool for the unbiased, comprehensive, and quantitative investigation of histone PTMs and variants. MS has been extensively used for the analysis of epigenetic marks in cell lines and animal tissue and, thanks to recent technological advances, is now ready to be applied also to clinical samples. In this review, we will provide an overview on the quantitative MS-based analysis of histones, their PTMs and their variants in cancer clinical samples, highlighting current achievements and future perspectives for this novel field of research. Among the different MS-based approaches currently available for histone PTM profiling, we will focus on the 'bottom-up' strategy, namely the analysis of short proteolytic peptides, as it has been already successfully employed for the analysis of clinical samples.
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Affiliation(s)
- Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Giulia Robusti
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
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Qian K, Yan C, Su H, Dang T, Zhou B, Wang Z, Zhao X, Ivanov I, Ho MC, Zheng YG. Pharmacophore-based screening of diamidine small molecule inhibitors for protein arginine methyltransferases. RSC Med Chem 2021; 12:95-102. [PMID: 34046601 PMCID: PMC8130551 DOI: 10.1039/d0md00259c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/13/2020] [Indexed: 11/21/2022] Open
Abstract
Protein arginine methyltransferases (PRMTs) are essential epigenetic and post-translational regulators in eukaryotic organisms. Dysregulation of PRMTs is intimately related to multiple types of human diseases, particularly cancer. Based on the previously reported PRMT1 inhibitors bearing the diamidine pharmacophore, we performed virtual screening to identify additional amidine-associated structural analogs. Subsequent enzymatic tests and characterization led to the discovery of a top lead K313 (2-(4-((4-carbamimidoylphenyl)amino)phenyl)-1H-indole-6-carboximidamide), which possessed low-micromolar potency with biochemical IC50 of 2.6 μM for human PRMT1. Limited selectivity was observed over some other PRMT isoforms such as CARM1 and PRMT7. Molecular modeling and inhibition pattern studies suggest that K313 is a nonclassic noncompetitive inhibitor to PRMT1. K313 significantly inhibited cell proliferation and reduced the arginine asymmetric dimethylation level in the leukaemia cancer cells.
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Affiliation(s)
- Kun Qian
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia Athens Georgia 30602 USA +(706) 542 0277
| | - Chunli Yan
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University Atlanta Georgia 30302 USA
| | - Hairui Su
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham Birmingham Alabama 35294 USA
| | - Tran Dang
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia Athens Georgia 30602 USA +(706) 542 0277
| | - Bo Zhou
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia Athens Georgia 30602 USA +(706) 542 0277
| | - Zhenyu Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University Atlanta Georgia 30302 USA
| | - Xinyang Zhao
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham Birmingham Alabama 35294 USA
| | - Ivaylo Ivanov
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University Atlanta Georgia 30302 USA
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica Nankang Taipei Taiwan
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia Athens Georgia 30602 USA +(706) 542 0277
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31
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Al Temimi AHK, Merx J, van Noortwijk CJ, Proietti G, Buijs R, White PB, Rutjes FPJT, Boltje TJ, Mecinović J. Fine-tuning of lysine side chain modulates the activity of histone lysine methyltransferases. Sci Rep 2020; 10:21574. [PMID: 33299050 PMCID: PMC7726145 DOI: 10.1038/s41598-020-78331-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/24/2020] [Indexed: 11/28/2022] Open
Abstract
Histone lysine methyltransferases (KMTs) play an important role in epigenetic gene regulation and have emerged as promising targets for drug discovery. However, the scope and limitation of KMT catalysis on substrates possessing substituted lysine side chains remain insufficiently explored. Here, we identify new unnatural lysine analogues as substrates for human methyltransferases SETD7, SETD8, G9a and GLP. Two synthetic amino acids that possess a subtle modification on the lysine side chain, namely oxygen at the γ position (KO, oxalysine) and nitrogen at the γ position (KN, azalysine) were incorporated into histone peptides and tested as KMTs substrates. Our results demonstrate that these lysine analogues are mono-, di-, and trimethylated to a different extent by trimethyltransferases G9a and GLP. In contrast to monomethyltransferase SETD7, SETD8 exhibits high specificity for both lysine analogues. These findings are important to understand the substrate scope of KMTs and to develop new chemical probes for biomedical applications.
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Affiliation(s)
- Abbas H K Al Temimi
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Jona Merx
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Christian J van Noortwijk
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Giordano Proietti
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Romano Buijs
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Paul B White
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Floris P J T Rutjes
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Thomas J Boltje
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Jasmin Mecinović
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands. .,Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark.
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32
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Cancela MB, Zugbi S, Winter U, Martinez AL, Sampor C, Sgroi M, Francis JH, Garippa R, Abramson DH, Chantada G, Schaiquevich P. A decision process for drug discovery in retinoblastoma. Invest New Drugs 2020; 39:426-441. [PMID: 33200242 DOI: 10.1007/s10637-020-01030-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/28/2020] [Indexed: 11/28/2022]
Abstract
Intraocular retinoblastoma treatment has changed radically over the last decade, leading to a notable improvement in ocular survival. However, eyes that relapse remain difficult to treat, as few alternative active drugs are available. More challenging is the scenario of central nervous system (CNS) metastasis, in which almost no advancements have been made. Both clinical scenarios represent an urgent need for new drugs. Using an integrated multidisciplinary approach, we developed a decision process for prioritizing drug selection for local (intravitreal [IVi], intrathecal/intraventricular [IT/IVt]), systemic, or intra-arterial chemotherapy (IAC) treatment by means of high-throughput pharmacological screening of primary cells from two patients with intraocular tumor and CNS metastasis and a thorough database search to identify clinical and biopharmaceutical data. This process identified 169 compounds to be cytotoxic; only 8 are FDA-approved, lack serious toxicities and available for IVi administration. Four of these agents could also be delivered by IT/IVt. Twelve FDA-approved drugs were identified for systemic delivery as they are able to cross the blood-brain barrier and lack serious adverse events; four drugs are of oral usage and six compounds that lack vesicant or neurotoxicity could be delivered by IAC. We also identified promising compounds in preliminary phases of drug development including inhibitors of survivin, antiapoptotic Bcl-2 family proteins, methyltransferase, and kinesin proteins. This systematic approach may be applied more broadly to prioritize drugs to be repurposed or to identify novel hits for use in retinoblastoma treatment.
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Affiliation(s)
- María Belen Cancela
- Precision Medicine, Hospital de Pediatría JP Garrahan, 1245, Buenos Aires, Argentina.,National Scientific and Technical Research Council, CONICET, 1425, Buenos Aires, Argentina
| | - Santiago Zugbi
- Precision Medicine, Hospital de Pediatría JP Garrahan, 1245, Buenos Aires, Argentina.,National Scientific and Technical Research Council, CONICET, 1425, Buenos Aires, Argentina
| | - Ursula Winter
- Pathology Service, Hospital de Pediatría JP Garrahan, 1245, Buenos Aires, Argentina
| | - Ana Laura Martinez
- Precision Medicine, Hospital de Pediatría JP Garrahan, 1245, Buenos Aires, Argentina
| | - Claudia Sampor
- Hematology-Oncology Service, Hospital de Pediatría JP Garrahan, 1245, Buenos Aires, Argentina
| | - Mariana Sgroi
- Ophthalmology Service, Hospital de Pediatría JP Garrahan, 1245, Buenos Aires, Argentina
| | - Jasmine H Francis
- Ophthalmic Oncology Service, Memorial Sloan-Kettering Institute and Cancer Center, New York, NY, 10065, USA
| | - Ralph Garippa
- Gene Editing And Screening Core facility, Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Institute and Cancer Center, New York, NY, 10065, USA
| | - David H Abramson
- Ophthalmic Oncology Service, Memorial Sloan-Kettering Institute and Cancer Center, New York, NY, 10065, USA
| | - Guillermo Chantada
- Precision Medicine, Hospital de Pediatría JP Garrahan, 1245, Buenos Aires, Argentina.,National Scientific and Technical Research Council, CONICET, 1425, Buenos Aires, Argentina
| | - Paula Schaiquevich
- Precision Medicine, Hospital de Pediatría JP Garrahan, 1245, Buenos Aires, Argentina. .,National Scientific and Technical Research Council, CONICET, 1425, Buenos Aires, Argentina.
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Fioravanti R, Tomassi S, Di Bello E, Romanelli A, Plateroti AM, Benedetti R, Conte M, Novellino E, Altucci L, Valente S, Mai A. Properly Substituted Cyclic Bis-(2-bromobenzylidene) Compounds Behaved as Dual p300/CARM1 Inhibitors and Induced Apoptosis in Cancer Cells. Molecules 2020; 25:molecules25143122. [PMID: 32650558 PMCID: PMC7397249 DOI: 10.3390/molecules25143122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 11/16/2022] Open
Abstract
Bis-(3-bromo-4-hydroxy)benzylidene cyclic compounds have been reported by us as epigenetic multiple ligands, but different substitutions at the two wings provided analogues with selective inhibition. Since the 1-benzyl-3,5-bis((E)-3-bromobenzylidene)piperidin-4-one 3 displayed dual p300/EZH2 inhibition joined to cancer-selective cell death in a panel of tumor cells and in in vivo xenograft models, we prepared a series of bis((E)-2-bromobenzylidene) cyclic compounds 4a–n to test in biochemical (p300, PCAF, SIRT1/2, EZH2, and CARM1) and cellular (NB4, U937, MCF-7, SH-SY5Y) assays. The majority of 4a–n exhibited potent dual p300 and CARM1 inhibition, sometimes reaching the submicromolar level, and induction of apoptosis mainly in the tested leukemia cell lines. The most effective compounds in both enzyme and cellular assays carried a 4-piperidone moiety and a methyl (4d), benzyl (4e), or acyl (4k–m) substituent at N1 position. Elongation of the benzyl portion to 2-phenylethyl (4f) and 3-phenylpropyl (4g) decreased the potency of compounds at both the enzymatic and cellular levels, but the activity was promptly restored by introduction of a ketone group into the phenylalkyl substituent (4h–j). Western blot analyses performed in NB4 and MCF-7 cells on selected compounds confirmed their inhibition of p300 and CARM1 through decrease of the levels of acetyl-H3 and acetyl-H4, marks for p300 inhibition, and of H3R17me2, mark for CARM1 inhibition.
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Affiliation(s)
- Rossella Fioravanti
- Dipartimento di Chimica e Tecnologie del Farmaco, ‘Sapienza’ Università di Roma, 00185 Roma, Italy; (R.F.); (E.D.B.); (A.R.)
| | - Stefano Tomassi
- Dipartimento di Farmacia, Università di Napoli ‘Federico II’, 80131 Napoli, Italy; (S.T.); (E.N.)
| | - Elisabetta Di Bello
- Dipartimento di Chimica e Tecnologie del Farmaco, ‘Sapienza’ Università di Roma, 00185 Roma, Italy; (R.F.); (E.D.B.); (A.R.)
| | - Annalisa Romanelli
- Dipartimento di Chimica e Tecnologie del Farmaco, ‘Sapienza’ Università di Roma, 00185 Roma, Italy; (R.F.); (E.D.B.); (A.R.)
| | - Andrea Maria Plateroti
- Dipartimento di Neuroscienze, Salute Mentale e Organi di Senso–Nesmos, ‘Sapienza’ Università di Roma, 00185 Roma, Italy;
| | - Rosaria Benedetti
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania Luigi Vanvitelli, 80138 Napoli, Italy; (R.B.); (M.C.); (L.A.)
| | - Mariarosaria Conte
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania Luigi Vanvitelli, 80138 Napoli, Italy; (R.B.); (M.C.); (L.A.)
| | - Ettore Novellino
- Dipartimento di Farmacia, Università di Napoli ‘Federico II’, 80131 Napoli, Italy; (S.T.); (E.N.)
| | - Lucia Altucci
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania Luigi Vanvitelli, 80138 Napoli, Italy; (R.B.); (M.C.); (L.A.)
| | - Sergio Valente
- Dipartimento di Chimica e Tecnologie del Farmaco, ‘Sapienza’ Università di Roma, 00185 Roma, Italy; (R.F.); (E.D.B.); (A.R.)
- Correspondence: (S.V.); (A.M.)
| | - Antonello Mai
- Dipartimento di Chimica e Tecnologie del Farmaco, ‘Sapienza’ Università di Roma, 00185 Roma, Italy; (R.F.); (E.D.B.); (A.R.)
- Correspondence: (S.V.); (A.M.)
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Lo Cigno I, Calati F, Borgogna C, Zevini A, Albertini S, Martuscelli L, De Andrea M, Hiscott J, Landolfo S, Gariglio M. Human Papillomavirus E7 Oncoprotein Subverts Host Innate Immunity via SUV39H1-Mediated Epigenetic Silencing of Immune Sensor Genes. J Virol 2020; 94:e01812-19. [PMID: 31776268 PMCID: PMC6997746 DOI: 10.1128/jvi.01812-19] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 11/20/2019] [Indexed: 12/23/2022] Open
Abstract
Subversion of innate immunity by oncoviruses, such as human papillomavirus (HPV), favors carcinogenesis because the mechanism(s) of viral immune evasion can also hamper cancer immunosurveillance. Previously, we demonstrated that high-risk (hr) HPVs trigger simultaneous epigenetic silencing of multiple effectors of innate immunity to promote viral persistence. Here, we expand on those observations and show that the HPV E7 oncoprotein upregulates the H3K9-specific methyltransferase, whose action shuts down the host innate immune response. Specifically, we demonstrate that SUV39H1 contributes to chromatin repression at the promoter regions of the viral nucleic acid sensors RIG-I and cGAS and the adaptor molecule STING in HPV-transformed cells. Inhibition of SUV39H1 leads to transcriptional activation of these genes, especially RIG-I, followed by increased beta interferon (IFN-β) and IFN-λ1 production after poly(dA·dT) or RIG-I agonist M8 transfection. Collectively, our findings provide new evidence that the E7 oncoprotein plays a central role in dampening host innate immunity and raise the possibility that targeting the downstream effector SUV39H1 or the RIG-I pathway is a viable strategy to treat viral and neoplastic disease.IMPORTANCE High-risk HPVs are major viral human carcinogens responsible for approximately 5% of all human cancers. The growth of HPV-transformed cells depends on the ability of viral oncoproteins to manipulate a variety of cellular circuits, including those involved in innate immunity. Here, we show that one of these strategies relies on E7-mediated transcriptional activation of the chromatin repressor SUV39H1, which then promotes epigenetic silencing of RIG-I, cGAS, and STING genes, thereby shutting down interferon secretion in HPV-transformed cells. Pharmacological or genetic inhibition of SUV39H1 restored the innate response in HPV-transformed cells, mostly through activation of RIG-I signaling. We also show that IFN production upon transfection of poly(dA·dT) or the RIG-I agonist M8 predominantly occurs through RIG-I signaling. Altogether, the reversible nature of the modifications associated with E7-mediated SUV39H1 upregulation provides a rationale for the design of novel anticancer and antiviral therapies targeting these molecules.
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Affiliation(s)
- Irene Lo Cigno
- University of Piemonte Orientale Medical School, Department of Translational Medicine, Molecular Virology Unit, Novara, Italy
| | - Federica Calati
- University of Piemonte Orientale Medical School, Department of Translational Medicine, Molecular Virology Unit, Novara, Italy
| | - Cinzia Borgogna
- University of Piemonte Orientale Medical School, Department of Translational Medicine, Molecular Virology Unit, Novara, Italy
| | | | - Silvia Albertini
- University of Piemonte Orientale Medical School, Department of Translational Medicine, Molecular Virology Unit, Novara, Italy
| | - Licia Martuscelli
- University of Piemonte Orientale Medical School, Department of Translational Medicine, Molecular Virology Unit, Novara, Italy
| | - Marco De Andrea
- Center for Translational Research on Autoimmune and Allergic Disease-CAAD, Novara, Italy
- University of Turin Medical School, Department of Public Health and Pediatric Sciences, Viral Pathogenesis Unit, Turin, Italy
| | - John Hiscott
- Istituto Pasteur-Fondazione Cenci Bolognetti, Rome, Italy
| | - Santo Landolfo
- University of Turin Medical School, Department of Public Health and Pediatric Sciences, Viral Pathogenesis Unit, Turin, Italy
| | - Marisa Gariglio
- University of Piemonte Orientale Medical School, Department of Translational Medicine, Molecular Virology Unit, Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Disease-CAAD, Novara, Italy
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35
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Tomaselli D, Lucidi A, Rotili D, Mai A. Epigenetic polypharmacology: A new frontier for epi-drug discovery. Med Res Rev 2020; 40:190-244. [PMID: 31218726 PMCID: PMC6917854 DOI: 10.1002/med.21600] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 05/10/2019] [Accepted: 05/14/2019] [Indexed: 12/11/2022]
Abstract
Recently, despite the great success achieved by the so-called "magic bullets" in the treatment of different diseases through a marked and specific interaction with the target of interest, the pharmacological research is moving toward the development of "molecular network active compounds," embracing the related polypharmacology approach. This strategy was born to overcome the main limitations of the single target therapy leading to a superior therapeutic effect, a decrease of adverse reactions, and a reduction of potential mechanism(s) of drug resistance caused by robustness and redundancy of biological pathways. It has become clear that multifactorial diseases such as cancer, neurological, and inflammatory disorders, may require more complex therapeutic approaches hitting a certain biological system as a whole. Concerning epigenetics, the goal of the multi-epi-target approach consists in the development of small molecules able to simultaneously and (often) reversibly bind different specific epi-targets. To date, two dual histone deacetylase/kinase inhibitors (CUDC-101 and CUDC-907) are in an advanced stage of clinical trials. In the last years, the growing interest in polypharmacology encouraged the publication of high-quality reviews on combination therapy and hybrid molecules. Hence, to update the state-of-the-art of these therapeutic approaches avoiding redundancy, herein we focused only on multiple medication therapies and multitargeting compounds exploiting epigenetic plus nonepigenetic drugs reported in the literature in 2018. In addition, all the multi-epi-target inhibitors known in literature so far, hitting two or more epigenetic targets, have been included.
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Affiliation(s)
- Daniela Tomaselli
- Department of Chemistry and Technologies of Drugs,
“Sapienza” University of Rome, P.le A. Moro 5, 00185 Roma, Italy
| | - Alessia Lucidi
- Department of Chemistry and Technologies of Drugs,
“Sapienza” University of Rome, P.le A. Moro 5, 00185 Roma, Italy
| | - Dante Rotili
- Department of Chemistry and Technologies of Drugs,
“Sapienza” University of Rome, P.le A. Moro 5, 00185 Roma, Italy
| | - Antonello Mai
- Department of Chemistry and Technologies of Drugs,
“Sapienza” University of Rome, P.le A. Moro 5, 00185 Roma, Italy
- Pasteur Institute - Cenci Bolognetti Foundation, Viale
Regina Elena 291, 00161 Roma, Italy
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Ganesan A, Arimondo PB, Rots MG, Jeronimo C, Berdasco M. The timeline of epigenetic drug discovery: from reality to dreams. Clin Epigenetics 2019; 11:174. [PMID: 31791394 PMCID: PMC6888921 DOI: 10.1186/s13148-019-0776-0] [Citation(s) in RCA: 205] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/05/2019] [Indexed: 12/14/2022] Open
Abstract
The flexibility of the epigenome has generated an enticing argument to explore its reversion through pharmacological treatments as a strategy to ameliorate disease phenotypes. All three families of epigenetic proteins—readers, writers, and erasers—are druggable targets that can be addressed through small-molecule inhibitors. At present, a few drugs targeting epigenetic enzymes as well as analogues of epigenetic modifications have been introduced into the clinic use (e.g. to treat haematological malignancies), and a wide range of epigenetic-based drugs are undergoing clinical trials. Here, we describe the timeline of epigenetic drug discovery and development beginning with the early design based solely on phenotypic observations to the state-of-the-art rational epigenetic drug discovery using validated targets. Finally, we will highlight some of the major aspects that need further research and discuss the challenges that need to be overcome to implement epigenetic drug discovery into clinical management of human disorders. To turn into reality, researchers from various disciplines (chemists, biologists, clinicians) need to work together to optimise the drug engineering, read-out assays, and clinical trial design.
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Affiliation(s)
- A Ganesan
- School of Pharmacy, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Paola B Arimondo
- Epigenetic Chemical Biology, Institut Pasteur, CNRS UMR3523, 28 rue du Docteur Roux, 75724, Paris, France
| | - Marianne G Rots
- Epigenetic Editing, Dept. Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713, GZ, Groningen, The Netherlands
| | - Carmen Jeronimo
- Cancer Biology & Epigenetics Group, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - María Berdasco
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain. .,Epigenetic Therapies, Josep Carreras Leukaemia Research Institute (IJC), IJC Building, Campus ICO-Germans Trias i Pujol, Ctra de Can Ruti, Camí de les Escoles s/n 08916 Badalona, Barcelona, Catalonia, Spain.
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Xiong Y, Greschik H, Johansson C, Seifert L, Bacher J, Park KS, Babault N, Martini M, Fagan V, Li F, Chau I, Christott T, Dilworth D, Barsyte-Lovejoy D, Vedadi M, Arrowsmith CH, Brennan P, Fedorov O, Jung M, Farnie G, Liu J, Oppermann U, Schüle R, Jin J. Discovery of a Potent and Selective Fragment-like Inhibitor of Methyllysine Reader Protein Spindlin 1 (SPIN1). J Med Chem 2019; 62:8996-9007. [PMID: 31260300 DOI: 10.1021/acs.jmedchem.9b00522] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
By screening an epigenetic compound library, we identified that UNC0638, a highly potent inhibitor of the histone methyltransferases G9a and GLP, was a weak inhibitor of SPIN1 (spindlin 1), a methyllysine reader protein. Our optimization of this weak hit resulted in the discovery of a potent, selective, and cell-active SPIN1 inhibitor, compound 3 (MS31). Compound 3 potently inhibited binding of trimethyllysine-containing peptides to SPIN1, displayed high binding affinity, was highly selective for SPIN1 over other epigenetic readers and writers, directly engaged SPIN1 in cells, and was not toxic to nontumorigenic cells. The crystal structure of the SPIN1-compound 3 complex indicated that it selectively binds tudor domain II of SPIN1. We also designed a structurally similar but inactive compound 4 (MS31N) as a negative control. Our results have demonstrated for the first time that potent, selective, and cell-active fragment-like inhibitors can be generated by targeting a single tudor domain.
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Affiliation(s)
- 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
| | - 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 OX37LD , U.K
| | - Ludwig Seifert
- Institute of Pharmaceutical Sciences , University of Freiburg , Freiburg 79104 , Germany
| | - Johannes Bacher
- Institute of Pharmaceutical Sciences , University of Freiburg , Freiburg 79104 , Germany
| | - Kwang-Su Park
- 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
| | - Nicolas Babault
- 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
| | - Michael Martini
- 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
| | - Vincent Fagan
- Structural Genomics Consortium & Target Discovery Institute , University of Oxford , Oxford OX37DQ and OX37FZ, U.K
| | | | | | - Thomas Christott
- Structural Genomics Consortium & Target Discovery Institute , University of Oxford , Oxford OX37DQ and OX37FZ, U.K
| | | | | | - Masoud Vedadi
- Department of Pharmacology and Toxicology , University of Toronto , Toronto , Ontario M5S 1A8 , Canada
| | | | - Paul Brennan
- Structural Genomics Consortium & Target Discovery Institute , University of Oxford , Oxford OX37DQ and OX37FZ, U.K
| | - Oleg Fedorov
- Structural Genomics Consortium & Target Discovery Institute , University of Oxford , Oxford OX37DQ and OX37FZ, 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 79106 , Germany
| | - Gillian Farnie
- Structural Genomics Consortium & Target Discovery Institute , University of Oxford , Oxford OX37DQ and OX37FZ, U.K
| | - Jing Liu
- 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
| | - Udo Oppermann
- Structural Genomics Consortium, Botnar Research Center, NIHR Oxford BRU , University of Oxford , Oxford OX37LD , U.K
| | - Roland Schüle
- Department of Urology and Center for Clinical Research , University Freiburg Medical Center , Freiburg 79106 , Germany
- BIOSS Centre of Biological Signalling Studies , University of Freiburg , Freiburg 79106 , Germany
- German Cancer Consortium (DKTK) , Freiburg 79106 , Germany
| | - 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
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38
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Vucicevic J, Nikolic K, Mitchell JB. Rational Drug Design of Antineoplastic Agents Using 3D-QSAR, Cheminformatic, and Virtual Screening Approaches. Curr Med Chem 2019; 26:3874-3889. [DOI: 10.2174/0929867324666170712115411] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/06/2017] [Accepted: 06/13/2017] [Indexed: 01/07/2023]
Abstract
Background:Computer-Aided Drug Design has strongly accelerated the development of novel antineoplastic agents by helping in the hit identification, optimization, and evaluation.Results:Computational approaches such as cheminformatic search, virtual screening, pharmacophore modeling, molecular docking and dynamics have been developed and applied to explain the activity of bioactive molecules, design novel agents, increase the success rate of drug research, and decrease the total costs of drug discovery. Similarity, searches and virtual screening are used to identify molecules with an increased probability to interact with drug targets of interest, while the other computational approaches are applied for the design and evaluation of molecules with enhanced activity and improved safety profile.Conclusion:In this review are described the main in silico techniques used in rational drug design of antineoplastic agents and presented optimal combinations of computational methods for design of more efficient antineoplastic drugs.
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Affiliation(s)
- Jelica Vucicevic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - John B.O. Mitchell
- EaStCHEM School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, United Kingdom
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39
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Batham J, Lim PS, Rao S. SETDB-1: A Potential Epigenetic Regulator in Breast Cancer Metastasis. Cancers (Basel) 2019; 11:cancers11081143. [PMID: 31405032 PMCID: PMC6721492 DOI: 10.3390/cancers11081143] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 02/06/2023] Open
Abstract
The full epigenetic repertoire governing breast cancer metastasis is not completely understood. Here, we discuss the histone methyltransferase SET Domain Bifurcated Histone Lysine Methyltransferase 1 (SETDB1) and its role in breast cancer metastasis. SETDB1 serves as an exemplar of the difficulties faced when developing therapies that not only specifically target cancer cells but also the more elusive and aggressive stem cells that contribute to metastasis via epithelial-to-mesenchymal transition and confer resistance to therapies.
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Affiliation(s)
- Jacob Batham
- Melanie Swan Memorial Translational Centre, Faculty of Sci-Tech, University of Canberra, Bruce ACT 2617, Australia
| | - Pek Siew Lim
- Melanie Swan Memorial Translational Centre, Faculty of Sci-Tech, University of Canberra, Bruce ACT 2617, Australia.
| | - Sudha Rao
- Melanie Swan Memorial Translational Centre, Faculty of Sci-Tech, University of Canberra, Bruce ACT 2617, Australia.
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40
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The Development of Tetrazole Derivatives as Protein Arginine Methyltransferase I (PRMT I) Inhibitors. Int J Mol Sci 2019; 20:ijms20153840. [PMID: 31390828 PMCID: PMC6695598 DOI: 10.3390/ijms20153840] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/01/2019] [Accepted: 08/01/2019] [Indexed: 02/07/2023] Open
Abstract
Protein arginine methyltransferase 1 (PRMT1) can catalyze protein arginine methylation by transferring the methyl group from S-adenosyl-L-methionine (SAM) to the guanidyl nitrogen atom of protein arginine, which influences a variety of biological processes. The dysregulation of PRMT1 is involved in a diverse range of diseases, including cancer. Therefore, there is an urgent need to develop novel and potent PRMT1 inhibitors. In the current manuscript, a series of 1-substituted 1H-tetrazole derivatives were designed and synthesized by targeting at the substrate arginine-binding site on PRMT1, and five compounds demonstrated significant inhibitory effects against PRMT1. The most potent PRMT1 inhibitor, compound 9a, displayed non-competitive pattern with respect to either SAM or substrate arginine, and showed the strong selectivity to PRMT1 compared to PRMT5, which belongs to the type II PRMT family. It was observed that the compound 9a inhibited the functions of PRMT1 and relative factors within this pathway, and down-regulated the canonical Wnt/β-catenin signaling pathway. The binding of compound 9a to PRMT1 was carefully analyzed by using molecular dynamic simulations and binding free energy calculations. These studies demonstrate that 9a was a potent PRMT1 inhibitor, which could be used as lead compound for further drug discovery.
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41
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Tewary SK, Zheng YG, Ho MC. Protein arginine methyltransferases: insights into the enzyme structure and mechanism at the atomic level. Cell Mol Life Sci 2019; 76:2917-2932. [PMID: 31123777 PMCID: PMC6741777 DOI: 10.1007/s00018-019-03145-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 02/06/2023]
Abstract
Protein arginine methyltransferases (PRMTs) catalyze the methyl transfer to the arginine residues of protein substrates and are classified into three major types based on the final form of the methylated arginine. Recent studies have shown a strong correlation between PRMT expression level and the prognosis of cancer patients. Currently, crystal structures of eight PRMT members have been determined. Kinetic and structural studies have shown that all PRMTs share similar, but unique catalytic and substrate recognition mechanism. In this review, we discuss the structural similarities and differences of different PRMT members, focusing on their overall structure, S-adenosyl-L-methionine-binding pocket, substrate arginine recognition and catalytic mechanisms. Since PRMTs are valuable targets for drug discovery, we also rationally classify the known PRMT inhibitors into five classes and discuss their mechanisms of action at the atomic level.
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Affiliation(s)
| | - Y George Zheng
- College of Pharmacy, University of Georgia, Athens, GA, 30602, USA
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 106, Taiwan.
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42
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Lin H, Wang M, Zhang YW, Tong S, Leal RA, Shetty R, Vaddi K, Luengo JI. Discovery of Potent and Selective Covalent Protein Arginine Methyltransferase 5 (PRMT5) Inhibitors. ACS Med Chem Lett 2019; 10:1033-1038. [PMID: 31312404 PMCID: PMC6627734 DOI: 10.1021/acsmedchemlett.9b00074] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/22/2019] [Indexed: 12/22/2022] Open
Abstract
Protein arginine methyltransferase 5 (PRMT5) is known to symmetrically dimethylate numerous cytosolic and nuclear proteins that are involved in a variety of cellular processes. Recent findings have revealed its potential as a cancer therapeutic target. PRMT5 possesses a cysteine (C449) in the active site, unique to PRMT5. Therefore, covalent PRMT5 inhibition is an attractive chemical approach. Herein, we report an exciting discovery of a series of novel hemiaminals that under physiological conditions can be converted to aldehydes and react with C449 to form covalent adducts, which presumably undergo an unprecedented elimination to form the thiol-vinyl ethers, as indicated by electron density in the co-crystal structure of the PRMT5/MEP50 complex.
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Affiliation(s)
- Hong Lin
- Prelude Therapeutics, 200 Powder Mill Road, Wilmington, Delaware 19803, United States
| | - Min Wang
- Prelude Therapeutics, 200 Powder Mill Road, Wilmington, Delaware 19803, United States
| | - Yang W. Zhang
- Prelude Therapeutics, 200 Powder Mill Road, Wilmington, Delaware 19803, United States
| | - Shuilong Tong
- VIVA Biotech Ltd., 334 Aidisheng Road, Zhangjiang High-Tech Park, Shanghai 201203, China
| | - Raul A. Leal
- Prelude Therapeutics, 200 Powder Mill Road, Wilmington, Delaware 19803, United States
| | - Rupa Shetty
- Prelude Therapeutics, 200 Powder Mill Road, Wilmington, Delaware 19803, United States
| | - Kris Vaddi
- Prelude Therapeutics, 200 Powder Mill Road, Wilmington, Delaware 19803, United States
| | - Juan I. Luengo
- Prelude Therapeutics, 200 Powder Mill Road, Wilmington, Delaware 19803, United States
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43
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Fulton MD, Brown T, Zheng YG. The Biological Axis of Protein Arginine Methylation and Asymmetric Dimethylarginine. Int J Mol Sci 2019; 20:ijms20133322. [PMID: 31284549 PMCID: PMC6651691 DOI: 10.3390/ijms20133322] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/04/2019] [Accepted: 07/04/2019] [Indexed: 12/20/2022] Open
Abstract
Protein post-translational modifications (PTMs) in eukaryotic cells play important roles in the regulation of functionalities of the proteome and in the tempo-spatial control of cellular processes. Most PTMs enact their regulatory functions by affecting the biochemical properties of substrate proteins such as altering structural conformation, protein-protein interaction, and protein-nucleic acid interaction. Amid various PTMs, arginine methylation is widespread in all eukaryotic organisms, from yeasts to humans. Arginine methylation in many situations can drastically or subtly affect the interactions of substrate proteins with their partnering proteins or nucleic acids, thus impacting major cellular programs. Recently, arginine methylation has become an important regulator of the formation of membrane-less organelles inside cells, a phenomenon of liquid-liquid phase separation (LLPS), through altering π-cation interactions. Another unique feature of arginine methylation lies in its impact on cellular physiology through its downstream amino acid product, asymmetric dimethylarginine (ADMA). Accumulation of ADMA in cells and in the circulating bloodstream is connected with endothelial dysfunction and a variety of syndromes of cardiovascular diseases. Herein, we review the current knowledge and understanding of protein arginine methylation in regards to its canonical function in direct protein regulation, as well as the biological axis of protein arginine methylation and ADMA biology.
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Affiliation(s)
- Melody D Fulton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Tyler Brown
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA.
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44
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Guo Z, Zhang Z, Yang H, Cao D, Xu X, Zheng X, Chen D, Wang Q, Li Y, Li J, Du Z, Wang X, Chen L, Ding J, Shen J, Geng M, Huang X, Xiong B. Design and Synthesis of Potent, Selective Inhibitors of Protein Arginine Methyltransferase 4 against Acute Myeloid Leukemia. J Med Chem 2019; 62:5414-5433. [PMID: 31117515 DOI: 10.1021/acs.jmedchem.9b00297] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
PRMT4 is a type I protein arginine methyltransferase and plays important roles in various cellular processes. Overexpression of PRMT4 has been found to be involved in several types of cancers. Selective and in vivo effective PRMT4 inhibitors are needed for demonstrating PRMT4 as a promising therapeutic target. On the basis of compound 6, a weak dual PRMT4/6 inhibitor, we constructed a tetrahydroisoquinoline scaffold through a cut-and-sew scaffold hopping strategy. The subsequent SAR optimization efforts employed structure-based approach led to the identification of a novel PRMT4 inhibitor 49. Compound 49 exhibited prominently high potency and selectivity, moderate pharmacokinetic profiles, and good antitumor efficacy in acute myeloid leukemia xenograft model via oral administration, thus demonstrating this compound as a useful pharmacological tool for further target validation and drug development in cancer therapy.
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Affiliation(s)
- Zuhao Guo
- Department of Medicinal Chemistry , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing 100049 , China
| | - Zhuqing Zhang
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing 100049 , China
| | - Hong Yang
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China
| | - Danyan Cao
- Department of Medicinal Chemistry , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China
| | - Xiaowei Xu
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing 100049 , China
| | - Xingling Zheng
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing 100049 , China
| | - Danqi Chen
- Department of Medicinal Chemistry , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China
| | - Qi Wang
- Department of Medicinal Chemistry , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing 100049 , China
| | - Yanlian Li
- Department of Medicinal Chemistry , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China
| | - Jian Li
- Department of Medicinal Chemistry , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China
| | - Zhiyan Du
- Department of Medicinal Chemistry , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China
| | - Xin Wang
- Department of Medicinal Chemistry , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China
| | - Lin Chen
- Department of Medicinal Chemistry , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China
| | - Jian Ding
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing 100049 , China
| | - Jingkang Shen
- Department of Medicinal Chemistry , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China
| | - Meiyu Geng
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing 100049 , China
| | - Xun Huang
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing 100049 , China
| | - Bing Xiong
- Department of Medicinal Chemistry , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing 100049 , China
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45
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Li F, Wan X, Xing J, Tan X, Li X, Wang Y, Zhao J, Wu X, Liu X, Li Z, Luo X, Lu W, Zheng M. Deep Neural Network Classifier for Virtual Screening Inhibitors of (S)-Adenosyl-L-Methionine (SAM)-Dependent Methyltransferase Family. Front Chem 2019; 7:324. [PMID: 31134191 PMCID: PMC6524412 DOI: 10.3389/fchem.2019.00324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 04/23/2019] [Indexed: 12/15/2022] Open
Abstract
The (S)-adenosyl-L-methionine (SAM)-dependent methyltransferases play essential roles in post-translational modifications (PTMs) and other miscellaneous biological processes, and are implicated in the pathogenesis of various genetic disorders and cancers. Increasing efforts have been committed toward discovering novel PTM inhibitors targeting the (S)-Adenosyl-L-methionine (SAM)-binding site and the substrate-binding site of methyltransferases, among which virtual screening (VS) and structure-based drug design (SBDD) are the most frequently used strategies. Here, we report the development of a target-specific scoring model for compound VS, which predict the likelihood of the compound being a potential inhibitor for the SAM-binding pocket of a given methyltransferase. Protein-ligand interaction characterized by Fingerprinting Triplets of Interaction Pseudoatoms was used as the input feature, and a binary classifier based on deep neural networks is trained to build the scoring model. This model enhances the efficiency of the existing strategies used for discovering novel chemical modulators of methyltransferase, which is crucial for understanding and exploring the complexity of epigenetic target space.
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Affiliation(s)
- Fei Li
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China.,State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xiaozhe Wan
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Xing
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI, United States
| | - Xiaoqin Tan
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Xutong Li
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Yulan Wang
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jihui Zhao
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolong Wu
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xiaohong Liu
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Zhaojun Li
- School of Information Management, Dezhou University, Dezhou, China
| | - Xiaomin Luo
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Wencong Lu
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China
| | - Mingyue Zheng
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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46
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Rezapour S, Hosseinzadeh E, Marofi F, Hassanzadeh A. Epigenetic-based therapy for colorectal cancer: Prospect and involved mechanisms. J Cell Physiol 2019; 234:19366-19383. [PMID: 31020647 DOI: 10.1002/jcp.28658] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/21/2019] [Accepted: 03/25/2019] [Indexed: 12/15/2022]
Abstract
Epigenetic modifications are heritable variations in gene expression not encoded by the DNA sequence. According to reports, a large number of studies have been performed to characterize epigenetic modification during normal development and also in cancer. Epigenetics can be regarded more widely to contain all of the changes in expression of genes that make by adjusted interactions between the regulatory portions of DNA or messenger RNAs that lead to indirect variation in the DNA sequence. In the last decade, epigenetic modification importance in colorectal cancer (CRC) pathogenesis was demonstrated powerfully. Although developments in CRC therapy have been made in the last years, much work is required as it remains the second leading cause of cancer death. Nowadays, epigenetic programs and genetic change have pivotal roles in the CRC incidence as well as progression. While our knowledge about epigenetic mechanism in CRC is not comprehensive, selective histone modifications and resultant chromatin conformation together with DNA methylation most likely regulate CRC pathogenesis that involved genes expression. Undoubtedly, the advanced understanding of epigenetic-based gene expression regulation in the CRC is essential to make epigenetic drugs for CRC therapy. The major aim of this review is to deliver a summary of valuable results that represent evidence of principle for epigenetic-based therapeutic approaches employment in CRC with a focus on the advantages of epigenetic-based therapy in the inhibition of the CRC metastasis and proliferation.
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Affiliation(s)
- Saleheh Rezapour
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Elham Hosseinzadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Faroogh Marofi
- Division of Hematology, Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Hassanzadeh
- Division of Hematology, Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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47
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Lin H, Luengo JI. Nucleoside protein arginine methyltransferase 5 (PRMT5) inhibitors. Bioorg Med Chem Lett 2019; 29:1264-1269. [PMID: 30956011 DOI: 10.1016/j.bmcl.2019.03.042] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/23/2019] [Accepted: 03/25/2019] [Indexed: 12/21/2022]
Abstract
Protein Arginine Methyltransferase 5 (PRMT5) is known to symmetrically dimethylate numerous cytosolic and nuclear proteins that are involved in a variety of cellular processes. Recent findings have revealed its potential as a cancer therapeutic target. PRMT5 selective inhibitors, GSK3326595, a substrate competitive inhibitor, and JNJ64619178, a SAM (S-adenosyl-l-methionine) mimetic/competitive inhibitor, have entered clinic trials for multiple cancer types. This review focuses on the recent developments in SAM mimetic nucleoside PRMT5 inhibitors, their SAR and structural insight based on published co-crystal structures.
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Affiliation(s)
- Hong Lin
- Prelude Therapeutics, 200 Powder Mill Road, Wilmington, DE 19803, United States
| | - Juan I Luengo
- Prelude Therapeutics, 200 Powder Mill Road, Wilmington, DE 19803, United States
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48
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Milite C, Feoli A, Horton JR, Rescigno D, Cipriano A, Pisapia V, Viviano M, Pepe G, Amendola G, Novellino E, Cosconati S, Cheng X, Castellano S, Sbardella G. Discovery of a Novel Chemotype of Histone Lysine Methyltransferase EHMT1/2 (GLP/G9a) Inhibitors: Rational Design, Synthesis, Biological Evaluation, and Co-crystal Structure. J Med Chem 2019; 62:2666-2689. [PMID: 30753076 DOI: 10.1021/acs.jmedchem.8b02008] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Since the discovery of compound BIX01294 over 10 years ago, only a very limited number of nonquinazoline inhibitors of H3K9-specific methyltransferases G9a and G9a-like protein (GLP) have been reported. Herein, we report the identification of a novel chemotype for G9a/GLP inhibitors, based on the underinvestigated 2-alkyl-5-amino- and 2-aryl-5-amino-substituted 3 H-benzo[ e][1,4]diazepine scaffold. Our research efforts resulted in the identification 12a (EML741), which not only maintained the high in vitro and cellular potency of its quinazoline counterpart, but also displayed improved inhibitory potency against DNA methyltransferase 1, improved selectivity against other methyltransferases, low cell toxicity, and improved apparent permeability values in both parallel artificial membrane permeability assay (PAMPA) and blood-brain barrier-specific PAMPA, and therefore might potentially be a better candidate for animal studies. Finally, the co-crystal structure of GLP in complex with 12a provides the basis for the further development of benzodiazepine-based G9a/GLP inhibitors.
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Affiliation(s)
| | | | - John R Horton
- Department of Molecular and Cellular Oncology , The University of Texas MD Anderson Cancer Center , Houston , Texas 77030 , United States
| | | | | | | | | | | | - Giorgio Amendola
- DiSTABiF , University of Campania "Luigi Vanvitelli" , Via Vivaldi 43 , 81100 Caserta , Italy
| | - Ettore Novellino
- Department of Pharmacy , University Federico II of Naples , Via D. Montesano 49 , 80131 Naples , Italy
| | - Sandro Cosconati
- DiSTABiF , University of Campania "Luigi Vanvitelli" , Via Vivaldi 43 , 81100 Caserta , Italy
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology , The University of Texas MD Anderson Cancer Center , Houston , Texas 77030 , United States
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49
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Lorentzian A, Uzozie A, Lange PF. Origins and clinical relevance of proteoforms in pediatric malignancies. Expert Rev Proteomics 2019; 16:185-200. [PMID: 30700156 DOI: 10.1080/14789450.2019.1575206] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Cancer changes the proteome in complex ways that reach well beyond simple changes in protein abundance. Genomic and transcriptional variations and post-translational protein modification create functional variants of a protein, known as proteoforms. Childhood cancers have fewer genomic alterations but show equally dramatic phenotypic changes as malignant cells in adults. Therefore, unraveling the complexities of the proteome is even more important in pediatric malignancies. Areas covered: In this review, the biological origins of proteoforms and technological advancements in the study of proteoforms are discussed. Particular emphasis is given to their implication in childhood malignancies and the critical role of cancer-specific proteoforms for the next generation of cancer therapies and diagnostics. Expert opinion: Recent advancements in technology have led to a better understanding of the underlying mechanisms of tumorigenesis. This has been critical for the development of more effective and less harmful treatments that are based on direct targeting of altered proteins and deregulated pathways. As proteome coverage and the ability to detect complex proteoforms increase, the most need for change is in data compilation and database availability to mediate high-level data analysis and allow for better functional annotation of proteoforms.
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Affiliation(s)
- Amanda Lorentzian
- a Department of Cell and Developmental Biology , University of British Columbia , Vancouver , BC , Canada.,b Michael Cuccione Childhood Cancer Research Program , BC Children's Hospital Research Institute , Vancouver , BC , Canada
| | - Anuli Uzozie
- b Michael Cuccione Childhood Cancer Research Program , BC Children's Hospital Research Institute , Vancouver , BC , Canada.,c Department of Pathology and Laboratory Medicine , University of British Columbia , Vancouver , BC , Canada
| | - Philipp F Lange
- a Department of Cell and Developmental Biology , University of British Columbia , Vancouver , BC , Canada.,b Michael Cuccione Childhood Cancer Research Program , BC Children's Hospital Research Institute , Vancouver , BC , Canada.,c Department of Pathology and Laboratory Medicine , University of British Columbia , Vancouver , BC , Canada
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50
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Jing P, Xie N, Zhu X, Dang H, Gu Z. The methylation induced by protein arginine methyltransferase 5 promotes tumorigenesis and progression of lung cancer. J Thorac Dis 2019; 10:7014-7019. [PMID: 30746248 DOI: 10.21037/jtd.2018.10.100] [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] [Indexed: 01/04/2023]
Abstract
Arginine methylation as a common pattern of post-translational modification is involved in many cellular biological processes. Protein arginine methyltransferase 5 (PRMT5) is a primary enzyme in charge of symmetric dimethylation (me2s) of arginine residues. Increasing literatures lead to the belief that PRMT5, as a potential oncogene, plays crucial roles in the tumorigenesis and progression of cancers. First of all, PRMT5 is overexpressed in several cancer cells, with various sub-cellular localization in different type of cells and different phases. Besides, PRMT5 participates in controlling cellular proliferation, differentiation, invasion, migration as well apoptosis through histone and other protein methylation. Moreover, PRMT5 is essential for growth and metastasis of lung cancer cells, and its overexpression indicates a poor clinical outcome of lung cancer. Therefore, in this review, we reviewed the substantial new literatures on PRMT5 and its functions, in order to highlight the significance of understanding this essential enzyme in lung cancer tumorigenesis and progression.
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Affiliation(s)
- Pengyu Jing
- Department of Thoracic Surgery, The Second Affiliated Hospital of AFMU, Air Force Medical University, Xi'an 710038, China
| | - Nianlin Xie
- Department of Thoracic Surgery, The Second Affiliated Hospital of AFMU, Air Force Medical University, Xi'an 710038, China
| | - Ximing Zhu
- Department of Thoracic Surgery, The Second Affiliated Hospital of AFMU, Air Force Medical University, Xi'an 710038, China
| | - Haizhou Dang
- Department of Thoracic Surgery, The Second Affiliated Hospital of AFMU, Air Force Medical University, Xi'an 710038, China
| | - Zhongping Gu
- Department of Thoracic Surgery, The Second Affiliated Hospital of AFMU, Air Force Medical University, Xi'an 710038, China
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