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Hsu KC, Huang YY, Chu JC, Huang YW, Hu JL, Lin TE, Yen SC, Weng JR, Huang WJ. Synthesis and biological evaluation of ortho-phenyl phenylhydroxamic acids containing phenothiazine with improved selectivity for class IIa histone deacetylases. J Enzyme Inhib Med Chem 2024; 39:2406025. [PMID: 39316378 PMCID: PMC11423540 DOI: 10.1080/14756366.2024.2406025] [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: 01/16/2024] [Revised: 08/27/2024] [Accepted: 09/13/2024] [Indexed: 09/25/2024] Open
Abstract
Class IIa histone deacetylases (HDACs) have been linked to tumorigenesis in various cancers. Previously, we designed phenylhydroxamic acid LH4f as a potent class IIa HDAC inhibitor. However, it also unselectively inhibited class I and class IIb HDACs. To enhance the compound's selectivity towards class IIa HDACs, the ortho-phenyl group from the selective HDAC7 inhibitor 1 is incorporated into ortho position of the phenylhydroxamic acid in LH4f. Compared to LH4f, most resulting compounds displayed substantially improved selectivity towards the class IIa HDACs. Notably, compound 7 g exhibited the strongest HDAC9 inhibition with an IC50 value of 40 nM. Molecular modelling further identified the key interactions of compound 7 g bound to HDAC9. Compound 7 g significantly inhibited several human cancer cells, induced apoptosis, modulated caspase-related proteins as well as p38, and caused DNA damage. These findings suggest the potential of class IIa HDAC inhibitors as lead compounds for the development of cancer therapeutics.
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Affiliation(s)
- Kai-Cheng Hsu
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Yun-Yi Huang
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Jung-Chun Chu
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Yu-Wen Huang
- Graduate Institute of Pharmacognosy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Jing-Lan Hu
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Tony Eight Lin
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Shih-Chung Yen
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong, China
| | - Jing-Ru Weng
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Wei-Jan Huang
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Graduate Institute of Pharmacognosy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
- School of Pharmacy, Taipei Medical University, Taipei, Taiwan
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2
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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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3
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Han H, Feng X, He T, Wu Y, He T, Yue Z, Zhou W. Discussion on structure classification and regulation function of histone deacetylase and their inhibitor. Chem Biol Drug Des 2024; 103:e14366. [PMID: 37776270 DOI: 10.1111/cbdd.14366] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 10/02/2023]
Abstract
Epigenetic regulation of genes through posttranslational regulation of proteins is a well-explored approach for disease treatment, particularly in cancer chemotherapy. Histone deacetylases have shown significant potential as effective drug targets in therapeutic studies aiming to restore epigenetic normality in oncology. Besides their role in modifying histones, histone deacetylases can also catalyze the deacetylation of various nonhistone proteins and participate in the regulation of multiple biological processes. This paper provides a review of the classification, structure, and functional characteristics of the four classes of human histone deacetylases. The increasing abundance of structural information on HDACs has led to the gradual elucidation of structural differences among subgroups and subtypes. This has provided a reasonable explanation for the selectivity of certain HDAC inhibitors. Currently, the US FDA has approved a total of six HDAC inhibitors for marketing, primarily for the treatment of various hematological tumors and a few solid tumors. These inhibitors all have a common pharmacodynamic moiety consisting of three parts: CAP, ZBG, and Linker. In this paper, the structure-effect relationship of HDAC inhibitors is explored by classifying the six HDAC inhibitors into three main groups: isohydroxamic acids, benzamides, and cyclic peptides, based on the type of inhibitor ZBG. However, there are still many questions that need to be answered in this field. In this paper, the structure-functional characteristics of HDACs and the structural information of the pharmacophore model and enzyme active region of HDAC is are considered, which can help to understand the inhibition mechanism of the compounds as well as the rational design of HDACs. This paper integrates the structural-functional characteristics of HDACs as well as the pharmacophore model of HDAC is and the structural information of the enzymatic active region, which not only contributes to the understanding of the inhibition mechanism of the compounds, but also provides a basis for the rational design of HDAC inhibitors.
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Affiliation(s)
- Han Han
- Department of Biochemistry and Molecular Biology, Shenyang Medical College, Shenyang City, P. R. China
| | - Xue Feng
- Department of Pathogen Biology, Shenyang Medical College, Shenyang City, P. R. China
| | - Ting He
- Department of Pathogen Biology, Shenyang Medical College, Shenyang City, P. R. China
| | - Yingfan Wu
- Department of Pathogen Biology, Shenyang Medical College, Shenyang City, P. R. China
| | - Tianmei He
- Department of Pathogen Biology, Shenyang Medical College, Shenyang City, P. R. China
| | - Ziwen Yue
- Department of Pathogen Biology, Shenyang Medical College, Shenyang City, P. R. China
| | - Weiqiang Zhou
- Department of Pathogen Biology, Shenyang Medical College, Shenyang City, P. R. China
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4
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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: 4] [Impact Index Per Article: 4.0] [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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5
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Moi D, Bonanni D, Belluti S, Linciano P, Citarella A, Franchini S, Sorbi C, Imbriano C, Pinzi L, Rastelli G. Discovery of potent pyrrolo-pyrimidine and purine HDAC inhibitors for the treatment of advanced prostate cancer. Eur J Med Chem 2023; 260:115730. [PMID: 37633202 DOI: 10.1016/j.ejmech.2023.115730] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/01/2023] [Accepted: 08/14/2023] [Indexed: 08/28/2023]
Abstract
The development of drugs for the treatment of advanced prostate cancer (PCA) remains a challenging task. In this study we have designed, synthesized and tested twenty-nine novel HDAC inhibitors based on three different zinc binding groups (trifluoromethyloxadiazole, hydroxamic acid, and 2-mercaptoacetamide). These warheads were conveniently tethered to variously substituted phenyl linkers and decorated with differently substituted pyrrolo-pyrimidine and purine cap groups. Remarkably, most of the compounds showed nanomolar inhibitory activity against HDAC6. To provide structural insights into the Structure-Activity Relationships (SAR) of the investigated compounds, docking of representative inhibitors and molecular dynamics of HDAC6-inhibitor complexes were performed. Compounds of the trifluoromethyloxadiazole and hydroxamic acid series exhibited promising anti-proliferative activities, HDAC6 targeting in PCA cells, and in vitro tumor selectivity. Representative compounds of the two series were tested for solubility, cell permeability and metabolic stability, demonstrating favorable in vitro drug-like properties. The more interesting compounds were subjected to migration assays, which revealed that compound 13 and, to a lesser extent, compound 15 inhibited the invasive behaviour of androgen-sensitive and -insensitive advanced prostate cancer cells. Compound 13 was profiled against all HDACs and found to inhibit all members of class II HDACs (except for HDAC10) and to be selective with respect to class I and class IV HDACs. Overall, compound 13 combines potent inhibitory activity and class II selectivity with favorable drug-like properties, an excellent anti-proliferative activity and marked anti-migration properties on PCA cells, making it an excellent lead candidate for further optimization.
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Affiliation(s)
- Davide Moi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Davide Bonanni
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Silvia Belluti
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Pasquale Linciano
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Andrea Citarella
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Silvia Franchini
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Claudia Sorbi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Carol Imbriano
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Luca Pinzi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy.
| | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy.
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6
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Sinatra L, Yang J, Schliehe-Diecks J, Dienstbier N, Vogt M, Gebing P, Bachmann LM, Sönnichsen M, Lenz T, Stühler K, Schöler A, Borkhardt A, Bhatia S, Hansen FK. Solid-Phase Synthesis of Cereblon-Recruiting Selective Histone Deacetylase 6 Degraders (HDAC6 PROTACs) with Antileukemic Activity. J Med Chem 2022; 65:16860-16878. [PMID: 36473103 DOI: 10.1021/acs.jmedchem.2c01659] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this work, we utilized the proteolysis targeting chimera (PROTAC) technology to achieve the chemical knock-down of histone deacetylase 6 (HDAC6). Two series of cereblon-recruiting PROTACs were synthesized via a solid-phase parallel synthesis approach, which allowed the rapid preparation of two HDAC6 degrader mini libraries. The PROTACs were either based on an unselective vorinostat-like HDAC ligand or derived from a selective HDAC6 inhibitor. Notably, both PROTAC series demonstrated selective degradation of HDAC6 in leukemia cell lines. The best degraders from each series (denoted A6 and B4) were capable of degrading HDAC6 via ternary complex formation and the ubiquitin-proteasome pathway, with DC50 values of 3.5 and 19.4 nM, respectively. PROTAC A6 demonstrated promising antiproliferative activity via inducing apoptosis in myeloid leukemia cell lines. These findings highlight the potential of this series of degraders as effective pharmacological tools for the targeted degradation of HDAC6.
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Affiliation(s)
- Laura Sinatra
- Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Jing Yang
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany.,Department of Medicine, Yangzhou Polytechnic College, West Wenchang Road 458, Yangzhou, 225009, P.R. China
| | - Julian Schliehe-Diecks
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Niklas Dienstbier
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Melina Vogt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Philip Gebing
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Luisa M Bachmann
- Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Melf Sönnichsen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Thomas Lenz
- Molecular Proteomics Laboratory, Biological Medical Research Center, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Kai Stühler
- Institute for Molecular Medicine, Proteome Research, University Hospital and Medical Faculty, Hein-rich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Andrea Schöler
- Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Sanil Bhatia
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Finn K Hansen
- Pharmaceutical Institute, Department of Pharmaceutical and Cell Biological Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
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7
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Vong P, Ouled-Haddou H, Garçon L. Histone Deacetylases Function in the Control of Early Hematopoiesis and Erythropoiesis. Int J Mol Sci 2022; 23:9790. [PMID: 36077192 PMCID: PMC9456231 DOI: 10.3390/ijms23179790] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Numerous studies have highlighted the role of post-translational modifications in the regulation of cell proliferation, differentiation and death. Among these modifications, acetylation modifies the physicochemical properties of proteins and modulates their activity, stability, localization and affinity for partner proteins. Through the deacetylation of a wide variety of functional and structural, nuclear and cytoplasmic proteins, histone deacetylases (HDACs) modulate important cellular processes, including hematopoiesis, during which different HDACs, by controlling gene expression or by regulating non-histone protein functions, act sequentially to provide a fine regulation of the differentiation process both in early hematopoietic stem cells and in more mature progenitors. Considering that HDAC inhibitors represent promising targets in cancer treatment, it is necessary to decipher the role of HDACs during hematopoiesis which could be impacted by these therapies. This review will highlight the main mechanisms by which HDACs control the hematopoietic stem cell fate, particularly in the erythroid lineage.
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Affiliation(s)
- Pascal Vong
- Université Picardie Jules Verne, HEMATIM UR4666, 80000 Amiens, France
| | | | - Loïc Garçon
- Université Picardie Jules Verne, HEMATIM UR4666, 80000 Amiens, France
- Service d’Hématologie Biologique, Centre Hospitalier Universitaire, CEDEX 1, 80054 Amiens, France
- Laboratoire de Génétique Constitutionnelle, Centre Hospitalier Universitaire, CEDEX 1, 80054 Amiens, France
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8
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Lisi S, Trovato M, Vitaloni O, Fantini M, Chirichella M, Tognini P, Cornuti S, Costa M, Groth M, Cattaneo A. Acetylation-Specific Interference by Anti-Histone H3K9ac Intrabody Results in Precise Modulation of Gene Expression. Int J Mol Sci 2022; 23:ijms23168892. [PMID: 36012156 PMCID: PMC9408029 DOI: 10.3390/ijms23168892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/01/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022] Open
Abstract
Among Histone post-translational modifications (PTMs), lysine acetylation plays a pivotal role in the epigenetic regulation of gene expression, mediated by chromatin modifying enzymes. Due to their activity in physiology and pathology, several chemical compounds have been developed to inhibit the function of these proteins. However, the pleiotropy of these classes of proteins represents a weakness of epigenetic drugs. Ideally, a new generation of epigenetic drugs should target with molecular precision individual acetylated lysines on the target protein. We exploit a PTM-directed interference, based on an intrabody (scFv-58F) that selectively binds acetylated lysine 9 of histone H3 (H3K9ac), to test the hypothesis that targeting H3K9ac yields more specific effects than inhibiting the corresponding HAT enzyme that installs that PTM. In yeast scFv-58F modulates, gene expression in a more specific way, compared to two well-established HAT inhibitors. This PTM-specific interference modulated expression of genes involved in ribosome biogenesis and function. In mammalian cells, the scFv-58F induces exclusive changes in the H3K9ac-dependent expression of specific genes. These results suggest the H3K9ac-specific intrabody as the founder of a new class of molecules to directly target histone PTMs, inverting the paradigm from inhibiting the writer enzyme to acting on the PTM.
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Affiliation(s)
- Simonetta Lisi
- Bio@SNS Laboratory, Scuola Normale Superiore, 56126 Pisa, Italy
| | - Matteo Trovato
- Bio@SNS Laboratory, Scuola Normale Superiore, 56126 Pisa, Italy
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | | | - Marco Fantini
- Bio@SNS Laboratory, Scuola Normale Superiore, 56126 Pisa, Italy
| | | | - Paola Tognini
- Bio@SNS Laboratory, Scuola Normale Superiore, 56126 Pisa, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy
| | - Sara Cornuti
- Bio@SNS Laboratory, Scuola Normale Superiore, 56126 Pisa, Italy
| | - Mario Costa
- Institute of Neurosciences, Consiglio Nazionale Delle Ricerche, 56124 Pisa, Italy
| | - Marco Groth
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Antonino Cattaneo
- Bio@SNS Laboratory, Scuola Normale Superiore, 56126 Pisa, Italy
- Correspondence: ; Tel.: +39-050-509320
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9
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Kumbhar N, Nimal S, Barale S, Kamble S, Bavi R, Sonawane K, Gacche R. Identification of novel leads as potent inhibitors of HDAC3 using ligand-based pharmacophore modeling and MD simulation. Sci Rep 2022; 12:1712. [PMID: 35110603 PMCID: PMC8810932 DOI: 10.1038/s41598-022-05698-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/03/2022] [Indexed: 02/08/2023] Open
Abstract
In the landscape of epigenetic regulation, histone deacetylase 3 (HDAC3) has emerged as a prominent therapeutic target for the design and development of candidate drugs against various types of cancers and other human disorders. Herein, we have performed ligand-based pharmacophore modeling, virtual screening, molecular docking, and MD simulations to design potent and selective inhibitors against HDAC3. The predicted best pharmacophore model 'Hypo 1' showed excellent correlation (R2 = 0.994), lowest RMSD (0.373), lowest total cost value (102.519), and highest cost difference (124.08). Hypo 1 consists of four salient pharmacophore features viz. one hydrogen bond acceptor (HBA), one ring aromatic (RA), and two hydrophobic (HYP). Hypo 1 was validated by Fischer's randomization with a 95% of confidence level and the external test set of 60 compounds with a good correlation coefficient (R2 = 0.970). The virtual screening of chemical databases, drug-like properties calculations followed by molecular docking resulted in identifying 22 representative hit compounds. Performed 50 ns of MD simulations on top three hits were retained the salient π-stacking, Zn2+ coordination, hydrogen bonding, and hydrophobic interactions with catalytic residues from the active site pocket of HDAC3. Total binding energy calculated by MM-PBSA showed that the Hit 1 and Hit 2 formed stable complexes with HDAC3 as compared to reference TSA. Further, the PLIP analysis showed a close resemblance between the salient pharmacophore features of Hypo 1 and the presence of molecular interactions in co-crystallized FDA-approved drugs. We conclude that the screened hit compounds may act as potent inhibitors of HDAC3 and further preclinical and clinical studies may pave the way for developing them as effective therapeutic agents for the treatment of different cancers and neurodegenerative disorders.
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Affiliation(s)
- Navanath Kumbhar
- Department of Biotechnology, Savitribai Phule Pune University Pune, Pune, Maharashtra (MS), 411007, India
| | - Snehal Nimal
- Department of Biotechnology, Savitribai Phule Pune University Pune, Pune, Maharashtra (MS), 411007, India
| | - Sagar Barale
- Department of Microbiology, Shivaji University, Kolhapur, Maharashtra (MS), 416004, India
| | - Subodh Kamble
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, Maharashtra (MS), 416004, India
| | - Rohit Bavi
- School of Chemical Science, Punyashlok Ahilyadevi Holkar Solapur University, Solapur, Maharashtra (MS), 413255, India
| | - Kailas Sonawane
- Department of Microbiology, Shivaji University, Kolhapur, Maharashtra (MS), 416004, India
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, Maharashtra (MS), 416004, India
| | - Rajesh Gacche
- Department of Biotechnology, Savitribai Phule Pune University Pune, Pune, Maharashtra (MS), 411007, India.
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10
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Collins JE, Lee JW, Bohmer MJ, Welden JD, Arshadi AK, Du L, Cichewicz RH, Chakrabarti D. Cyclic Tetrapeptide HDAC Inhibitors with Improved Plasmodium falciparum Selectivity and Killing Profile. ACS Infect Dis 2021; 7:2889-2903. [PMID: 34491031 DOI: 10.1021/acsinfecdis.1c00341] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cyclic tetrapeptide histone deacetylase inhibitors represent a promising class of antiplasmodial agents that epigenetically disrupt a wide range of cellular processes in Plasmodium falciparum. Unfortunately, certain limitations, including reversible killing effects and host cell toxicity, prevented these inhibitors from further development and clinical use as antimalarials. In this study, we present a series of cyclic tetrapeptide analogues derived primarily from the fungus Wardomyces dimerus that inhibit P. falciparum with low nanomolar potency and high selectivity. This cyclic tetrapeptide scaffold was diversified further via semisynthesis, leading to the identification of several key structural changes that positively impacted the selectivity, potency, and in vitro killing profiles of these compounds. We confirmed their effectiveness as HDAC inhibitors through the inhibition of PfHDAC1 catalytic activity, in silico modeling, and the hyperacetylation of histone H4. Additional analysis revealed the in vitro inhibition of the most active epoxide-containing analogue was plasmodistatic, exhibiting reversible inhibitory effects upon compound withdrawal after 24 or 48 h. In contrast, one of the new diacetyloxy semisynthetic analogues, CTP-NPDG 19, displayed a rapid and irreversible action against the parasite following compound exposure for 24 h.
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Affiliation(s)
- Jennifer E. Collins
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, 12722 Research Parkway, Orlando, Florida 32826, United States
| | - Jin Woo Lee
- Department of Chemistry and Biochemistry, Institute for Natural Products Applications & Research Technologies, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Monica J. Bohmer
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, 12722 Research Parkway, Orlando, Florida 32826, United States
| | - Joshua D. Welden
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, 12722 Research Parkway, Orlando, Florida 32826, United States
| | - Arash K. Arshadi
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, 12722 Research Parkway, Orlando, Florida 32826, United States
| | - Lin Du
- Department of Chemistry and Biochemistry, Institute for Natural Products Applications & Research Technologies, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Robert H. Cichewicz
- Department of Chemistry and Biochemistry, Institute for Natural Products Applications & Research Technologies, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Debopam Chakrabarti
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, 12722 Research Parkway, Orlando, Florida 32826, United States
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11
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Bonanni D, Citarella A, Moi D, Pinzi L, Bergamini E, Rastelli G. Dual Targeting Strategies On Histone Deacetylase 6 (HDAC6) And Heat Shock Protein 90 (Hsp90). Curr Med Chem 2021; 29:1474-1502. [PMID: 34477503 DOI: 10.2174/0929867328666210902145102] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 07/08/2021] [Accepted: 07/23/2021] [Indexed: 11/22/2022]
Abstract
The design of multi-target drugs acting simultaneously on multiple signaling pathways is a growing field in medicinal chemistry, especially for the treatment of complex diseases such as cancer. Histone deacetylase 6 (HDAC6) is an established anticancer drug target involved in tumor cells transformation. Being an epigenetic enzyme at the interplay of many biological processes, HDAC6 has become an attractive target for polypharmacology studies aimed at improving therapeutic efficacy of anticancer drugs. For example, the molecular chaperone Heat shock protein 90 (Hsp90) is a substrate of HDAC6 deacetylation, and several lines of evidence demonstrate that simultaneous inhibition of HDAC6 and Hsp90 promote synergistic antitumor effects on different cancer cell lines, highlighting the potential benefits of developing a single molecule endowed with multi-target activity. This review will summarize the complex interplay between HDAC6 and Hsp90, providing also useful hints for multi-target drug design and discovery approaches in this field. To this end, crystallographic structures of HDAC6 and Hsp90 complexes will be extensively reviewed in the light of discussing binding pockets features and pharmacophore requirements and providing useful guidelines for the design of dual inhibitors. The few examples of multi-target inhibitors obtained so far, mostly based on chimeric approaches, will be summarized and put into context. Finally, the main features of HDAC6 and Hsp90 inhibitors will be compared, and ligand- and structure-based strategies potentially useful for the development of small molecular weight dual inhibitors will be proposed and discussed.
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Affiliation(s)
- Davide Bonanni
- Department of Life Sciences, University of Modena and Reggio Emilia Via Campi 183, 41125 Modena, Italy
| | - Andrea Citarella
- Department of Life Sciences, University of Modena and Reggio Emilia Via Campi 183, 41125 Modena, Italy
| | - Davide Moi
- Department of Life Sciences, University of Modena and Reggio Emilia Via Campi 183, 41125 Modena, Italy
| | - Luca Pinzi
- Department of Life Sciences, University of Modena and Reggio Emilia Via Campi 183, 41125 Modena, Italy
| | - Elisa Bergamini
- Department of Life Sciences, University of Modena and Reggio Emilia Via Campi 183, 41125 Modena, Italy
| | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia Via Campi 183, 41125 Modena, Italy
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12
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Elmezayen AD, Kemal Y. Structure-based virtual screening for novel potential selective inhibitors of class IIa histone deacetylases for cancer treatment. Comput Biol Chem 2021; 92:107491. [PMID: 33930743 DOI: 10.1016/j.compbiolchem.2021.107491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
Abstract
The fundamental cause of human cancer is strongly influenced by down- or up-regulations of epigenetic factors. Upregulated histone deacetylases (HDAC) have been shown to be effectively neutralized by the action of HDACs inhibitors (HDACi). However, cytotoxicity has been reported in normal cells because of non-specificity of several available HDACis that are in clinical use or at different phases of clinical trials. Because of the high amino acid sequence and structural similarity among HDAC enzymes, it is believed to be a challenging task to obtain isoform-selectivity. The essential aim of the present research work was to identify isoform-selective inhibitors against class IIa HDACs via structure-based drug design. Based on the highest binding affinity and isoform-selectivity, the top-ranked inhibitors were in silico tested for their absorption, distribution, metabolism, elimination, and toxicity (ADMET) properties, which were classified as drug-like compounds. Later, molecular dynamics simulation (MD) was carried out for all compound-protein complexes to evaluate the structural stability and the biding mode of the inhibitors, which showed high stability throughout the 100 ns simulation. Free binding energy predictions by MM-PBSA method showed the high binding affinity of the identified compounds toward their respective targets. Hence, these inhibitors could be used as drug candidates or as lead compounds for more in silico or in vitro optimization to design safe isoform-selective HDACs inhibitors.
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Affiliation(s)
- Ammar D Elmezayen
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Cibali, Istanbul, Turkey
| | - Yelekçi Kemal
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Cibali, Istanbul, Turkey.
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13
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Das Gupta K, Shakespear MR, Curson JEB, Murthy AMV, Iyer A, Hodson MP, Ramnath D, Tillu VA, von Pein JB, Reid RC, Tunny K, Hohenhaus DM, Moradi SV, Kelly GM, Kobayashi T, Gunter JH, Stevenson AJ, Xu W, Luo L, Jones A, Johnston WA, Blumenthal A, Alexandrov K, Collins BM, Stow JL, Fairlie DP, Sweet MJ. Class IIa Histone Deacetylases Drive Toll-like Receptor-Inducible Glycolysis and Macrophage Inflammatory Responses via Pyruvate Kinase M2. Cell Rep 2021; 30:2712-2728.e8. [PMID: 32101747 DOI: 10.1016/j.celrep.2020.02.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 09/30/2019] [Accepted: 02/03/2020] [Indexed: 12/14/2022] Open
Abstract
Histone deacetylases (HDACs) drive innate immune cell-mediated inflammation. Here we identify class IIa HDACs as key molecular links between Toll-like receptor (TLR)-inducible aerobic glycolysis and macrophage inflammatory responses. A proteomic screen identified the glycolytic enzyme pyruvate kinase M isoform 2 (Pkm2) as a partner of proinflammatory Hdac7 in murine macrophages. Myeloid-specific Hdac7 overexpression in transgenic mice amplifies lipopolysaccharide (LPS)-inducible lactate and promotes a glycolysis-associated inflammatory signature. Conversely, pharmacological or genetic targeting of Hdac7 and other class IIa HDACs attenuates LPS-inducible glycolysis and accompanying inflammatory responses in macrophages. We show that an Hdac7-Pkm2 complex acts as an immunometabolism signaling hub, whereby Pkm2 deacetylation at lysine 433 licenses its proinflammatory functions. Disrupting this complex suppresses inflammatory responses in vitro and in vivo. Class IIa HDACs are thus pivotal intermediates connecting TLR-inducible glycolysis to inflammation via Pkm2.
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Affiliation(s)
- Kaustav Das Gupta
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland 4072, Australia; IMB Centre for Inflammation and Disease Research and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Melanie R Shakespear
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland 4072, Australia; IMB Centre for Inflammation and Disease Research and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - James E B Curson
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland 4072, Australia; IMB Centre for Inflammation and Disease Research and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ambika M V Murthy
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland 4072, Australia; IMB Centre for Inflammation and Disease Research and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Abishek Iyer
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland 4072, Australia; IMB Centre for Inflammation and Disease Research and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, IMB, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mark P Hodson
- School of Pharmacy, The University of Queensland, Brisbane, Queensland 4072, Australia; Metabolomics Australia, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia; Victor Chang Cardiac Research Institute, Sydney, New South Wales 2010, Australia
| | - Divya Ramnath
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland 4072, Australia; IMB Centre for Inflammation and Disease Research and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Vikas A Tillu
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jessica B von Pein
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland 4072, Australia; IMB Centre for Inflammation and Disease Research and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Robert C Reid
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland 4072, Australia; IMB Centre for Inflammation and Disease Research and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, IMB, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kathryn Tunny
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Daniel M Hohenhaus
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Shayli Varasteh Moradi
- CSIRO-QUT Synthetic Biology Alliance, Centre for Tropical Crops and Biocommodities, Queensland University of Technology (QUT), Gardens Point Campus, Brisbane, Queensland 4000, Australia
| | - Gregory M Kelly
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Takumi Kobayashi
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jennifer H Gunter
- Australian Prostate Cancer Research Centre-Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Translational Research Institute, Queensland University of Technology (QUT), Brisbane, Queensland 4102, Australia
| | - Alexander J Stevenson
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Weijun Xu
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland 4072, Australia; IMB Centre for Inflammation and Disease Research and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, IMB, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Lin Luo
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland 4072, Australia; IMB Centre for Inflammation and Disease Research and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Alun Jones
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Wayne A Johnston
- CSIRO-QUT Synthetic Biology Alliance, Centre for Tropical Crops and Biocommodities, Queensland University of Technology (QUT), Gardens Point Campus, Brisbane, Queensland 4000, Australia
| | - Antje Blumenthal
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kirill Alexandrov
- CSIRO-QUT Synthetic Biology Alliance, Centre for Tropical Crops and Biocommodities, Queensland University of Technology (QUT), Gardens Point Campus, Brisbane, Queensland 4000, Australia
| | - Brett M Collins
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jennifer L Stow
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland 4072, Australia; IMB Centre for Inflammation and Disease Research and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P Fairlie
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland 4072, Australia; IMB Centre for Inflammation and Disease Research and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, IMB, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Matthew J Sweet
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland 4072, Australia; IMB Centre for Inflammation and Disease Research and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia.
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14
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Mangiatordi GF, Intranuovo F, Delre P, Abatematteo FS, Abate C, Niso M, Creanza TM, Ancona N, Stefanachi A, Contino M. Cannabinoid Receptor Subtype 2 (CB2R) in a Multitarget Approach: Perspective of an Innovative Strategy in Cancer and Neurodegeneration. J Med Chem 2020; 63:14448-14469. [PMID: 33094613 DOI: 10.1021/acs.jmedchem.0c01357] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The cannabinoid receptor subtype 2 (CB2R) represents an interesting and new therapeutic target for its involvement in the first steps of neurodegeneration as well as in cancer onset and progression. Several studies, focused on different types of tumors, report a promising anticancer activity induced by CB2R agonists due to their ability to reduce inflammation and cell proliferation. Moreover, in neuroinflammation, the stimulation of CB2R, overexpressed in microglial cells, exerts beneficial effects in neurodegenerative disorders. With the aim to overcome current treatment limitations, new drugs can be developed by specifically modulating, together with CB2R, other targets involved in such multifactorial disorders. Building on successful case studies of already developed multitarget strategies involving CB2R, in this Perspective we aim at prompting the scientific community to consider new promising target associations involving HDACs (histone deacetylases) and σ receptors by employing modern approaches based on molecular hybridization, computational polypharmacology, and machine learning algorithms.
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Affiliation(s)
| | - Francesca Intranuovo
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy
| | - Pietro Delre
- CNR-Institute of Crystallography, Via Amendola 122/o, 70126 Bari, Italy.,Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Francesca Serena Abatematteo
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy
| | - Carmen Abate
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy
| | - Mauro Niso
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy
| | - Teresa Maria Creanza
- CNR-Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing, Via Amendola 122/o, 70126 Bari, Italy
| | - Nicola Ancona
- CNR-Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing, Via Amendola 122/o, 70126 Bari, Italy
| | - Angela Stefanachi
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy
| | - Marialessandra Contino
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy
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15
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Hassan MM, Israelian J, Nawar N, Ganda G, Manaswiyoungkul P, Raouf YS, Armstrong D, Sedighi A, Olaoye OO, Erdogan F, Cabral AD, Angeles F, Altintas R, de Araujo ED, Gunning PT. Characterization of Conformationally Constrained Benzanilide Scaffolds for Potent and Selective HDAC8 Targeting. J Med Chem 2020; 63:8634-8648. [PMID: 32672458 DOI: 10.1021/acs.jmedchem.0c01025] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Histone deacetylases (HDACs) are an attractive therapeutic target for a variety of human diseases. Currently, all four FDA-approved HDAC-targeting drugs are nonselective, pan-HDAC inhibitors, exhibiting adverse side effects at therapeutic doses. Although selective HDAC inhibition has been proposed to mitigate toxicity, the targeted catalytic domains are highly conserved. Herein, we describe a series of rationally designed, conformationally constrained, benzanilide foldamers which selectively bind the catalytic tunnel of HDAC8. The series includes benzanilides, MMH371, MMH409, and MMH410, which exhibit potent in vitro HDAC8 activity (IC50 = 66, 23, and 66 nM, respectively) and up to 410-fold selectivity for HDAC8 over the next targeted HDAC. Experimental and computational analyses of the benzanilide structure docked with human HDAC8 enzyme showed the adoption of a low-energy L-shaped conformer that favors HDAC8 selectivity. The conformationally constrained HDAC8 inhibitors present an alternative biological probe for further determining the clinical utility and safety of pharmacological knockdown of HDAC8 in diseased cells.
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Affiliation(s)
- Muhammad Murtaza Hassan
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga ON L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto ON M5S 3H6, Canada
| | - Johan Israelian
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga ON L5L 1C6, Canada
| | - Nabanita Nawar
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga ON L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto ON M5S 3H6, Canada
| | - Giovanni Ganda
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga ON L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto ON M5S 3H6, Canada
| | - Pimyupa Manaswiyoungkul
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga ON L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto ON M5S 3H6, Canada
| | - Yasir S Raouf
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga ON L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto ON M5S 3H6, Canada
| | - David Armstrong
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga ON L5L 1C6, Canada
| | - Abootaleb Sedighi
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga ON L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto ON M5S 3H6, Canada
| | - Olasunkanmi O Olaoye
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga ON L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto ON M5S 3H6, Canada
| | - Fettah Erdogan
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga ON L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto ON M5S 3H6, Canada
| | - Aaron D Cabral
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga ON L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto ON M5S 3H6, Canada
| | - Fabrizio Angeles
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga ON L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto ON M5S 3H6, Canada
| | - Rabia Altintas
- Clinical Cooperation Unit Pediatric Oncology (G340), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany.,Heidelberg Medical Faculty, University of Heidelberg, Heidelberg 691171, Germany
| | - Elvin D de Araujo
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga ON L5L 1C6, Canada
| | - Patrick T Gunning
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga ON L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto ON M5S 3H6, Canada
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16
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Elmezayen AD, Yelekçi K. Homology modeling and in silico design of novel and potential dual-acting inhibitors of human histone deacetylases HDAC5 and HDAC9 isozymes. J Biomol Struct Dyn 2020; 39:6396-6414. [PMID: 32715940 DOI: 10.1080/07391102.2020.1798812] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Histone deacetylases (HDACs) are a group of enzymes that have prominent and crucial effect on various biological systems, mainly by their suppressive effect on transcription. Searching for inhibitors targeting their respective isoforms without affecting other targets is greatly needed. Some histone deacetylases have no crystal structures, such as HDAC5 and HDAC9. Lacking proper and suitable crystal structure is obstructing the designing of appropriate isoform selective inhibitors. Here in this study, we constructed human HDAC5 and HDAC9 protein models using human HDAC4 (PDB:2VQM_A) as a template by the means of homology modeling approach. Based on the Z-score of the built models, model M0014 of HDAC5 and model M0020 of HDAC9 were selected. The models were verified by MODELLER and validated using the Web-based PROCHECK server. All selected known inhibitors displayed reasonable binding modes and equivalent predicted Ki values in comparison to the experimental binding affinities (Ki/IC50). The known inhibitor Rac26 showed the best binding affinity for HDAC5, while TMP269 showed the best binding affinity for HDAC9. The best two compounds, CHEMBL2114980 and CHEMBL217223, had relatively similar inhibition constants against HDAC5 and HDAC9. The built models and their complexes were subjected to molecular dynamic simulations (MD) for 100 ns. Examining the MD simulation results of all studied structures, including the RMSD, RMSF, radius of gyration and potential energy suggested the stability and reliability of the built models. Accordingly, the results obtained in this study could be used for designing de novo inhibitors against HDAC5 and HDAC9. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ammar D Elmezayen
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
| | - Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
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17
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Pflüger-Müller B, Oo JA, Heering J, Warwick T, Proschak E, Günther S, Looso M, Rezende F, Fork C, Geisslinger G, Thomas D, Gurke R, Steinhilber D, Schulz M, Leisegang MS, Brandes RP. The endocannabinoid anandamide has an anti-inflammatory effect on CCL2 expression in vascular smooth muscle cells. Basic Res Cardiol 2020; 115:34. [PMID: 32323032 PMCID: PMC7176595 DOI: 10.1007/s00395-020-0793-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/14/2020] [Indexed: 11/29/2022]
Abstract
Endocannabinoids are important lipid-signaling mediators. Both protective and deleterious effects of endocannabinoids in the cardiovascular system have been reported but the mechanistic basis for these contradicting observations is unclear. We set out to identify anti-inflammatory mechanisms of endocannabinoids in the murine aorta and in human vascular smooth muscle cells (hVSMC). In response to combined stimulation with cytokines, IL-1β and TNFα, the murine aorta released several endocannabinoids, with anandamide (AEA) levels being the most significantly increased. AEA pretreatment had profound effects on cytokine-induced gene expression in hVSMC and murine aorta. As revealed by RNA-Seq analysis, the induction of a subset of 21 inflammatory target genes, including the important cytokine CCL2 was blocked by AEA. This effect was not mediated through AEA-dependent interference of the AP-1 or NF-κB pathways but rather through an epigenetic mechanism. In the presence of AEA, ATAC-Seq analysis and chromatin-immunoprecipitations revealed that CCL2 induction was blocked due to increased levels of H3K27me3 and a decrease of H3K27ac leading to compacted chromatin structure in the CCL2 promoter. These effects were mediated by recruitment of HDAC4 and the nuclear corepressor NCoR1 to the CCL2 promoter. This study therefore establishes a novel anti-inflammatory mechanism for the endogenous endocannabinoid AEA in vascular smooth muscle cells. Furthermore, this work provides a link between endogenous endocannabinoid signaling and epigenetic regulation.
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Affiliation(s)
- Beatrice Pflüger-Müller
- Fachbereich Medizin, Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.,German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt, Germany
| | - James A Oo
- Fachbereich Medizin, Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.,German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt, Germany
| | - Jan Heering
- Branch for Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, 60438, Frankfurt, Germany
| | - Timothy Warwick
- Fachbereich Medizin, Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.,German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt, Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe-University, 60438, Frankfurt, Germany
| | - Stefan Günther
- Max-Planck-Institute for Heart- and Lung Research (MPI-HLR), 61231, Bad Nauheim, Germany
| | - Mario Looso
- Max-Planck-Institute for Heart- and Lung Research (MPI-HLR), 61231, Bad Nauheim, Germany
| | - Flávia Rezende
- Fachbereich Medizin, Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.,German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt, Germany
| | - Christian Fork
- Fachbereich Medizin, Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.,German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt, Germany
| | - Gerd Geisslinger
- Branch for Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, 60438, Frankfurt, Germany.,Faculty of Medicine, Pharmazentrum Frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe-University, 60590, Frankfurt, Germany
| | - Dominique Thomas
- Faculty of Medicine, Pharmazentrum Frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe-University, 60590, Frankfurt, Germany
| | - Robert Gurke
- Branch for Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, 60438, Frankfurt, Germany.,Faculty of Medicine, Pharmazentrum Frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe-University, 60590, Frankfurt, Germany
| | - Dieter Steinhilber
- Branch for Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, 60438, Frankfurt, Germany.,Institute of Pharmaceutical Chemistry, Goethe-University, 60438, Frankfurt, Germany
| | - Marcel Schulz
- Vascular Research Centre, Goethe-University, 60596, Frankfurt, Germany
| | - Matthias S Leisegang
- Fachbereich Medizin, Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.,German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt, Germany
| | - Ralf P Brandes
- Fachbereich Medizin, Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany. .,German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt, Germany.
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18
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Grbić E, Gorkič N, Pleskovič A, Zorc M, Ljuca F, Gasparini M, Mrđa B, Cilenšek I, Mankoč S, Banach M, Petrovič D, Fras Z. Association between rs2107595 HDAC9 gene polymorphism and advanced carotid atherosclerosis in the Slovenian cohort. Lipids Health Dis 2020; 19:71. [PMID: 32284067 PMCID: PMC7155263 DOI: 10.1186/s12944-020-01255-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022] Open
Abstract
Background Histone deacetylase 9 (HDAC9) plays an important role in transcriptional regulation, cell cycle progression and developmental events; moreover, it has been investigated as a candidate gene in a number of conditions, including the onset and progression of atherosclerosis. We hypothesized that the rs2107595 HDAC9 gene polymorphism may be associated with advanced carotid artery disease in a Slovenian cohort. We also investigated the effect of this polymorphism on HDAC9 receptor expression in the internal carotid artery (ICA) specimens obtained by endarterectomy. Methods This case-control study enrolled 619 unrelated Slovenian patients: 311 patients with ICA stenosis > 75% as the study group and 308 patients with ICA stenosis < 50% as the control group. Patient laboratory and clinical data were obtained from the medical records. The rs2107595 polymorphisms were genotyped using TaqMan SNP Genotyping assay. HDAC9 expression was assessed by immunohistochemistry in 30 ICA specimens from patients with ICA atherosclerosis > 75%, and the numerical areal density of HDAC9 positive cells was calculated. Results The occurrence of advanced ICA atherosclerosis in the Slovenian cohort was 3.81 times higher in the codominant genetic model (OR = 3.81, 95%CI = 1.06–13.77, p = 0.04), and 3.10 times higher in the recessive genetic model (OR = 3.10, 95%CI = 1.16–8.27, p = 0.02). In addition, the A allele of rs2107595 was associated with increased HDAC9 expression in the ICA specimens obtained by endarterectomy. Conclusions We observed a significant association between the AA genotype of rs2107595 with the advanced carotid artery disease in our Slovenian cohort, indicating that this polymorphism may be a genetic risk factor for ICA atherosclerosis.
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Affiliation(s)
- Emin Grbić
- Department of Physiology, Faculty of Medicine, University of Tuzla, Tuzla, Bosnia and Herzegovina
| | - Nataša Gorkič
- International Center for Cardiovascular Diseases MC Medicor d.d, Izola, Slovenia
| | - Aleš Pleskovič
- Department of Cardiology, Division of Medicine, University Medical Centre of Ljubljana, Ljubljana, Slovenia
| | - Marjeta Zorc
- International Center for Cardiovascular Diseases MC Medicor d.d, Izola, Slovenia
| | - Farid Ljuca
- Department of Physiology, Faculty of Medicine, University of Tuzla, Tuzla, Bosnia and Herzegovina
| | - Mladen Gasparini
- Department of Vascular Surgery, General Hospital Izola, Izola, Slovenia
| | - Božidar Mrđa
- Department of Vascular Surgery, University Medical Centre Maribor, Maribor, Slovenia
| | - Ines Cilenšek
- Institute of Histology and Embryology, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000, Ljubljana, Slovenia
| | - Sara Mankoč
- Institute of Histology and Embryology, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000, Ljubljana, Slovenia
| | - Maciej Banach
- Cardiovascular Research Centre, University of Zielona-Gora, Zielona Gora, Poland.,Polish Mother's Memorial Hospital Research Institute (PMMHRI), Lodz, Poland
| | - Daniel Petrovič
- International Center for Cardiovascular Diseases MC Medicor d.d, Izola, Slovenia. .,Institute of Histology and Embryology, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000, Ljubljana, Slovenia.
| | - Zlatko Fras
- Department of Cardiology, Division of Medicine, University Medical Centre of Ljubljana, Ljubljana, Slovenia. .,Division of Medicine, Centre for Preventive Cardiology, Division of Medicine, University Medical Centre Ljubljana, Zaloška cesta 7, SI-1525, Ljubljana, Slovenia. .,Chair of Internal Medicine, Medical Faculty, University of Ljubljana, Ljubljana, Slovenia.
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19
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Hassell KN. Histone Deacetylases and their Inhibitors in Cancer Epigenetics. Diseases 2019; 7:diseases7040057. [PMID: 31683808 PMCID: PMC6955926 DOI: 10.3390/diseases7040057] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/25/2019] [Accepted: 10/30/2019] [Indexed: 02/06/2023] Open
Abstract
Histone deacetylases (HDAC) and histone deacetylase inhibitors (HDACi) have greatly impacted the war on cancer. Their role in epigenetics has significantly altered the development of anticancer drugs used to treat the most rare, persistent forms of cancer. During transcription, HDAC and HDACi are used to regulate the genetic mutations found in cancerous cells by removing and/or preventing the removal of the acetyl group on specific histones. This activity determines the relaxed or condensed conformation of the nucleosome, changing the accessibility zones for transcription factors. These modifications lead to other biological processes for the cell, including cell cycle progression, proliferation, and differentiation. Each HDAC and HDACi class or group has a distinctive mechanism of action that can be utilized to halt the progression of cancerous cell growth. While the use of HDAC- and HDACi-derived compounds are relatively new in treatment of cancers, they have a proven efficacy when the appropriately utilized. This following manuscript highlights the mechanisms of action utilized by HDAC and HDACi in various cancer, their role in epigenetics, current drug manufacturers, and the impact predicative modeling systems have on cancer therapeutic drug discovery.
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Affiliation(s)
- Kelly N Hassell
- Department of Biology, College of St. Elizabeth, Morristown, NJ 07960, USA.
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20
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Choi MA, Park SY, Chae HY, Song Y, Sharma C, Seo YH. Design, synthesis and biological evaluation of a series of CNS penetrant HDAC inhibitors structurally derived from amyloid-β probes. Sci Rep 2019; 9:13187. [PMID: 31515509 PMCID: PMC6742641 DOI: 10.1038/s41598-019-49784-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 08/19/2019] [Indexed: 12/17/2022] Open
Abstract
To develop novel CNS penetrant HDAC inhibitors, a new series of HDAC inhibitors having benzoheterocycle were designed, synthesized, and biologically evaluated. Among the synthesized compounds, benzothiazole derivative 9b exhibited a remarkable anti-proliferative activity (GI50 = 2.01 μM) against SH-SY5Y cancer cell line in a dose and time-dependent manner, better than the reference drug SAHA (GI50 = 2.90 μM). Moreover, compound 9b effectively promoted the accumulation of acetylated Histone H3 and α-tubulin through inhibition of HDAC1 and HDAC6 enzymes, respectively. HDAC enzyme assay also confirmed that compound 9b efficiently inhibited HDAC1 and HDAC6 isoforms with IC50 values of 84.9 nM and 95.9 nM. Furthermore, compound 9b inhibited colony formation capacity of SH-SY5Y cells, which is considered a hallmark of cell carcinogenesis and metastatic potential. The theoretical prediction, in vitro PAMPA-BBB assay, and in vivo brain pharmacokinetic studies confirmed that compound 9b had much higher BBB permeability than SAHA. In silico docking study demonstrated that compound 9b fitted in the substrate binding pocket of HDAC1 and HDAC6. Taken together, compound 9b provided a novel scaffold for developing CNS penetrant HDAC inhibitors and therapeutic potential for CNS-related diseases.
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Affiliation(s)
- Myeong A Choi
- College of Pharmacy, Keimyung University, Daegu, 42601, South Korea
| | - Sun You Park
- College of Pharmacy, Keimyung University, Daegu, 42601, South Korea
| | - Hye Yun Chae
- College of Pharmacy, Keimyung University, Daegu, 42601, South Korea
| | - Yoojin Song
- College of Pharmacy, Keimyung University, Daegu, 42601, South Korea
| | | | - Young Ho Seo
- College of Pharmacy, Keimyung University, Daegu, 42601, South Korea.
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21
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Asfaha Y, Schrenk C, Alves Avelar LA, Hamacher A, Pflieger M, Kassack MU, Kurz T. Recent advances in class IIa histone deacetylases research. Bioorg Med Chem 2019; 27:115087. [PMID: 31561937 DOI: 10.1016/j.bmc.2019.115087] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/25/2019] [Accepted: 09/03/2019] [Indexed: 12/16/2022]
Abstract
Epigenetic control plays an important role in gene regulation through chemical modifications of DNA and post-translational modifications of histones. An essential post-translational modification is the histone acetylation/deacetylation-process which is regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs). The mammalian zinc dependent HDAC family is subdivided into three classes: class I (HDACs 1-3, 8), class II (IIa: HDACs 4, 5, 7, 9; IIb: HDACs 6, 10) and class IV (HDAC 11). In this review, recent studies on the biological role and regulation of class IIa HDACs as well as their contribution in neurodegenerative diseases, immune disorders and cancer will be presented. Furthermore, the development, synthesis, and future perspectives of selective class IIa inhibitors will be highlighted.
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Affiliation(s)
- Yodita Asfaha
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Christian Schrenk
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Leandro A Alves Avelar
- 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
| | - Marc Pflieger
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Matthias U Kassack
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.
| | - Thomas Kurz
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.
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22
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Ishola AA, Adewole KE. Phytosterols and triterpenes from Morinda lucida Benth. exhibit binding tendency against class I HDAC and HDAC7 isoforms. Mol Biol Rep 2019; 46:2307-2325. [PMID: 30771146 DOI: 10.1007/s11033-019-04689-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/07/2019] [Indexed: 12/22/2022]
Abstract
The important role of histone deacetylases (HDACs) in the development of cancer has been demonstrated by various studies. Thus targeting HDACs with inhibitors is a major focus in anticancer drug research. Although few synthetic HDAC inhibitors (HDIs) have been approved for cancer treatment, they have significant undesirable side effects. Therefore emphases have been placed on natural HDIs as substitutes for the synthetic ones. In a bid to identify more HDIs, this study evaluated the binding tendency of compounds derived from Morinda lucida Benth. towards selected HDACs for the discovery of potent HDIs as potential candidates for anticancer therapeutics, based on the report of anticancer potentials of Morinda lucida-derived extracts and compounds. Givinostat and 49 Morinda-lucida derived compounds were docked against selected HDAC isoforms using AutodockVina, while binding interactions were viewed with Discovery Studio Visualizer, BIOVIA, 2016. Druglikeness and Absorption-Distribution-Metabolism-Excretion (ADME) parameters of the top 7 compounds were evaluated using the Swiss online ADME web tool. The results revealed that out of the 49 compounds, 3 phytosterols (campesterol, cycloartenol, and stigmasterol) and 2 triterpenes (oleanolic acid and ursolic acid) exhibited high HDAC inhibitory activity compared to givinostat. These 5 compounds also fulfill oral drugability of Lipinski rule of five. Morinda lucida-derived phytosterols and triterpenes show high binding tendency towards the selected HDACs and exhibited good drugability characteristics and are therefore good candidates for further studies in the search for therapies against abnormalities linked with over-activity of HDACs.
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Affiliation(s)
- Ahmed Adebayo Ishola
- Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin, Nigeria
| | - Kayode Ezekiel Adewole
- Biochemistry Unit, Department of Chemical Sciences, Faculty of Natural Sciences, Ajayi Crowther University Oyo, Oyo, Oyo State, Nigeria.
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23
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Veale CGL. Unpacking the Pathogen Box-An Open Source Tool for Fighting Neglected Tropical Disease. ChemMedChem 2019; 14:386-453. [PMID: 30614200 DOI: 10.1002/cmdc.201800755] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Indexed: 12/13/2022]
Abstract
The Pathogen Box is a 400-strong collection of drug-like compounds, selected for their potential against several of the world's most important neglected tropical diseases, including trypanosomiasis, leishmaniasis, cryptosporidiosis, toxoplasmosis, filariasis, schistosomiasis, dengue virus and trichuriasis, in addition to malaria and tuberculosis. This library represents an ensemble of numerous successful drug discovery programmes from around the globe, aimed at providing a powerful resource to stimulate open source drug discovery for diseases threatening the most vulnerable communities in the world. This review seeks to provide an in-depth analysis of the literature pertaining to the compounds in the Pathogen Box, including structure-activity relationship highlights, mechanisms of action, related compounds with reported activity against different diseases, and, where appropriate, discussion on the known and putative targets of compounds, thereby providing context and increasing the accessibility of the Pathogen Box to the drug discovery community.
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Affiliation(s)
- Clinton G L Veale
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa
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24
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Targeting the Oxytocin System: New Pharmacotherapeutic Approaches. Trends Pharmacol Sci 2019; 40:22-37. [DOI: 10.1016/j.tips.2018.11.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/27/2018] [Accepted: 11/01/2018] [Indexed: 12/27/2022]
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25
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Habibian J, Ferguson BS. The Crosstalk between Acetylation and Phosphorylation: Emerging New Roles for HDAC Inhibitors in the Heart. Int J Mol Sci 2018; 20:E102. [PMID: 30597863 PMCID: PMC6337125 DOI: 10.3390/ijms20010102] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 12/20/2018] [Accepted: 12/22/2018] [Indexed: 12/22/2022] Open
Abstract
Approximately five million United States (U.S.) adults are diagnosed with heart failure (HF), with eight million U.S. adults projected to suffer from HF by 2030. With five-year mortality rates following HF diagnosis approximating 50%, novel therapeutic treatments are needed for HF patients. Pre-clinical animal models of HF have highlighted histone deacetylase (HDAC) inhibitors as efficacious therapeutics that can stop and potentially reverse cardiac remodeling and dysfunction linked with HF development. HDACs remove acetyl groups from nucleosomal histones, altering DNA-histone protein electrostatic interactions in the regulation of gene expression. However, HDACs also remove acetyl groups from non-histone proteins in various tissues. Changes in histone and non-histone protein acetylation plays a key role in protein structure and function that can alter other post translational modifications (PTMs), including protein phosphorylation. Protein phosphorylation is a well described PTM that is important for cardiac signal transduction, protein activity and gene expression, yet the functional role for acetylation-phosphorylation cross-talk in the myocardium remains less clear. This review will focus on the regulation and function for acetylation-phosphorylation cross-talk in the heart, with a focus on the role for HDACs and HDAC inhibitors as regulators of acetyl-phosphorylation cross-talk in the control of cardiac function.
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Affiliation(s)
- Justine Habibian
- Cellular and Molecular Biology, University of Nevada, Reno, NV 89557, USA.
- Department of Nutrition, University of Nevada, Reno, NV 89557, USA.
- Center for Cardiovascular Research, University of Nevada, Reno, NV 89557, USA.
| | - Bradley S Ferguson
- Department of Nutrition, University of Nevada, Reno, NV 89557, USA.
- Center for Cardiovascular Research, University of Nevada, Reno, NV 89557, USA.
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26
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Cattaneo A, Chirichella M. Targeting the Post-translational Proteome with Intrabodies. Trends Biotechnol 2018; 37:578-591. [PMID: 30577991 DOI: 10.1016/j.tibtech.2018.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/18/2018] [Accepted: 11/19/2018] [Indexed: 12/22/2022]
Abstract
The complexity of the proteome exceeds that of the genome. Post-translational modifications (PTMs) and conformational changes of proteins trigger new molecular interactions whose systematic elucidation is hampered by the lack of specific tools. PTMs are particularly relevant for epigenetic regulation of gene expression; a field of translational interest. However, state-of-the-art inhibitors used in epigenetic studies and therapies target modifier enzymes such as acetylases and deacetylases, rather than a single PTM protein per se. The systematic development of anti-PTM intrabodies, which allow targeting of intracellular proteins in the context of living cells, will help reaching a new level of precision and specificity in the description of epigenetics, paving the way to new therapeutic opportunities.
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Affiliation(s)
- Antonino Cattaneo
- Bio@SNS Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri, 7 - 56126 Pisa, Italy.
| | - Michele Chirichella
- Bio@SNS Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri, 7 - 56126 Pisa, Italy; Current address: Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
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27
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Cincinelli R, Musso L, Artali R, Guglielmi MB, La Porta I, Melito C, Colelli F, Cardile F, Signorino G, Fucci A, Frusciante M, Pisano C, Dallavalle S. Hybrid topoisomerase I and HDAC inhibitors as dual action anticancer agents. PLoS One 2018; 13:e0205018. [PMID: 30300374 PMCID: PMC6177136 DOI: 10.1371/journal.pone.0205018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/18/2018] [Indexed: 12/29/2022] Open
Abstract
Recent studies have shown that HDAC inhibitors act synergistically with camptothecin derivatives in combination therapies. To exploit this synergy, new hybrid molecules targeting simultaneously topoisomerase I and HDAC were designed. In particular, a selected multivalent agent containing a camptothecin and a SAHA-like template showed a broad spectrum of antiproliferative activity, with IC50 values in the nanomolar range. Preliminary in vivo results indicated a strong antitumor activity on human mesothelioma primary cell line MM473 orthotopically xenografted in CD-1 nude mice and very high tolerability.
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Affiliation(s)
- Raffaella Cincinelli
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milano, Italy
| | - Loana Musso
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milano, Italy
| | | | | | | | - Carmela Melito
- Biogem, Research Institute, Ariano Irpino, Avellino, Italy
| | | | | | | | | | | | - Claudio Pisano
- Biogem, Research Institute, Ariano Irpino, Avellino, Italy
- * E-mail: (SD); (CP)
| | - Sabrina Dallavalle
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milano, Italy
- * E-mail: (SD); (CP)
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28
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Kollar J, Frecer V. Diarylcyclopropane hydroxamic acid inhibitors of histone deacetylase 4 designed by combinatorial approach and QM/MM calculations. J Mol Graph Model 2018; 85:97-110. [PMID: 30145395 DOI: 10.1016/j.jmgm.2018.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/12/2018] [Accepted: 08/13/2018] [Indexed: 12/01/2022]
Abstract
Inhibitors of histone deacetylase superfamily (HDAC), which induce cell cycle arrest, trigger cell death and reduce angiogenesis appear as promising anti-cancer drugs targeting the epigenetic regulation of gene expression. Approved HDAC inhibitors were found effective against haematological and solid malignancies, other HDACIs are currently in clinical trials for the treatment of neurological diseases or immune disorders. Among those, diarylcyclopropane hydroxamic acids (DCHA) were found to be potent and selective inhibitors of the class IIa HDACs, specifically HDAC4, a pharmacological target for the treatment of Huntington's disease and muscular atrophy. Crystallographic analysis revealed that one of the aryl groups of the DCHA fills the lower specificity pocket of the HDAC4 catalytic site that is specific for the class IIa HDACs. We have used computer-assisted combinatorial chemistry, hybrid quantum mechanics/molecular mechanics (QM/MM) with implicit solvation and QSAR models to optimize DCHA inhibitors and propose more potent DCHA analogues. The QM/MM approach has been selected since the process of inhibitor binding to the catalytic zinc and polar amino acid residues of the deacetylase active site induces considerable rearrangement of electron density of the inhibitor. Virtual combinatorial library consisting of 12180 DCHA analogues was focused by means of structure-based evaluation to form a small combinatorial subset enriched in potentially interesting inhibitor candidates. Two validated QSAR models making use of computed relative binding affinities of the DCHA inhibitors to the HDAC4 (ΔΔGcomQM/MM) were utilized to estimate the inhibitory potencies of the new analogues. The predicted half-maximal inhibitory concentrations (IC50pre) of the designed analogues fall into the low nanomolar concentration range and their predicted ADME properties are also favourable. The best designed DCHA analogues contain indazole, phenylpiperidine, phenyloxazole or hydroxypyridine moieties and stabilize bound inhibitors by hydrogen bonds to the catalytic water molecule and backbone carbonyl groups of the deacetylase active site residues. This makes them more potent and more specific inhibitors towards the HDAC4 isoform than the known diarylcyclopropane hydroxamic acids. The analogues are recommended for synthesis and experimental verification of inhibitory potencies in medicinal chemistry laboratories.
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Affiliation(s)
- Jakub Kollar
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava SK-84215, Slovakia; Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava SK-83232, Slovakia
| | - Vladimir Frecer
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava SK-83232, Slovakia; International Centre for Applied Research and Sustainable Technology (ICARST n.o.), Bratislava SK-84104, Slovakia.
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29
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30
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Berishvili VP, Voronkov AE, Radchenko EV, Palyulin VA. Machine Learning Classification Models to Improve the Docking-based Screening: A Case of PI3K-Tankyrase Inhibitors. Mol Inform 2018; 37:e1800030. [DOI: 10.1002/minf.201800030] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/28/2018] [Indexed: 01/20/2023]
Affiliation(s)
- Vladimir P. Berishvili
- Department of Chemistry; Lomonosov Moscow State University; Leninskie gory 1/3 Moscow 119991 Russia
| | - Andrew E. Voronkov
- Department of Chemistry; Lomonosov Moscow State University; Leninskie gory 1/3 Moscow 119991 Russia
- Digital BioPharm Ltd.; Hovseterveien 42 A, H0301 Oslo 0768 Norway
| | - Eugene V. Radchenko
- Department of Chemistry; Lomonosov Moscow State University; Leninskie gory 1/3 Moscow 119991 Russia
| | - Vladimir A. Palyulin
- Department of Chemistry; Lomonosov Moscow State University; Leninskie gory 1/3 Moscow 119991 Russia
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31
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Lu W, Zhang R, Jiang H, Zhang H, Luo C. Computer-Aided Drug Design in Epigenetics. Front Chem 2018; 6:57. [PMID: 29594101 PMCID: PMC5857607 DOI: 10.3389/fchem.2018.00057] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 02/23/2018] [Indexed: 12/31/2022] Open
Abstract
Epigenetic dysfunction has been widely implicated in several diseases especially cancers thus highlights the therapeutic potential for chemical interventions in this field. With rapid development of computational methodologies and high-performance computational resources, computer-aided drug design has emerged as a promising strategy to speed up epigenetic drug discovery. Herein, we make a brief overview of major computational methods reported in the literature including druggability prediction, virtual screening, homology modeling, scaffold hopping, pharmacophore modeling, molecular dynamics simulations, quantum chemistry calculation, and 3D quantitative structure activity relationship that have been successfully applied in the design and discovery of epi-drugs and epi-probes. Finally, we discuss about major limitations of current virtual drug design strategies in epigenetics drug discovery and future directions in this field.
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Affiliation(s)
- Wenchao Lu
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Rukang Zhang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Hao Jiang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Huimin Zhang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Cheng Luo
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
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