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Curcio A, Rocca R, Alcaro S, Artese A. The Histone Deacetylase Family: Structural Features and Application of Combined Computational Methods. Pharmaceuticals (Basel) 2024; 17:620. [PMID: 38794190 PMCID: PMC11124352 DOI: 10.3390/ph17050620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Histone deacetylases (HDACs) are crucial in gene transcription, removing acetyl groups from histones. They also influence the deacetylation of non-histone proteins, contributing to the regulation of various biological processes. Thus, HDACs play pivotal roles in various diseases, including cancer, neurodegenerative disorders, and inflammatory conditions, highlighting their potential as therapeutic targets. This paper reviews the structure and function of the four classes of human HDACs. While four HDAC inhibitors are currently available for treating hematological malignancies, numerous others are undergoing clinical trials. However, their non-selective toxicity necessitates ongoing research into safer and more efficient class-selective or isoform-selective inhibitors. Computational methods have aided the discovery of HDAC inhibitors with the desired potency and/or selectivity. These methods include ligand-based approaches, such as scaffold hopping, pharmacophore modeling, three-dimensional quantitative structure-activity relationships, and structure-based virtual screening (molecular docking). Moreover, recent developments in the field of molecular dynamics simulations, combined with Poisson-Boltzmann/molecular mechanics generalized Born surface area techniques, have improved the prediction of ligand binding affinity. In this review, we delve into the ways in which these methods have contributed to designing and identifying HDAC inhibitors.
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Affiliation(s)
- Antonio Curcio
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
| | - Roberta Rocca
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
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2
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Kraft FB, Enns J, Honin I, Engelhardt J, Schöler A, Smith ST, Meiler J, Schäker-Hübner L, Weindl G, Hansen FK. Groebke Blackburn Bienaymé-mediated multi-component synthesis of selective HDAC6 inhibitors with anti-inflammatory properties. Bioorg Chem 2024; 143:107072. [PMID: 38185013 DOI: 10.1016/j.bioorg.2023.107072] [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: 10/09/2023] [Revised: 12/19/2023] [Accepted: 12/27/2023] [Indexed: 01/09/2024]
Abstract
Histone deacetylases (HDACs) are a class of enzymes that cleave acyl groups from lysine residues of histone and non-histone proteins. There are 18 human HDAC isoforms with different cellular targets and functions. Among them, HDAC6 was found to be overexpressed in different types of cancer. However, when used in monotherapy, HDAC6 inhibition by selective inhibitors fails to show pronounced anti-cancer effects. The HDAC6 enzyme also addresses non-histone proteins like α-tubulin and cortactin, making it important for cell migration and angiogenesis. Recently, the NLRP3 inflammasome was identified as an important regulator of inflammation and immune responses and, importantly, HDAC6 is critically involved the activation of the inflammasome. We herein report the design, synthesis and biological evaluation of a library of selective HDAC6 inhibitors. Starting from the previously published crystal structure of MAIP-032 in complex with CD2 of zHDAC6, we performed docking studies to evaluate additional possible interactions of the cap group with the L1-loop pocket. Based on the results we synthesized 13 novel HDAC6 inhibitors via the Groebke-Blackburn-Bienaymé three component reaction as the key step. Compounds 8k (HDAC1 IC50: 5.87 μM; HDAC6 IC50: 0.024 μM; selectivity factor (SF1/6): 245) and 8m (HDAC1 IC50: 3.07 μM; HDAC6 IC50: 0.026 μM; SF1/6: 118) emerged as the most potent and selective inhibitors of HDAC6 and outperformed the lead structure MAIP-032 (HDAC1 IC50: 2.20 μM; HDAC6 IC50: 0.058 μM; SF1/6: 38) both in terms of inhibitory potency and selectivity. Subsequent immunoblot analysis confirmed the high selectivity of 8k and 8m for HDAC6 in a cellular environment. While neither 8k and 8m nor the selectivity HDAC6 inhibitor tubastatin A showed antiproliferative effects in the U-87 MG glioblastoma cell line, compound 8m attenuated cell migration significantly in wound healing assays in U-87 MG cells. Moreover, in macrophages compounds 8k and 8m demonstrated significant inhibition of LPS-induced IL1B mRNA expression and TNF release. These findings suggest that our imidazo[1,2-a]pyridine-capped HDAC6 inhibitors may serve as promising candidates for the development of drugs to effectively treat NLRP3 inflammasome-driven inflammatory diseases.
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Affiliation(s)
- Fabian B Kraft
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Jana Enns
- Department of Pharmacology and Toxicology, Pharmaceutical Institute, University of Bonn, Gerhard-Domagk-Str.3, 53121 Bonn, Germany
| | - Irina Honin
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Jonas Engelhardt
- Department of Pharmacology and Toxicology, Pharmaceutical Institute, University of Bonn, Gerhard-Domagk-Str.3, 53121 Bonn, Germany
| | - Andrea Schöler
- Institute for Drug Discovery, Medicinal Faculty, University Leipzig, Brüderstraße 34, 04103 Leipzig, Germany
| | - Shannon T Smith
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Jens Meiler
- Institute for Drug Discovery, Medicinal Faculty, University Leipzig, Brüderstraße 34, 04103 Leipzig, Germany; Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Linda Schäker-Hübner
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Günther Weindl
- Department of Pharmacology and Toxicology, Pharmaceutical Institute, University of Bonn, Gerhard-Domagk-Str.3, 53121 Bonn, Germany
| | - Finn K Hansen
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany.
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Abe Y, Kofman ER, Ouyang Z, Cruz-Becerra G, Spann NJ, Seidman JS, Troutman TD, Stender JD, Taylor H, Fan W, Link VM, Shen Z, Sakai J, Downes M, Evans RM, Kadonaga JT, Rosenfeld MG, Glass CK. A TLR4/TRAF6-dependent signaling pathway mediates NCoR coactivator complex formation for inflammatory gene activation. Proc Natl Acad Sci U S A 2024; 121:e2316104121. [PMID: 38165941 PMCID: PMC10786282 DOI: 10.1073/pnas.2316104121] [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: 09/15/2023] [Accepted: 11/21/2023] [Indexed: 01/04/2024] Open
Abstract
The nuclear receptor corepressor (NCoR) forms a complex with histone deacetylase 3 (HDAC3) that mediates repressive functions of unliganded nuclear receptors and other transcriptional repressors by deacetylation of histone substrates. Recent studies provide evidence that NCoR/HDAC3 complexes can also exert coactivator functions in brown adipocytes by deacetylating and activating PPARγ coactivator 1α (PGC1α) and that signaling via receptor activator of nuclear factor kappa-B (RANK) promotes the formation of a stable NCoR/HDAC3/PGC1β complex that coactivates nuclear factor kappa-B (NFκB)- and activator protein 1 (AP-1)-dependent genes required for osteoclast differentiation. Here, we demonstrate that activation of Toll-like receptor (TLR) 4, but not TLR3, the interleukin 4 (IL4) receptor nor the Type I interferon receptor, also promotes assembly of an NCoR/HDAC3/PGC1β coactivator complex. Receptor-specific utilization of TNF receptor-associated factor 6 (TRAF6) and downstream activation of extracellular signal-regulated kinase 1 (ERK1) and TANK-binding kinase 1 (TBK1) accounts for the common ability of RANK and TLR4 to drive assembly of an NCoR/HDAC3/PGC1β complex in macrophages. ERK1, the p65 component of NFκB, and the p300 histone acetyltransferase (HAT) are also components of the induced complex and are associated with local histone acetylation and transcriptional activation of TLR4-dependent enhancers and promoters. These observations identify a TLR4/TRAF6-dependent signaling pathway that converts NCoR from a corepressor of nuclear receptors to a coactivator of NFκB and AP-1 that may be relevant to functions of NCoR in other developmental and homeostatic processes.
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Affiliation(s)
- Yohei Abe
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Eric R. Kofman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
- Stem Cell Program, University of California San Diego, La Jolla, CA92093
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA92093
| | - Zhengyu Ouyang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Grisel Cruz-Becerra
- Department of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Nathanael J. Spann
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Jason S. Seidman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Ty D. Troutman
- Department of Medicine, University of California San Diego, La Jolla, CA92093
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, OH45229
| | - Joshua D. Stender
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Havilah Taylor
- Department and School of Medicine, University of California San Diego, La Jolla, CA92093
| | - Weiwei Fan
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA92037
| | - Verena M. Link
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
- Faculty of Biology, Department II, Ludwig-Maximilians Universität München, Munich82152, Germany
| | - Zeyang Shen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA92093
| | - Juro Sakai
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo153-8904, Japan
- Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai980-8575, Japan
| | - Michael Downes
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA92037
| | - Ronald M. Evans
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA92037
| | - James T. Kadonaga
- Department of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Michael G. Rosenfeld
- Department and School of Medicine, University of California San Diego, La Jolla, CA92093
| | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
- Department of Medicine, University of California San Diego, La Jolla, CA92093
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Patel P, Shrivastava SK, Sharma P, Kurmi BD, Shirbhate E, Rajak H. Hydroxamic acid derivatives as selective HDAC3 inhibitors: computer-aided drug design strategies. J Biomol Struct Dyn 2024; 42:362-383. [PMID: 36995068 DOI: 10.1080/07391102.2023.2192804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 03/13/2023] [Indexed: 03/31/2023]
Abstract
Histone deacetylases (HDACs) are critical epigenetic drug targets that have gained significant attention in the scientific community for the treatment of cancer. The currently marketed HDAC inhibitors lack selectivity for the various HDAC isoenzymes. Here, we describe our protocol for the discovery of novel potential hydroxamic acid based HDAC3 inhibitors through pharmacophore modeling, virtual screening, docking, molecular dynamics (MD) simulation and toxicity studies. The ten pharmacophore hypotheses were established, and their reliability was validated by different ROC (receiving operator curve) analysis. Among them, the best model (Hypothesis 9 or RRRA) was employed for searching SCHEMBL, ZINC and MolPort database to screen out hit molecules as selective HDAC3 inhibitors, followed by different docking stages. MD simulation (50 ns) and MMGBSA study were performed to study the stability of ligand binding modes and with the help of trajectory analysis, to calculate the ligand-receptor complex RMSD (root-mean-square deviation), RMSF (root-mean-square fluctuation) and H-bond distance, etc. Finally, in-silico toxicity studies were performed on top screened molecules and compared with reference drug SAHA and established structure-activity relationship (SAR). The results indicated that compound 31, with high inhibitory potency and less toxicity (probability value 0.418), is suitable for further experimental analysis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Preeti Patel
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Guru Ghasidas University, Bilaspur, Chhattisgarh, India
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, Punjab, India
| | - Sushant Kumar Shrivastava
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Piyoosh Sharma
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Balak Das Kurmi
- Department of Pharmaceutics, ISF College of Pharmacy, Moga, Punjab, India
| | - Ekta Shirbhate
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Guru Ghasidas University, Bilaspur, Chhattisgarh, India
| | - Harish Rajak
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Guru Ghasidas University, Bilaspur, Chhattisgarh, India
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5
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Uba AI, Zengin G. In the quest for histone deacetylase inhibitors: current trends in the application of multilayered computational methods. Amino Acids 2023; 55:1709-1726. [PMID: 37367966 DOI: 10.1007/s00726-023-03297-y] [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: 04/15/2023] [Accepted: 06/20/2023] [Indexed: 06/28/2023]
Abstract
Histone deacetylase (HDAC) inhibitors have gained attention over the past three decades because of their potential in the treatment of different diseases including various forms of cancers, neurodegenerative disorders, autoimmune, inflammatory diseases, and other metabolic disorders. To date, 5 HDAC inhibitor drugs are marketed for the treatment of hematological malignancies and several drug-candidate HDAC inhibitors are at different stages of clinical trials. However, due to the toxic side effects of these drugs resulting from the lack of target selectivity, active studies are ongoing to design and develop either class-selective or isoform-selective inhibitors. Computational methods have aided the discovery of HDAC inhibitors with the desired potency and/or selectivity. These methods include ligand-based approaches such as scaffold hopping, pharmacophore modeling, three-dimensional quantitative structure-activity relationships (3D-QSAR); and structure-based virtual screening (molecular docking). The current trends involve the application of the combination of these methods and incorporating molecular dynamics simulations coupled with Poisson-Boltzmann/molecular mechanics generalized Born surface area (MM-PBSA/MM-GBSA) to improve the prediction of ligand binding affinity. This review aimed at understanding the current trends in applying these multilayered strategies and their contribution to the design/identification of HDAC inhibitors.
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Affiliation(s)
- Abdullahi Ibrahim Uba
- Department of Molecular Biology and Genetics, Istanbul AREL University, Istanbul, 34537, Turkey.
| | - Gokhan Zengin
- Department of Biology, Science Faculty, Selcuk University, Konya, 42130, Turkey.
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6
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Lanka G, Begum D, Banerjee S, Adhikari N, P Y, Ghosh B. Pharmacophore-based virtual screening, 3D QSAR, Docking, ADMET, and MD simulation studies: An in silico perspective for the identification of new potential HDAC3 inhibitors. Comput Biol Med 2023; 166:107481. [PMID: 37741229 DOI: 10.1016/j.compbiomed.2023.107481] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/19/2023] [Accepted: 09/15/2023] [Indexed: 09/25/2023]
Abstract
Histone deacetylase 3 (HDAC3) is an epigenetic regulator that involves gene expression, apoptosis, and cell cycle progression, and the overexpression of HDAC3 is accountable for several cancers, neurodegeneracy, and many other diseases. Therefore, HDAC3 emerged as a promising drug target for the novel drug design. Here, we carried out the pharmacophore modeling using 50 benzamide-based HDAC3 selective inhibitors and utilized it for PHASE ligand screening to retrieve the hits with similar pharmacophore features. The dataset inhibitors of best hypotheses used to build the 3D QSAR model and the generated 3D QSAR model resulted in good PLS statistics with a regression coefficient (R2) of 0.89, predictive coefficient (Q2) of 0.88, and Pearson-R factor of 0.94 indicating its excellent predictive ability. The hits retrieved from pharmacophore-based virtual screening were subjected to docking against HDAC3 for the identification of potential inhibitors. A total of 10 hitsM1 to M10 were ranked using their scoring functions and further subject to lead optimization. The Prime MM/GBSA, AutoDock binding free energies, and ADMET studies were implemented for the selection of lead candidates. The four ligand molecules M1, M2, M3, and M4 were identified as potential leads against HDAC3 after lead optimization. The top two leads M1 and M2 were subjected to MD simulations for their stability evaluation with HDAC3. The newly designed leads M11 and M12 were identified as HDAC3 potential inhibitors from MD simulations studies. Therefore, the outcomes of the present study could provide insights into the discovery of new potential HDAC3 inhibitors with improved selectivity and activity against a variety of cancers and neurodegenerative diseases.
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Affiliation(s)
- Goverdhan Lanka
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
| | - Darakhshan Begum
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
| | - Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P. O. Box 17020, Jadavpur University, Kolkata, 700032, West Bengal, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P. O. Box 17020, Jadavpur University, Kolkata, 700032, West Bengal, India
| | - Yogeeswari P
- Computer Aided Drug Design Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, 500078, India.
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7
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Abe Y, Kofman ER, Almeida M, Ouyang Z, Ponte F, Mueller JR, Cruz-Becerra G, Sakai M, Prohaska TA, Spann NJ, Resende-Coelho A, Seidman JS, Stender JD, Taylor H, Fan W, Link VM, Cobo I, Schlachetzki JCM, Hamakubo T, Jepsen K, Sakai J, Downes M, Evans RM, Yeo GW, Kadonaga JT, Manolagas SC, Rosenfeld MG, Glass CK. RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression. Mol Cell 2023; 83:3421-3437.e11. [PMID: 37751740 PMCID: PMC10591845 DOI: 10.1016/j.molcel.2023.08.029] [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: 04/03/2023] [Revised: 07/17/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023]
Abstract
The nuclear receptor co-repressor (NCoR) complex mediates transcriptional repression dependent on histone deacetylation by histone deacetylase 3 (HDAC3) as a component of the complex. Unexpectedly, we found that signaling by the receptor activator of nuclear factor κB (RANK) converts the NCoR/HDAC3 co-repressor complex to a co-activator of AP-1 and NF-κB target genes that are required for mouse osteoclast differentiation. Accordingly, the dominant function of NCoR/HDAC3 complexes in response to RANK signaling is to activate, rather than repress, gene expression. Mechanistically, RANK signaling promotes RNA-dependent interaction of the transcriptional co-activator PGC1β with the NCoR/HDAC3 complex, resulting in the activation of PGC1β and inhibition of HDAC3 activity for acetylated histone H3. Non-coding RNAs Dancr and Rnu12, which are associated with altered human bone homeostasis, promote NCoR/HDAC3 complex assembly and are necessary for RANKL-induced osteoclast differentiation in vitro. These findings may be prototypic for signal-dependent functions of NCoR in other biological contexts.
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Affiliation(s)
- Yohei Abe
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Eric R Kofman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Maria Almeida
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Department of Orthopedic Surgery, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
| | - Zhengyu Ouyang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Filipa Ponte
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jasmine R Mueller
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Grisel Cruz-Becerra
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Mashito Sakai
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Biochemistry and Molecular Biology, Nippon Medical School Hospital, Tokyo 113-8602, Japan
| | - Thomas A Prohaska
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Ana Resende-Coelho
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jason S Seidman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Joshua D Stender
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Havilah Taylor
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Weiwei Fan
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Verena M Link
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Faculty of Biology, Department II, Ludwig-Maximilians Universität München, Planegg-Martinsried 82152, Germany
| | - Isidoro Cobo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Takao Hamakubo
- Department of Protein-Protein Interaction Research, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo 113-8602, Japan
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Juro Sakai
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Michael Downes
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ronald M Evans
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - James T Kadonaga
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Stavros C Manolagas
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Department of Orthopedic Surgery, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
| | - Michael G Rosenfeld
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.
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8
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Abdallah DI, de Araujo ED, Patel NH, Hasan LS, Moriggl R, Krämer OH, Gunning PT. Medicinal chemistry advances in targeting class I histone deacetylases. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:757-779. [PMID: 37711592 PMCID: PMC10497394 DOI: 10.37349/etat.2023.00166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/22/2023] [Indexed: 09/16/2023] Open
Abstract
Histone deacetylases (HDACs) are a class of zinc (Zn)-dependent metalloenzymes that are responsible for epigenetic modifications. HDACs are largely associated with histone proteins that regulate gene expression at the DNA level. This tight regulation is controlled by acetylation [via histone acetyl transferases (HATs)] and deacetylation (via HDACs) of histone and non-histone proteins that alter the coiling state of DNA, thus impacting gene expression as a downstream effect. For the last two decades, HDACs have been studied extensively and indicated in a range of diseases where HDAC dysregulation has been strongly correlated with disease emergence and progression-most prominently, cancer, neurodegenerative diseases, HIV, and inflammatory diseases. The involvement of HDACs as regulators in these biochemical pathways established them as an attractive therapeutic target. This review summarizes the drug development efforts exerted to create HDAC inhibitors (HDACis), specifically class I HDACs, with a focus on the medicinal chemistry, structural design, and pharmacology aspects of these inhibitors.
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Affiliation(s)
- Diaaeldin I. Abdallah
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 2E8, Canada
| | - Elvin D. de Araujo
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
| | - Naman H. Patel
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
| | - Lina S. Hasan
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
| | - Richard Moriggl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Oliver H. Krämer
- Department of Toxicology, University of Mainz Medical Center, 55131 Mainz, Germany
| | - Patrick T. Gunning
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 2E8, Canada
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9
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He R, Liu B, Geng B, Li N, Geng Q. The role of HDAC3 and its inhibitors in regulation of oxidative stress and chronic diseases. Cell Death Discov 2023; 9:131. [PMID: 37072432 PMCID: PMC10113195 DOI: 10.1038/s41420-023-01399-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 04/20/2023] Open
Abstract
HDAC3 is a specific and crucial member of the HDAC family. It is required for embryonic growth, development, and physiological function. The regulation of oxidative stress is an important factor in intracellular homeostasis and signal transduction. Currently, HDAC3 has been found to regulate several oxidative stress-related processes and molecules dependent on its deacetylase and non-enzymatic activities. In this review, we comprehensively summarize the knowledge of the relationship of HDAC3 with mitochondria function and metabolism, ROS-produced enzymes, antioxidant enzymes, and oxidative stress-associated transcription factors. We also discuss the role of HDAC3 and its inhibitors in some chronic cardiovascular, kidney, and neurodegenerative diseases. Due to the simultaneous existence of enzyme activity and non-enzyme activity, HDAC3 and the development of its selective inhibitors still need further exploration in the future.
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Affiliation(s)
- Ruyuan He
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Bohao Liu
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Boxin Geng
- School of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing, China
| | - Ning Li
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China.
| | - Qing Geng
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China.
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10
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Cheng BX, Shao GY, Li Y, Tian QQ, Wang SY, Liu F. Molecular cloning and characterisation of the PmEglin cDNA in the leech Hirudinaria sp. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01277-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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11
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Current trends in development of HDAC-based chemotherapeutics. Life Sci 2022; 308:120946. [PMID: 36096240 DOI: 10.1016/j.lfs.2022.120946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 11/20/2022]
Abstract
BACKGROUND Histone deacetylases (HDACs) are one of the essential epigenetic targets in cancer treatment. These enzymes play key roles in post-translation modification (PTM) and gene expression, and consequently, their inhibitors are about to find their place in pharmacotherapy. Most of the currently approved HDAC inhibitors (HDACIs) are wide-spectrum with poor clinical outcomes and numerous side effects. Therefore, new generations of HDAC-based chemotherapeutics with better clinical outcomes are emerging, e.g., isoform-selective inhibitors, multitargeted HDACIs, as well as HDAC degraders. AIM The review intended to introduce drug design approaches which were used for designing novel agents which can be beneficial in the process of finding new and more effective HDACI-based therapeutics. METHODS PubMed and other databases were searched for literature regarding the structure-function of HDAC isoforms, and strategies used to design HDAC inhibitors. Also, all clinical trials available from the ClinicalTrials site for years 2021-2022 were investigated. KEY FINDINGS It is expected that the future of drug discovery projects in HDAC field will concentrate mostly on issues such as isoform-selectivity, multitargeted HDAC inhibitors and HDAC degraders. Deeper knowledge of the 3D structure of HDACs complexed with inhibitors and extensive delineation of biological roles of HDACs are needed for efficient investigations leading to the discovery of novel potent inhibitors. SIGNIFICANCE Histone deacetylases (HDACs) are one of the important epigenetic targets in cancer treatment drug discovery. Comprehending the structure of HDAC isoforms along with applied drug design strategies can inspire new ideas.
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12
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Pulya S, Patel T, Paul M, Adhikari N, Banerjee S, Routholla G, Biswas S, Jha T, Ghosh B. Selective inhibition of histone deacetylase 3 by novel hydrazide based small molecules as therapeutic intervention for the treatment of cancer. Eur J Med Chem 2022; 238:114470. [DOI: 10.1016/j.ejmech.2022.114470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/14/2022] [Accepted: 05/15/2022] [Indexed: 11/25/2022]
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13
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Silencing of histone deacetylase 3 suppresses the development of esophageal squamous cell carcinoma through regulation of miR-494-mediated TGIF1. Cancer Cell Int 2022; 22:191. [PMID: 35578338 PMCID: PMC9109300 DOI: 10.1186/s12935-022-02581-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 04/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Deacetylation of histones by histone deacetylase 3 (HDAC3) acts importantly in modulating apoptosis, DNA damage and cellular progression. Herein, we aimed to unravel the functional role of HDAC3 in a lethal disease, esophageal squamous cell carcinoma (ESCC). METHODS The expression of HDAC3 in clinically collected ESCC tissues was determined by RT-qPCR and immunohistochemistry. As revealed from bioinformatics analysis, the putative relations between HDAC3 and microRNA-494 (miR-494) and between miR-494 and transforming growth factor beta (TGFβ)-inducing factor 1 (TGIF1) were further verified by chromatin immunoprecipitation and dual-luciferase reporter gene assay. Functional roles of shRNA-mediated depletion of HDAC3, miR-494 mimic and overexpressed TGIF1 were explored by gain- and loss-of-function assays with regard to ESCC cell biological behaviors. A nude mouse model of ESCC was developed for in vivo validation. RESULTS HDAC3 was highly expressed in ESCC tissues, suggestive of poor prognosis while TGIF1 was upregulated and miR-494 was downregulated. Mechanistic investigation revealed that HDAC3 inhibited miR-494 expression and TGIF1 was a direct target of miR-494. Furthermore, silencing HDAC3 or overexpressing miR-494 was demonstrated to suppress aggressive phenotypes of ESCC cells both in vitro through the activated TGFβ signaling pathway and in vivo, while TGIF1 overexpression induced opposite results. CONCLUSION Collectively, our findings provided demonstration regarding the oncogenic property of HDAC3 in ESCC via the miR-494/TGIF1/TGFβ axis.
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14
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Smalley JP, Baker IM, Pytel WA, Lin LY, Bowman KJ, Schwabe JWR, Cowley SM, Hodgkinson JT. Optimization of Class I Histone Deacetylase PROTACs Reveals that HDAC1/2 Degradation is Critical to Induce Apoptosis and Cell Arrest in Cancer Cells. J Med Chem 2022; 65:5642-5659. [PMID: 35293758 PMCID: PMC9014412 DOI: 10.1021/acs.jmedchem.1c02179] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Class I histone deacetylase (HDAC) enzymes 1, 2, and 3 organize chromatin as the catalytic subunits within seven distinct multiprotein corepressor complexes and are established drug targets. We report optimization studies of benzamide-based Von Hippel-Lindau (VHL) E3-ligase proteolysis targeting chimeras (PROTACs) and for the first time describe transcriptome perturbations resulting from these degraders. By modifying the linker and VHL ligand, we identified PROTACs 7, 9, and 22 with submicromolar DC50 values for HDAC1 and/or HDAC3 in HCT116 cells. A hook effect was observed for HDAC3 that could be negated by modifying the position of attachment of the VHL ligand to the linker. The more potent HDAC1/2 degraders correlated with greater total differentially expressed genes and enhanced apoptosis in HCT116 cells. We demonstrate that HDAC1/2 degradation by PROTACs correlates with enhanced global gene expression and apoptosis, important for the development of more efficacious HDAC therapeutics with reduced side effects.
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Affiliation(s)
- Joshua P Smalley
- Leicester Institute of Structural and Chemical Biology, School of Chemistry, University of Leicester, Leicester LE1 7RH, U.K
| | - India M Baker
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, U.K
| | - Wiktoria A Pytel
- Leicester Institute of Structural and Chemical Biology, School of Chemistry, University of Leicester, Leicester LE1 7RH, U.K
| | - Li-Ying Lin
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, U.K
| | - Karen J Bowman
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, U.K
| | - John W R Schwabe
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, U.K
| | - Shaun M Cowley
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, U.K
| | - James T Hodgkinson
- Leicester Institute of Structural and Chemical Biology, School of Chemistry, University of Leicester, Leicester LE1 7RH, U.K
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15
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Serganova I, Chakraborty S, Yamshon S, Isshiki Y, Bucktrout R, Melnick A, Béguelin W, Zappasodi R. Epigenetic, Metabolic, and Immune Crosstalk in Germinal-Center-Derived B-Cell Lymphomas: Unveiling New Vulnerabilities for Rational Combination Therapies. Front Cell Dev Biol 2022; 9:805195. [PMID: 35071240 PMCID: PMC8777078 DOI: 10.3389/fcell.2021.805195] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 11/30/2021] [Indexed: 12/24/2022] Open
Abstract
B-cell non-Hodgkin lymphomas (B-NHLs) are highly heterogenous by genetic, phenotypic, and clinical appearance. Next-generation sequencing technologies and multi-dimensional data analyses have further refined the way these diseases can be more precisely classified by specific genomic, epigenomic, and transcriptomic characteristics. The molecular and genetic heterogeneity of B-NHLs may contribute to the poor outcome of some of these diseases, suggesting that more personalized precision-medicine approaches are needed for improved therapeutic efficacy. The germinal center (GC) B-cell like diffuse large B-cell lymphomas (GCB-DLBCLs) and follicular lymphomas (FLs) share specific epigenetic programs. These diseases often remain difficult to treat and surprisingly do not respond advanced immunotherapies, despite arising in secondary lymphoid organs at sites of antigen recognition. Epigenetic dysregulation is a hallmark of GCB-DLBCLs and FLs, with gain-of-function (GOF) mutations in the histone methyltransferase EZH2, loss-of-function (LOF) mutations in histone acetyl transferases CREBBP and EP300, and the histone methyltransferase KMT2D representing the most prevalent genetic lesions driving these diseases. These mutations have the common effect to disrupt the interactions between lymphoma cells and the immune microenvironment, via decreased antigen presentation and responsiveness to IFN-γ and CD40 signaling pathways. This indicates that immune evasion is a key step in GC B-cell lymphomagenesis. EZH2 inhibitors are now approved for the treatment of FL and selective HDAC3 inhibitors counteracting the effects of CREBBP LOF mutations are under development. These treatments can help restore the immune control of GCB lymphomas, and may represent optimal candidate agents for more effective combination with immunotherapies. Here, we review recent progress in understanding the impact of mutant chromatin modifiers on immune evasion in GCB lymphomas. We provide new insights on how the epigenetic program of these diseases may be regulated at the level of metabolism, discussing the role of metabolic intermediates as cofactors of epigenetic enzymes. In addition, lymphoma metabolic adaptation can negatively influence the immune microenvironment, further contributing to the development of immune cold tumors, poorly infiltrated by effector immune cells. Based on these findings, we discuss relevant candidate epigenetic/metabolic/immune targets for rational combination therapies to investigate as more effective precision-medicine approaches for GCB lymphomas.
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Affiliation(s)
- Inna Serganova
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, United States.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Sanjukta Chakraborty
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, United States
| | - Samuel Yamshon
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, United States
| | - Yusuke Isshiki
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, United States
| | - Ryan Bucktrout
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, United States
| | - Ari Melnick
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, United States
| | - Wendy Béguelin
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, United States
| | - Roberta Zappasodi
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, United States.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, United States.,Parker Institute for Cancer Immunotherapy, San Francisco, CA, United States
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16
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Ibrahim HS, Abdelsalam M, Zeyn Y, Zessin M, Mustafa AHM, Fischer MA, Zeyen P, Sun P, Bülbül EF, Vecchio A, Erdmann F, Schmidt M, Robaa D, Barinka C, Romier C, Schutkowski M, Krämer OH, Sippl W. Synthesis, Molecular Docking and Biological Characterization of Pyrazine Linked 2-Aminobenzamides as New Class I Selective Histone Deacetylase (HDAC) Inhibitors with Anti-Leukemic Activity. Int J Mol Sci 2021; 23:ijms23010369. [PMID: 35008795 PMCID: PMC8745332 DOI: 10.3390/ijms23010369] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 12/19/2022] Open
Abstract
Class I histone deacetylases (HDACs) are key regulators of cell proliferation and they are frequently dysregulated in cancer cells. We report here the synthesis of a novel series of class-I selective HDAC inhibitors (HDACi) containing a 2-aminobenzamide moiety as a zinc-binding group connected with a central (piperazin-1-yl)pyrazine or (piperazin-1-yl)pyrimidine moiety. Some of the compounds were additionally substituted with an aromatic capping group. Compounds were tested in vitro against human HDAC1, 2, 3, and 8 enzymes and compared to reference class I HDACi (Entinostat (MS-275), Mocetinostat, CI994 and RGFP-966). The most promising compounds were found to be highly selective against HDAC1, 2 and 3 over the remaining HDAC subtypes from other classes. Molecular docking studies and MD simulations were performed to rationalize the in vitro data and to deduce a complete structure activity relationship (SAR) analysis of this novel series of class-I HDACi. The most potent compounds, including 19f, which blocks HDAC1, HDAC2, and HDAC3, as well as the selective HDAC1/HDAC2 inhibitors 21a and 29b, were selected for further cellular testing against human acute myeloid leukemia (AML) and erythroleukemic cancer (HEL) cells, taking into consideration their low toxicity against human embryonic HEK293 cells. We found that 19f is superior to the clinically tested class-I HDACi Entinostat (MS-275). Thus, 19f is a new and specific HDACi with the potential to eliminate blood cancer cells of various origins.
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Affiliation(s)
- Hany S. Ibrahim
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo 11829, Egypt
| | - Mohamed Abdelsalam
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Yanira Zeyn
- Department of Toxicology, University Medical Center, 55131 Mainz, Germany; (Y.Z.); (A.-H.M.M.); (M.A.F.)
| | - Matthes Zessin
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
- Department of Enzymology, Institute of Biochemistry, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany;
| | - Al-Hassan M. Mustafa
- Department of Toxicology, University Medical Center, 55131 Mainz, Germany; (Y.Z.); (A.-H.M.M.); (M.A.F.)
- Department of Zoology, Faculty of Science, Aswan University, Aswan 81528, Egypt
| | - Marten A. Fischer
- Department of Toxicology, University Medical Center, 55131 Mainz, Germany; (Y.Z.); (A.-H.M.M.); (M.A.F.)
| | - Patrik Zeyen
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
| | - Ping Sun
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
| | - Emre F. Bülbül
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
| | - Anita Vecchio
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
| | - Frank Erdmann
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
| | - Matthias Schmidt
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
| | - Dina Robaa
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
| | - Cyril Barinka
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 25250 Vestec, Czech Republic;
| | - Christophe Romier
- Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS, INSERM, Université de Strasbourg, CEDEX, 67404 Illkirch, France;
| | - Mike Schutkowski
- Department of Enzymology, Institute of Biochemistry, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany;
| | - Oliver H. Krämer
- Department of Toxicology, University Medical Center, 55131 Mainz, Germany; (Y.Z.); (A.-H.M.M.); (M.A.F.)
- Correspondence: (O.H.K.); (W.S.)
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
- Correspondence: (O.H.K.); (W.S.)
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17
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Depleted histone deacetylase 3 or restored microRNA-19b-1-5p facilitates recovery of spinal cord injury via inactivating JAK2/STAT3 signaling pathway. Genomics 2021; 114:110262. [PMID: 34971719 DOI: 10.1016/j.ygeno.2021.12.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/13/2021] [Accepted: 12/20/2021] [Indexed: 11/23/2022]
Abstract
We intended to discuss the influence of histone deacetylase 3 (HDAC3) on spinal cord injury (SCI) by regulating microRNA-19b-1-5p (miR-19b-1-5p) and janus kinase 2/signal transducer and activator of transcription 3 (JAK2/STAT3) pathway. In a rat model, the role of HDAC3 and miR-19b-1-5p in SCI was identified through detecting motor function, serum inflammation, pathological damage, cell apoptosis and GFAP expression. Also, by measuring GFAP expression and migration of spinal cord astrocytes, the effects of HDAC3 and miR-19b-1-5p in SCI were identified in vitro. Restoration of miR-19b-1-5p or depletion of HDAC3 attenuated motor function, inflammation, pathological damage and apoptosis, and reduced GFAP expression in the spinal cord tissue of SCI rats. Up-regulating miR-19b-1-5p or down-regulating HDAC3 decreased migration and GFAP expression of injured astrocytes. Our study presents that down-regulated HDAC3 can facilitate the recovery of SCI via inhibiting the activation of JAK2/STAT3 pathway by up-regulating miR-19b-1-5p.
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18
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Zhang L, Cao W. Histone deacetylase 3 (HDAC3) as an important epigenetic regulator of kidney diseases. J Mol Med (Berl) 2021; 100:43-51. [PMID: 34698870 DOI: 10.1007/s00109-021-02141-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/18/2021] [Accepted: 09/09/2021] [Indexed: 12/18/2022]
Abstract
Development and progression of many kidney diseases are substantially influenced by aberrant protein acetylation modifications of gene expression crucial for kidney functions. Histone deacetylase (HDAC) expression alterations are detected from renal samples of patients and animal models of various kidney diseases, and the administrations of HDAC inhibitors display impressive renal protective effects in vitro and in vivo. However, when the expression alterations of multiple HDACs occur, not all the HDACs causally affect the disease onset or progression. Identification of a single HDAC as a disease-causing factor will allow subtype-targeted intervention with less side effect. HDAC3 is a unique HDAC with distinct structural and subcellular distribution features and co-repressor dependency. HDAC3 is required for kidney development and its aberrations actively participate in many pathological processes, such as cancer, cardiovascular diseases, diabetes, and neurodegenerative disorders, and contribute significantly to the pathogenesis of kidney diseases. This review will discuss the recent studies that investigate the critical roles of HDAC3 aberrations in kidney development, renal aging, renal cell carcinoma, renal fibrosis, chronic kidney disease, polycystic kidney disease, glomerular podocyte injury, and diabetic nephropathy. These studies reveal the distinct characters of HDAC3 aberrations that act on different molecules/signaling pathways under various renal pathological conditions, which might shed lights into the epigenetic mechanisms of renal diseases and the potentially therapeutic strategies.
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Affiliation(s)
- Lijun Zhang
- Department of Nephrology, Northern Jiangsu People's Hospital, Nanjing University School of Medicine, Yangzhou, 225001, China
- Jiangsu Key Lab of Molecular Medicine, Nanjing University School of Medicine, Nanjing, 210093, China
| | - Wangsen Cao
- Department of Nephrology, Northern Jiangsu People's Hospital, Nanjing University School of Medicine, Yangzhou, 225001, China.
- Jiangsu Key Lab of Molecular Medicine, Nanjing University School of Medicine, Nanjing, 210093, China.
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19
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Dong L, Huang J, Zu P, Liu J, Gao X, Du J, Li Y. Transcription factor 3 (TCF3) combined with histone deacetylase 3 (HDAC3) down-regulates microRNA-101 to promote Burkitt lymphoma cell proliferation and inhibit apoptosis. Bioengineered 2021; 12:7995-8005. [PMID: 34658308 PMCID: PMC8806859 DOI: 10.1080/21655979.2021.1977557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
To explore the function of transcription factor 3 (TCF3) on the proliferation and apoptosis of Burkitt lymphoma cells and its mechanism. qRT-PCR was performed to determine the expression of TCF3, histone deacetylase 3 (HDAC3), and microRNA-101 (miR-101) in the Burkitt lymphoma (BL) tumor tissues and lymph node tissues with reactive lymph node hyperplasia (RLNH). We found that the expression of TCF3 and HDAC3 was up-regulated in BL tumor tissues and lymphoma cells, and the miR-101 expression was down-regulated. And TCF3 and HDAC3 were negatively correlated with the expression of miR-101, respectively. In addition, knockdown of TCF3 can inhibit BL cell proliferation, reduce cell viability and promote cell apoptosis, retain the cell cycle in the G0/G1 phase, and inhibit the expression of Akt/mTOR pathway-related proteins (p-Akt and p-mTOR). When miR-101 was overexpressed, the results were the same as when TCF3 was knocked down. Moreover, we used Co-immunoprecipitation (Co-IP) to detect the interaction between TCF3 and HDAC3, and performed the Chromatin immunoprecipitation (ChIP) experiment to detect the enrichment of TCF3 and HDAC3 in the promoter region of miR-101. We found that TCF3 can interact with HDAC3 and is enriched in the miR-101 promoter region. In conclusion, TCF3 combined with HDAC3 down-regulates the expression of miR-101, thereby promoting the proliferation of BL cells and inhibiting their apoptosis.
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Affiliation(s)
- Lihua Dong
- Department of Hematology, Henan Institute of Hematology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Jingjing Huang
- Department of Hematology, Henan Institute of Hematology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Peng Zu
- Department of Hematology, Henan Institute of Hematology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Jing Liu
- Department of Hematology, Henan Institute of Hematology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Xue Gao
- Department of Hematology, Henan Institute of Hematology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Jianwei Du
- Department of Hematology, Henan Institute of Hematology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yufu Li
- Department of Hematology, Henan Institute of Hematology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
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20
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Ning L, Rui X, Bo W, Qing G. The critical roles of histone deacetylase 3 in the pathogenesis of solid organ injury. Cell Death Dis 2021; 12:734. [PMID: 34301918 PMCID: PMC8302660 DOI: 10.1038/s41419-021-04019-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/11/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023]
Abstract
Histone deacetylase 3 (HDAC3) plays a crucial role in chromatin remodeling, which, in turn, regulates gene transcription. Hence, HDAC3 has been implicated in various diseases, including ischemic injury, fibrosis, neurodegeneration, infections, and inflammatory conditions. In addition, HDAC3 plays vital roles under physiological conditions by regulating circadian rhythms, metabolism, and development. In this review, we summarize the current knowledge of the physiological functions of HDAC3 and its role in organ injury. We also discuss the therapeutic value of HDAC3 in various diseases.
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Affiliation(s)
- Li Ning
- grid.412632.00000 0004 1758 2270Department of Thoracic Surgery, Renmin Hospital of Wuhan University, 430060 Wuhan, China
| | - Xiong Rui
- grid.412632.00000 0004 1758 2270Department of Thoracic Surgery, Renmin Hospital of Wuhan University, 430060 Wuhan, China
| | - Wang Bo
- grid.412632.00000 0004 1758 2270Department of Thoracic Surgery, Renmin Hospital of Wuhan University, 430060 Wuhan, China
| | - Geng Qing
- grid.412632.00000 0004 1758 2270Department of Thoracic Surgery, Renmin Hospital of Wuhan University, 430060 Wuhan, China
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21
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Biosimilar Interchangeability and Emerging Treatment Strategies for Inflammatory Bowel Diseases: A Commentary. GASTROENTEROLOGY INSIGHTS 2021. [DOI: 10.3390/gastroent12030026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This commentary summarizes a collection of key references published within the last ten years, and identifies pharmacologic research directions to improve treatment access and success through greater biosimilar or “follow-on” biologic utilization combined with other targeted small molecule agents that possess unique pathophysiologic mechanisms for inflammatory bowel diseases (IBD) in adult and pediatric patients. Since they are not identical to the originator or reference biologic agent, all biosimilars are not generically equivalent. However, in the US and other countries, they are considered therapeutically interchangeable if the manufacturer has demonstrated no clinically meaningful differences from the reference product. Comparisons of different clinical initiation and switching scenarios are discussed with reference to interchangeability, immunogenicity, nocebo effect, cost effectiveness, and time courses for discontinuation rates.
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22
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Ghiboub M, Elfiky AMI, de Winther MPJ, Harker NR, Tough DF, de Jonge WJ. Selective Targeting of Epigenetic Readers and Histone Deacetylases in Autoimmune and Inflammatory Diseases: Recent Advances and Future Perspectives. J Pers Med 2021; 11:336. [PMID: 33922725 PMCID: PMC8145108 DOI: 10.3390/jpm11050336] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023] Open
Abstract
Histone deacetylases (HDACs) and bromodomain-containing proteins (BCPs) play a key role in chromatin remodeling. Based on their ability to regulate inducible gene expression in the context of inflammation and cancer, HDACs and BCPs have been the focus of drug discovery efforts, and numerous small-molecule inhibitors have been developed. However, dose-limiting toxicities of the first generation of inhibitors, which typically target multiple HDACs or BCPs, have limited translation to the clinic. Over the last decade, an increasing effort has been dedicated to designing class-, isoform-, or domain-specific HDAC or BCP inhibitors, as well as developing strategies for cell-specific targeted drug delivery. Selective inhibition of the epigenetic modulators is helping to elucidate the functions of individual epigenetic proteins and has the potential to yield better and safer therapeutic strategies. In accordance with this idea, several in vitro and in vivo studies have reported the ability of more selective HDAC/BCP inhibitors to recapitulate the beneficial effects of pan-inhibitors with less unwanted adverse events. In this review, we summarize the most recent advances with these strategies, discussing advantages and limitations of these approaches as well as some therapeutic perspectives, focusing on autoimmune and inflammatory diseases.
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Affiliation(s)
- Mohammed Ghiboub
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (M.G.); (A.M.I.E.)
- Adaptive Immunity Research Unit, Medicines Research Centre, GlaxoSmithKline, Stevenage SG1 2NY, UK; (N.R.H.); (D.F.T.)
| | - Ahmed M. I. Elfiky
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (M.G.); (A.M.I.E.)
- Adaptive Immunity Research Unit, Medicines Research Centre, GlaxoSmithKline, Stevenage SG1 2NY, UK; (N.R.H.); (D.F.T.)
| | - Menno P. J. de Winther
- Department of Medical Biochemistry, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
- Department of Medicine, Institute for Cardiovascular Prevention (IPEK), 80336 Munich, Germany
| | - Nicola R. Harker
- Adaptive Immunity Research Unit, Medicines Research Centre, GlaxoSmithKline, Stevenage SG1 2NY, UK; (N.R.H.); (D.F.T.)
| | - David F. Tough
- Adaptive Immunity Research Unit, Medicines Research Centre, GlaxoSmithKline, Stevenage SG1 2NY, UK; (N.R.H.); (D.F.T.)
| | - Wouter J. de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (M.G.); (A.M.I.E.)
- Department of Surgery, University of Bonn, 53127 Bonn, Germany
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23
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Melesina J, Simoben CV, Praetorius L, Bülbül EF, Robaa D, Sippl W. Strategies To Design Selective Histone Deacetylase Inhibitors. ChemMedChem 2021; 16:1336-1359. [PMID: 33428327 DOI: 10.1002/cmdc.202000934] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Indexed: 12/15/2022]
Abstract
This review classifies drug-design strategies successfully implemented in the development of histone deacetylase (HDAC) inhibitors, which have many applications including cancer treatment. Our focus is on especially demanded selective HDAC inhibitors and their structure-activity relationships in relation to corresponding protein structures. The main part of the paper is divided into six subsections each narrating how optimization of one of six structural features can influence inhibitor selectivity. It starts with the impact of the zinc binding group on selectivity, continues with the optimization of the linker placed in the substrate binding tunnel as well as the adjustment of the cap group interacting with the surface of the protein, and ends with the addition of groups targeting class-specific sub-pockets: the side-pocket-, lower-pocket- and foot-pocket-targeting groups. The review is rounded off with a conclusion and an outlook on the future of HDAC inhibitor design.
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Affiliation(s)
- Jelena Melesina
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
| | - Conrad V Simoben
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
| | - Lucas Praetorius
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
| | - Emre F Bülbül
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
| | - Dina Robaa
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
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24
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Su M, Gong X, Liu F. An update on the emerging approaches for histone deacetylase (HDAC) inhibitor drug discovery and future perspectives. Expert Opin Drug Discov 2021; 16:745-761. [PMID: 33530771 DOI: 10.1080/17460441.2021.1877656] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION HDACs catalyze the removal of acetyl groups from the ε-N-acetylated lysine residues of various protein substrates including both histone and nonhistone proteins. Different HDACs have distinct biological functions and are recruited to specific regions of the genome. HDAC inhibitors have attracted much attention in recent decades; indeed, there have been more than thirty HDAC inhibitors investigated in clinic trials with five approvals being achieved. AREAS COVERED This review covers the emerging approaches for HDAC inhibitor drug discovery from the past five years and includes discussion of structure-based rational design, isoform selectivity, and dual mechanism/multi-targeting. Chemical structures in addition to the in vitro and in vivo inhibiting activity of these compounds have also been discussed. EXPERT OPINION The exact role and biological functions of HDACs is still under investigation with a variety of HDAC inhibitors having been designed and evaluated. HDAC inhibitors have shown promise in treating cancer, AD, metabolic disease, viral infection, and multiple sclerosis, but there is still a lot of room for clinical improvement. In the future, more efforts should be put into (i) HDAC isoform identification (ii) the optimization of selectivity, activity, and pharmacokinetics; and (iii) unconventional approaches for discovering different effective scaffolds and pharmacophores.
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Affiliation(s)
- Ma Su
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University, Suzhou, PR China
| | - Xingyu Gong
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University, Suzhou, PR China
| | - Feng Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University, Suzhou, PR China
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25
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Luo Y, Li H. Structure-Based Inhibitor Discovery of Class I Histone Deacetylases (HDACs). Int J Mol Sci 2020; 21:E8828. [PMID: 33266366 PMCID: PMC7700698 DOI: 10.3390/ijms21228828] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 12/17/2022] Open
Abstract
Class I histone deacetylases (HDACs) are promising targets for epigenetic therapies for a range of diseases such as cancers, inflammations, infections and neurological diseases. Although six HDAC inhibitors are now licensed for clinical treatments, they are all pan-inhibitors with little or no HDAC isoform selectivity, exhibiting undesirable side effects. A major issue with the currently available HDAC inhibitors is that they have limited specificity and target multiple deacetylases. Except for HDAC8, Class I HDACs (1, 2 and 3) are recruited to large multiprotein complexes to function. Therefore, there are rising needs to develop new, hopefully, therapeutically efficacious HDAC inhibitors with isoform or complex selectivity. Here, upon the introduction of the structures of Class I HDACs and their complexes, we provide an up-to-date overview of the structure-based discovery of Class I HDAC inhibitors, including pan-, isoform-selective and complex-specific inhibitors, aiming to provide an insight into the discovery of additional HDAC inhibitors with greater selectivity, specificity and therapeutic utility.
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Affiliation(s)
- Yuxiang Luo
- School of Pharmaceutical Sciences, Sun Yat-sen University, No.132 Wai Huan Dong lu, Guangzhou Higher Education Mega Center, Guangzhou 510006, Guangdong, China;
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, No.132 Wai Huan Dong lu, Guangzhou Higher Education Mega Center, Guangzhou 510006, Guangdong, China;
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, Guangdong, China
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26
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Sarkar R, Banerjee S, Amin SA, Adhikari N, Jha T. Histone deacetylase 3 (HDAC3) inhibitors as anticancer agents: A review. Eur J Med Chem 2020; 192:112171. [DOI: 10.1016/j.ejmech.2020.112171] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/18/2020] [Accepted: 02/19/2020] [Indexed: 01/18/2023]
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Krieger V, Hamacher A, Cao F, Stenzel K, Gertzen CGW, Schäker-Hübner L, Kurz T, Gohlke H, Dekker FJ, Kassack MU, Hansen FK. Synthesis of Peptoid-Based Class I-Selective Histone Deacetylase Inhibitors with Chemosensitizing Properties. J Med Chem 2019; 62:11260-11279. [DOI: 10.1021/acs.jmedchem.9b01489] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Viktoria Krieger
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Alexandra Hamacher
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Fangyuan Cao
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katharina Stenzel
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Christoph G. W. Gertzen
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute for Complex Systems - Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52425 Jülich, Germany
- Center for Structural Studies (CSS), Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Linda Schäker-Hübner
- Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Medical Faculty, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany
| | - Thomas Kurz
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute for Complex Systems - Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52425 Jülich, Germany
| | - Frank J. Dekker
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Matthias U. Kassack
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Finn K. Hansen
- Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Medical Faculty, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany
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28
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The inflammatory effect of epigenetic factors and modifications in type 2 diabetes. Inflammopharmacology 2019; 28:345-362. [PMID: 31707555 DOI: 10.1007/s10787-019-00663-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/30/2019] [Indexed: 02/06/2023]
Abstract
Inflammation has a central role in the etiology of type 2 diabetes (T2D) and its complications. Both genetic and epigenetic factors have been implicated in the development of T2D-associated inflammation. Epigenetic mechanisms regulate the function of several components of the immune system. Diabetic conditions trigger aberrant epigenetic alterations that contribute to the progression of insulin resistance and β-cell dysfunction by induction of inflammatory responses. Thus, targeting epigenetic factors and modifications, as one of the underlying causes of inflammation, could lead to the development of novel immune-based strategies for the treatment of T2D. The aim of this review is to provide an overview of the epigenetic mechanisms involved in the propagation and perpetuation of chronic inflammation in T2D. We also discuss the possible anti-inflammatory approaches that target epigenetic factors for the treatment of T2D.
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29
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Design, Synthesis, and Docking Study of Acyl Thiourea Derivatives as Possible Histone Deacetylase Inhibitors with a Novel Zinc Binding Group. Sci Pharm 2019. [DOI: 10.3390/scipharm87040028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Histone deacetylase inhibitors with zinc binding groups often exhibit drawbacks like non-selectivity or toxic effects. Thus, there are continuous efforts to modify the currently available inhibitors or to discover new derivatives to overcome these problems. One approach is to synthesize new compounds with novel zinc binding groups. The present study describes the utilization of acyl thiourea functionality, known to possess the ability to complex with metals, to be a novel zinc binding group incorporated into the designed histone deacetylase inhibitors. N-adipoyl monoanilide thiourea (4) and N-pimeloyl monoanilide thiourea (5) have been synthesized and characterized successfully. They showed inhibition of growth of human colon adenocarcinoma and mouse hepatoblastoma cells with low cytotoxic effect against normal human breast cells. Their binding mode to the active site of several histone deacetylases has been studied by docking and the results gave a preliminary indication that they could be successful histone deacetylase inhibitors.
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30
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Zwinderman MRH, de Weerd S, Dekker FJ. Targeting HDAC Complexes in Asthma and COPD. EPIGENOMES 2019; 3:19. [PMID: 34968229 PMCID: PMC8594684 DOI: 10.3390/epigenomes3030019] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/02/2019] [Accepted: 09/04/2019] [Indexed: 01/08/2023] Open
Abstract
Around three million patients die due to airway inflammatory diseases each year. The most notable of these diseases are asthma and chronic obstructive pulmonary disease (COPD). Therefore, new therapies are urgently needed. Promising targets are histone deacetylases (HDACs), since they regulate posttranslational protein acetylation. Over a thousand proteins are reversibly acetylated, and acetylation critically influences aberrant intracellular signaling pathways in asthma and COPD. The diverse set of selective and non-selective HDAC inhibitors used in pre-clinical models of airway inflammation show promising results, but several challenges still need to be overcome. One such challenge is the design of HDAC inhibitors with unique selectivity profiles, such as selectivity towards specific HDAC complexes. Novel strategies to disrupt HDAC complexes should be developed to validate HDACs further as targets for new anti-inflammatory pulmonary treatments.
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Affiliation(s)
| | | | - Frank J. Dekker
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, 9713 AV Groningen, The Netherlands (M.R.H.Z.) (S.d.W.)
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31
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Stamatovic SM, Phillips CM, Martinez-Revollar G, Keep RF, Andjelkovic AV. Involvement of Epigenetic Mechanisms and Non-coding RNAs in Blood-Brain Barrier and Neurovascular Unit Injury and Recovery After Stroke. Front Neurosci 2019; 13:864. [PMID: 31543756 PMCID: PMC6732937 DOI: 10.3389/fnins.2019.00864] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/31/2019] [Indexed: 12/13/2022] Open
Abstract
Cessation of blood flow leads to a complex cascade of pathophysiological events at the blood-vascular-parenchymal interface which evolves over time and space, and results in damage to neural cells and edema formation. Cerebral ischemic injury evokes a profound and deleterious upregulation in inflammation and triggers multiple cell death pathways, but it also induces a series of the events associated with regenerative responses, including vascular remodeling, angiogenesis, and neurogenesis. Emerging evidence suggests that epigenetic reprograming could play a pivotal role in ongoing post-stroke neurovascular unit (NVU) changes and recovery. This review summarizes current knowledge about post-stroke recovery processes at the NVU, as well as epigenetic mechanisms and modifiers (e.g., DNA methylation, histone modifying enzymes and microRNAs) associated with stroke injury, and NVU repair. It also discusses novel drug targets and therapeutic strategies for enhancing post-stroke recovery.
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Affiliation(s)
- Svetlana M Stamatovic
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Chelsea M Phillips
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, United States
| | | | - Richard F Keep
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI, United States.,Department of Molecular Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Anuska V Andjelkovic
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, United States.,Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI, United States
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32
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Epigenetics and meditation. Curr Opin Psychol 2019; 28:76-80. [DOI: 10.1016/j.copsyc.2018.11.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/09/2018] [Accepted: 11/17/2018] [Indexed: 12/13/2022]
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33
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Bresciani A, Ontoria JM, Biancofiore I, Cellucci A, Ciammaichella A, Di Marco A, Ferrigno F, Francone A, Malancona S, Monteagudo E, Nizi E, Pace P, Ponzi S, Rossetti I, Veneziano M, Summa V, Harper S. Improved Selective Class I HDAC and Novel Selective HDAC3 Inhibitors: Beyond Hydroxamic Acids and Benzamides. ACS Med Chem Lett 2019; 10:481-486. [PMID: 30996783 DOI: 10.1021/acsmedchemlett.8b00517] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 11/27/2018] [Indexed: 12/11/2022] Open
Abstract
The application of class I HDAC inhibitors as cancer therapies is well established, but more recently their development for nononcological indications has increased. We report here on the generation of improved class I selective human HDAC inhibitors based on an ethylketone zinc binding group (ZBG) in place of the hydroxamic acid that features the majority of HDAC inhibitors. We also describe a novel set of HDAC3 isoform selective inhibitors that show stronger potency and selectivity than the most commonly used HDAC3 selective tool compound RGFP966. These compounds are again based on an alternative ZBG with respect to the ortho-anilide that is featured in HDAC3 selective compounds reported to date.
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Affiliation(s)
- Alberto Bresciani
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Jesus M. Ontoria
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | | | | | | | - Annalise Di Marco
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Federica Ferrigno
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | | | - Savina Malancona
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Edith Monteagudo
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Emanuela Nizi
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Paola Pace
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Simona Ponzi
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Ilaria Rossetti
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Maria Veneziano
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Vincenzo Summa
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Steven Harper
- IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
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34
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Apoptosis Induction byHistone Deacetylase Inhibitors in Cancer Cells: Role of Ku70. Int J Mol Sci 2019; 20:ijms20071601. [PMID: 30935057 PMCID: PMC6480544 DOI: 10.3390/ijms20071601] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/16/2019] [Accepted: 03/18/2019] [Indexed: 01/02/2023] Open
Abstract
Histone deacetylases (HDACs) are a group of enzymes that regulate gene transcription by controlling deacetylation of histones and non-histone proteins. Overexpression of HDACs is found in some types of tumors and predicts poor prognosis. Five HDAC inhibitors are approved for the treatment of cutaneous T-cell lymphoma, peripheral T-cell lymphoma, and multiple myeloma. Treatment with HDAC inhibitors regulates gene expression with increased acetylated histones with unconfirmed connection with therapy. Apoptosis is a key mechanism by which HDAC inhibitors selectively kill cancer cells, probably due to acetylation of non-histone proteins. Ku70 is a protein that repairs DNA breaks and stabilizes anti-apoptotic protein c-FLIP and proapoptotic protein Bax, which is regulated by acetylation. HDAC inhibitors induce Ku70 acetylation with repressed c-FLIP and activated Bax in cancer cells. Current studies indicate that Ku70 is a potential target of HDAC inhibitors and plays an important role during the induction of apoptosis.
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35
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Dziewulska A, Dobosz AM, Dobrzyn A. High-Throughput Approaches onto Uncover (Epi)Genomic Architecture of Type 2 Diabetes. Genes (Basel) 2018; 9:E374. [PMID: 30050001 PMCID: PMC6115814 DOI: 10.3390/genes9080374] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 07/20/2018] [Accepted: 07/23/2018] [Indexed: 12/20/2022] Open
Abstract
Type 2 diabetes (T2D) is a complex disorder that is caused by a combination of genetic, epigenetic, and environmental factors. High-throughput approaches have opened a new avenue toward a better understanding of the molecular bases of T2D. A genome-wide association studies (GWASs) identified a group of the most common susceptibility genes for T2D (i.e., TCF7L2, PPARG, KCNJ1, HNF1A, PTPN1, and CDKAL1) and illuminated novel disease-causing pathways. Next-generation sequencing (NGS)-based techniques have shed light on rare-coding genetic variants that account for an appreciable fraction of T2D heritability (KCNQ1 and ADRA2A) and population risk of T2D (SLC16A11, TPCN2, PAM, and CCND2). Moreover, single-cell sequencing of human pancreatic islets identified gene signatures that are exclusive to α-cells (GCG, IRX2, and IGFBP2) and β-cells (INS, ADCYAP1, INS-IGF2, and MAFA). Ongoing epigenome-wide association studies (EWASs) have progressively defined links between epigenetic markers and the transcriptional activity of T2D target genes. Differentially methylated regions were found in TCF7L2, THADA, KCNQ1, TXNIP, SOCS3, SREBF1, and KLF14 loci that are related to T2D. Additionally, chromatin state maps in pancreatic islets were provided and several non-coding RNAs (ncRNA) that are key to T2D pathogenesis were identified (i.e., miR-375). The present review summarizes major progress that has been made in mapping the (epi)genomic landscape of T2D within the last few years.
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Affiliation(s)
- Anna Dziewulska
- Laboratory of Cell Signaling and Metabolic Disorders, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland.
| | - Aneta M Dobosz
- Laboratory of Cell Signaling and Metabolic Disorders, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland.
| | - Agnieszka Dobrzyn
- Laboratory of Cell Signaling and Metabolic Disorders, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland.
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