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Carullo G, Orsini N, Piano I, Pozzetti L, Papa A, Fontana A, Napoli D, Corsi F, Marco BD, Galante A, Marotta L, Panzeca G, O'Brien J, Sanchez AG, Doherty H, Mahon N, Clarke L, Contri C, Pasquini S, Gorelli B, Saponara S, Valoti M, Vincenzi F, Varani K, Ramunno A, Brogi S, Butini S, Gemma S, Kennedy BN, Gargini C, Strettoi E, Campiani G. Targeting Relevant HDACs to Support the Survival of Cone Photoreceptors in Inherited Retinal Diseases: Identification of a Potent Pharmacological Tool with In Vitro and In Vivo Efficacy. J Med Chem 2024. [PMID: 38961727 DOI: 10.1021/acs.jmedchem.4c00477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Inherited retinal diseases, which include retinitis pigmentosa, are a family of genetic disorders characterized by gradual rod-cone degeneration and vision loss, without effective pharmacological treatments. Experimental approaches aim to delay disease progression, supporting cones' survival, crucial for human vision. Histone deacetylases (HDACs) mediate the activation of epigenetic and nonepigenetic pathways that modulate cone degeneration in RP mouse models. We developed new HDAC inhibitors (5a-p), typified by a tetrahydro-γ-carboline scaffold, characterized by high HDAC6 inhibition potency with balanced physicochemical properties for in vivo studies. Compound 5d (repistat, IC50 HDAC6 = 6.32 nM) increased the levels of acetylated α-tubulin compared to histone H3 in ARPE-19 and 661W cells. 5d promoted vision rescue in the atp6v0e1-/- zebrafish model of photoreceptor dysfunction. A single intravitreal injection of 5d in the rd10 mouse model of RP supported morphological and functional preservation of cone cells and maintenance of the retinal pigment epithelium array.
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Affiliation(s)
- Gabriele Carullo
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Noemi Orsini
- Neuroscience Institute, Italian National Research Council (CNR) Area della Ricerca, Via Giuseppe Moruzzi 1, 56124 Pisa, Italy
- Regional Doctorate School in Neuroscience of Universities of Florence, Pisa, Siena, Florence, CNR Via Giuseppe Moruzzi 1, 56124 Pisa, Italy
| | - Ilaria Piano
- Department of Pharmacy, Via Bonanno 6, 56124 Pisa, Italy
| | - Luca Pozzetti
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Alessandro Papa
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Anna Fontana
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Debora Napoli
- Neuroscience Institute, Italian National Research Council (CNR) Area della Ricerca, Via Giuseppe Moruzzi 1, 56124 Pisa, Italy
- Regional Doctorate School in Neuroscience of Universities of Florence, Pisa, Siena, Florence, CNR Via Giuseppe Moruzzi 1, 56124 Pisa, Italy
| | | | - Beatrice Di Marco
- Neuroscience Institute, Italian National Research Council (CNR) Area della Ricerca, Via Giuseppe Moruzzi 1, 56124 Pisa, Italy
- Regional Doctorate School in Neuroscience of Universities of Florence, Pisa, Siena, Florence, CNR Via Giuseppe Moruzzi 1, 56124 Pisa, Italy
| | | | - Ludovica Marotta
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Giovanna Panzeca
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Justine O'Brien
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Alicia Gomez Sanchez
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Harry Doherty
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Niamh Mahon
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Leni Clarke
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Chiara Contri
- Department of Translational Medicine, University of Ferrara, Via Fossato di Mortara 17-19, 44121 Ferrara, Italy
| | - Silvia Pasquini
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Fossato di Mortara 17-19, 44121 Ferrara, Italy
| | - Beatrice Gorelli
- Department of Life Sciences, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Simona Saponara
- Department of Life Sciences, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Massimo Valoti
- Department of Life Sciences, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Fabrizio Vincenzi
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Fossato di Mortara 17-19, 44121 Ferrara, Italy
| | - Katia Varani
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Fossato di Mortara 17-19, 44121 Ferrara, Italy
| | - Anna Ramunno
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84100 Fisciano (SA), Italy
| | - Simone Brogi
- Department of Pharmacy, Via Bonanno 6, 56124 Pisa, Italy
| | - Stefania Butini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Sandra Gemma
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Breandán N Kennedy
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute, University College Dublin, D04 V1W8 Dublin, Ireland
| | | | - Enrica Strettoi
- Neuroscience Institute, Italian National Research Council (CNR) Area della Ricerca, Via Giuseppe Moruzzi 1, 56124 Pisa, Italy
| | - Giuseppe Campiani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan 81746-7346, Iran
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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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Efficacy of selective histone deacetylase 6 inhibition in mouse models of Pseudomonas aeruginosa infection: A new glimpse for reducing inflammation and infection in cystic fibrosis. Eur J Pharmacol 2022; 936:175349. [DOI: 10.1016/j.ejphar.2022.175349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 11/22/2022]
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Lindman J, Gopalan G, Palo-Nieto C, Brandt P, Gising J, Larhed M. Diastereoselective Synthesis of N-Methylspiroindolines by Intramolecular Mizoroki-Heck Annulations. ACS OMEGA 2022; 7:32525-32535. [PMID: 36120037 PMCID: PMC9476516 DOI: 10.1021/acsomega.2c04111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
Spiroindolines represent a privileged structure in medicinal chemistry, although stereocontrol around the spirocarbon can be a synthetic challenge. Here we present a palladium(0)-catalyzed intramolecular Mizoroki-Heck annulation reaction from (+)-Vince lactam-derived cyclopentenyl-tethered 2-bromo-N-methylanilines for the formation of N-methylspiroindolines. A series of 14 N-methylspiroindolines were synthesized in 59-81% yield with diastereoselectivity >98%, which was rationalized by density functional theory calculations and confirmed through X-ray crystallography. One spiroindoline was converted to an N- and C-terminal protected rigidified unnatural amino acid, which could be orthogonally deprotected.
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Fontana A, Cursaro I, Carullo G, Gemma S, Butini S, Campiani G. A Therapeutic Perspective of HDAC8 in Different Diseases: An Overview of Selective Inhibitors. Int J Mol Sci 2022; 23:ijms231710014. [PMID: 36077415 PMCID: PMC9456347 DOI: 10.3390/ijms231710014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Histone deacetylases (HDACs) are epigenetic enzymes which participate in transcriptional repression and chromatin condensation mechanisms by removing the acetyl moiety from acetylated ε-amino group of histone lysines and other non-histone proteins. In recent years, HDAC8, a class I HDAC, has emerged as a promising target for different disorders, including X-linked intellectual disability, fibrotic diseases, cancer, and various neuropathological conditions. Selective HDAC8 targeting is required to limit side effects deriving from the treatment with pan-HDAC inhibitors (HDACis); thus, many endeavours have focused on the development of selective HDAC8is. In addition, polypharmacological approaches have been explored to achieve a synergistic action on multi-factorial diseases or to enhance the drug efficacy. In this frame, proteolysis-targeting chimeras (PROTACs) might be regarded as a dual-targeting approach for attaining HDAC8 proteasomal degradation. This review highlights the most relevant and recent advances relative to HDAC8 validation in various diseases, providing a snapshot of the current selective HDAC8is, with a focus on polyfunctional modulators.
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Affiliation(s)
- Anna Fontana
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Ilaria Cursaro
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Gabriele Carullo
- Department of Life Sciences, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Sandra Gemma
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Stefania Butini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
- Correspondence: ; Tel.: +39-057-723-4161
| | - Giuseppe Campiani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
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6
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Azetidin-2-one-based small molecules as dual hHDAC6/HDAC8 inhibitors: Investigation of their mechanism of action and impact of dual inhibition profile on cell viability. Eur J Med Chem 2022; 238:114409. [DOI: 10.1016/j.ejmech.2022.114409] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/11/2022] [Accepted: 04/20/2022] [Indexed: 01/28/2023]
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7
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Relitti N, Saraswati AP, Carullo G, Papa A, Monti A, Benedetti R, Passaro E, Brogi S, Calderone V, Butini S, Gemma S, Altucci L, Campiani G, Doti N. Design and Synthesis of New Oligopeptidic Parvulin Inhibitors. ChemMedChem 2022; 17:e202200050. [PMID: 35357776 PMCID: PMC9321596 DOI: 10.1002/cmdc.202200050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/28/2022] [Indexed: 11/12/2022]
Abstract
Pin1 catalyzes the cis-trans isomerization of pThr-Pro or pSer-Pro amide bonds of different proteins involved in several physio/pathological processes. In this framework, recent research activity is directed towards the identification of new selective Pin1 inhibitors. Here, we developed a set ( 5a - p ) of peptide-based Pin1 inhibitors. Direct-binding experiments allowed the identification of the peptide-based inhibitor 5k as a potent ligand of Pin1. Notably, 5k binds Pin1 with a higher affinity compared to Pin4. The comparative analysis of molecular models of Pin1 and Pin4 with the selected compound, gave a rational explanation of the biochemical activity, and pinpointed the chemical elements that, if opportunely modified, may further improve inhibitory potency, pharmacological properties and selectivity of future peptide-based Parvulin inhibitors. Since 5k showed a limited cell penetration and no antiproliferative activity, it was conjugated to a polyarginine stretch, known to promote cell penetration of peptides, to obtain R8-5k derivative, which displayed an anti-proliferative effect on cancer cell lines compared to non-tumor cells. The effect of R8 on cell proliferation was also investigated. This work doubts the application of the R8 strategy for the development of cell penetrating antiproliferative peptides since it is not inert.
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Affiliation(s)
- Nicola Relitti
- University of Siena: Universita degli Studi di Siena, DBCF, ITALY
| | | | - Gabriele Carullo
- University of Siena: Universita degli Studi di Siena, DBCF, 2, Aldo Moro, 53100 Siena Italy, 53100, Siena, ITALY
| | - Alessandro Papa
- University of Siena: Universita degli Studi di Siena, DBCF, ITALY
| | | | - Rosaria Benedetti
- University of Campania Luigi Vanvitelli: Universita degli Studi della Campania Luigi Vanvitelli, Medicine, ITALY
| | - Eugenia Passaro
- University of Pisa Department of Pharmaceutical Sciences: Universita degli Studi di Pisa Dipartimento di Farmacia, Pharmacy, ITALY
| | - Simone Brogi
- University of Pisa Department of Pharmaceutical Sciences: Universita degli Studi di Pisa Dipartimento di Farmacia, Pharmacy, ITALY
| | - Vincenzo Calderone
- University of Pisa Department of Pharmaceutical Sciences: Universita degli Studi di Pisa Dipartimento di Farmacia, Pharmacy, ITALY
| | - Stefania Butini
- University of Siena: Universita degli Studi di Siena, DBCF, ITALY
| | - Sandra Gemma
- University of Siena: Universita degli Studi di Siena, DBCF, ITALY
| | - Lucia Altucci
- University of Campania Luigi Vanvitelli: Universita degli Studi della Campania Luigi Vanvitelli, Medicine, ITALY
| | - Giuseppe Campiani
- Universita degli Studi di Siena, Dipartimento di Biotecnologie, Via Aldo Moro 2, 53100, Siena, ITALY
| | - Nunzianna Doti
- CNR: Consiglio Nazionale delle Ricerche, Bioimaging, ITALY
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Virtual Combinatorial Library Screening of Quinadoline B Derivatives against SARS-CoV-2 RNA-Dependent RNA Polymerase. COMPUTATION 2022. [DOI: 10.3390/computation10010007] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The unprecedented global health threat of SARS-CoV-2 has sparked a continued interest in discovering novel anti-COVID-19 agents. To this end, we present here a computer-based protocol for identifying potential compounds targeting RNA-dependent RNA polymerase (RdRp). Starting from our previous study wherein, using a virtual screening campaign, we identified a fumiquinazolinone alkaloid quinadoline B (Q3), an antiviral fungal metabolite with significant activity against SARS-CoV-2 RdRp, we applied in silico combinatorial methodologies for generating and screening a library of anti-SARS-CoV-2 candidates with strong in silico affinity for RdRp. For this study, the quinadoline pharmacophore was subjected to structural iteration, obtaining a Q3-focused library of over 900,000 unique structures. This chemical library was explored to identify binders of RdRp with greater affinity with respect to the starting compound Q3. Coupling this approach with the evaluation of physchem profile, we found 26 compounds with significant affinities for the RdRp binding site. Moreover, top-ranked compounds were submitted to molecular dynamics to evaluate the stability of the systems during a selected time, and to deeply investigate the binding mode of the most promising derivatives. Among the generated structures, five compounds, obtained by inserting nucleotide-like scaffolds (1, 2, and 5), heterocyclic thiazolyl benzamide moiety (compound 3), and a peptide residue (compound 4), exhibited enhanced binding affinity for SARS-CoV-2 RdRp, deserving further investigation as possible antiviral agents. Remarkably, the presented in silico procedure provides a useful computational procedure for hit-to-lead optimization, having implications in anti-SARS-CoV-2 drug discovery and in general in the drug optimization process.
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Wang J, Cao Z, Wang F, Wang P, An J, Fu X, Liu T, Li Y, Li Y, Zhao Y, Lin H, He B. Cysteine derivatives as acetyl lysine mimics to inhibit zinc-dependent histone deacetylases for treating cancer. Eur J Med Chem 2021; 225:113799. [PMID: 34500130 DOI: 10.1016/j.ejmech.2021.113799] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/09/2021] [Accepted: 08/22/2021] [Indexed: 12/12/2022]
Abstract
Zinc-dependent histone deacetylases (HDACs) are important epigenetic regulators that have become important drug targets for treating cancer. Although five HDAC inhibitors have been approved for treating several cancers, there is still a huge demand on discovering new HDAC inhibitors to explore the therapeutic potentials for treating solid tumor cancers. Substrate mimics are a powerful rational design approach for the development of potent inhibitors. Here we describe the rational design, synthesis, biological evaluation, molecular docking and in vivo efficacy study of a class of HDAC inhibitors using Nε-acetyl lysine mimics that are derived from cysteine. As a result, compounds 7a, 9b and 13d demonstrated pan-HDAC inhibition and broad cytotoxicity against several cancer cell lines, comparable to the approved HDAC inhibitor SAHA. Furthermore, 13d significantly inhibited tumor growth in a A549 xenograft mice model without any obvious weight loss, supporting that the cysteine-derived acetyl lysine mimics are promising HDAC inhibitors with therapeutic potentials for treating cancer.
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Affiliation(s)
- Jie Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Zhuoxian Cao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Fang Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Pan Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Jianxiong An
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Xiaozhong Fu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Ting Liu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Yan Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Yongjun Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Yonglong Zhao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Hening Lin
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, United States
| | - Bin He
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medicine, Guizhou Medical University, Guiyang, 550004, China.
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10
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Flori L, Petrarolo G, Brogi S, La Motta C, Testai L, Calderone V. Identification of novel SIRT1 activators endowed with cardioprotective profile. Eur J Pharm Sci 2021; 165:105930. [PMID: 34265406 DOI: 10.1016/j.ejps.2021.105930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/16/2021] [Accepted: 07/03/2021] [Indexed: 12/25/2022]
Abstract
Drugs targeting epigenetic mechanisms are attracting the attention of scientists since it was observed that the modulation of this post-translational apparatus, could help to identify innovative therapeutic strategies. Among the epigenetic druggable targets, the positive modulation of SIRT1 has also been related to significant cardioprotective effects. Unfortunately, actual SIRT1 activators (natural products and synthetic molecules) suffer from several drawbacks, particularly poor pharmacokinetic profiles. Accordingly, in this article we present the development of an integrated screening platform aimed at identifying novel SIRT1 activators with favorable drug-like features as cardioprotective agents. Encompassing several competencies (in silico, medicinal chemistry, and pharmacology), we describe a multidisciplinary approach for rapidly identifying SIRT1 activators and their preliminary pharmacological characterization. In the first step, we virtually screened an in-house chemical library comprising synthetic molecules inspired by nature, against SIRT1 enzyme. To this end, we combined molecular docking-based approach with the estimation of relative ligand binding energy, using the crystal structure of SIRT1 enzyme in complex with resveratrol. Eleven computational hits were identified, synthesized and tested against the isolated enzyme for validating the in silico strategy. Among the tested molecules, five of them behave as SIRT1 enzyme activators. Due to the superior response in activating the enzyme and its favorable calculated physico-chemical properties, compound 8 was further characterized in ex vivo studies on isolated and perfused rat hearts submitted to ischemia/reperfusion (I/R) period. The pharmacological profile of compound 8, suggests that this molecule represents a prototypic SIRT1 activator with satisfactory drug-like profile, paving the way for developing novel epigenetic cardioprotective agents.
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Affiliation(s)
- Lorenzo Flori
- Department of Pharmacy, University of Pisa, Via Bonanno, 6, I-56126 Pisa, Italy
| | - Giovanni Petrarolo
- Department of Pharmacy, University of Pisa, Via Bonanno, 6, I-56126 Pisa, Italy
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, Via Bonanno, 6, I-56126 Pisa, Italy.
| | - Concettina La Motta
- Department of Pharmacy, University of Pisa, Via Bonanno, 6, I-56126 Pisa, Italy.
| | - Lara Testai
- Department of Pharmacy, University of Pisa, Via Bonanno, 6, I-56126 Pisa, Italy.
| | - Vincenzo Calderone
- Department of Pharmacy, University of Pisa, Via Bonanno, 6, I-56126 Pisa, Italy
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11
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Sirous H, Campiani G, Calderone V, Brogi S. Discovery of novel hit compounds as potential HDAC1 inhibitors: The case of ligand- and structure-based virtual screening. Comput Biol Med 2021; 137:104808. [PMID: 34478925 DOI: 10.1016/j.compbiomed.2021.104808] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/24/2021] [Accepted: 08/24/2021] [Indexed: 11/28/2022]
Abstract
Histone deacetylases (HDACs) as an important family of epigenetic regulatory enzymes are implicated in the onset and progression of carcinomas. As a result, HDAC inhibition has been proven as a compelling strategy for reversing the aberrant epigenetic changes associated with cancer. However, non-selective profile of most developed HDAC inhibitors (HDACIs) leads to the occurrence of various side effects, limiting their clinical utility. This evidence provides a solid ground for ongoing research aimed at identifying isoform-selective inhibitors. Among the isoforms, HDAC1 have particularly gained increased attention as a preferred target for the design of selective HDACIs. Accordingly, in this paper, we have developed a reliable virtual screening process, combining different ligand- and structure-based methods, to identify novel benzamide-based analogs with potential HDAC1 inhibitory activity. For this purpose, a focused library of 736,160 compounds from PubChem database was first compiled based on 80% structural similarity with four known benzamide-based HDAC1 inhibitors, Mocetinostat, Entinostat, Tacedinaline, and Chidamide. Our inclusive in-house 3D-QSAR model, derived from pharmacophore-based alignment, was then employed as a 3D-query to discriminate hits with the highest predicted HDAC1 inhibitory activity. The selected hits were subjected to subsequent structure-based approaches (induced-fit docking (IFD), MM-GBSA calculations and molecular dynamics (MD) simulation) to retrieve potential compounds with the highest binding affinity for HDAC1 active site. Additionally, in silico ADMET properties and PAINS filtration were also considered for selecting an enriched set of the best drug-like molecules. Finally, six top-ranked hit molecules, CID_38265326, CID_56064109, CID_8136932, CID_55802151, CID_133901641 and CID_18150975 were identified to expose the best stability profiles and binding mode in the HDAC1 active site. The IFD and MD results cooperatively confirmed the interactions of the promising selected hits with critical residues within HDAC1 active site. In summary, the presented computational approach can provide a set of guidelines for the further development of improved benzamide-based derivatives targeting HDAC1 isoform.
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Affiliation(s)
- Hajar Sirous
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, 81746-73461 Isfahan, Iran.
| | - Giuseppe Campiani
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, 2018-2022, University of Siena, Via Aldo Moro 2, I-53100 Siena, Italy
| | - Vincenzo Calderone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, I-56126 Pisa, Italy
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, I-56126 Pisa, Italy.
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12
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Campiani G, Cavella C, Osko JD, Brindisi M, Relitti N, Brogi S, Saraswati AP, Federico S, Chemi G, Maramai S, Carullo G, Jaeger B, Carleo A, Benedetti R, Sarno F, Lamponi S, Rottoli P, Bargagli E, Bertucci C, Tedesco D, Herp D, Senger J, Ruberti G, Saccoccia F, Saponara S, Gorelli B, Valoti M, Kennedy B, Sundaramurthi H, Butini S, Jung M, Roach KM, Altucci L, Bradding P, Christianson DW, Gemma S, Prasse A. Harnessing the Role of HDAC6 in Idiopathic Pulmonary Fibrosis: Design, Synthesis, Structural Analysis, and Biological Evaluation of Potent Inhibitors. J Med Chem 2021; 64:9960-9988. [PMID: 34251197 PMCID: PMC8300879 DOI: 10.1021/acs.jmedchem.1c00184] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is an interstitial lung disease characterized by a progressive-fibrosing phenotype. IPF has been associated with aberrant HDAC activities confirmed by our immunohistochemistry studies on HDAC6 overexpression in IPF lung tissues. We herein developed a series of novel hHDAC6 inhibitors, having low inhibitory potency over hHDAC1 and hHDAC8, as potential pharmacological tools for IPF treatment. Their inhibitory potency was combined with low in vitro and in vivo toxicity. Structural analysis of 6h and structure-activity relationship studies contributed to the optimization of the binding mode of the new molecules. The best-performing analogues were tested for their efficacy in inhibiting fibrotic sphere formation and cell viability, proving their capability in reverting the IPF phenotype. The efficacy of analogue 6h was also determined in a validated human lung model of TGF-β1-dependent fibrogenesis. The results highlighted in this manuscript may pave the way for the identification of first-in-class molecules for the treatment of IPF.
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Affiliation(s)
- Giuseppe Campiani
- University of Siena, Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, via Aldo Moro 2, 53100 Siena, Italy
| | - Caterina Cavella
- University of Siena, Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, via Aldo Moro 2, 53100 Siena, Italy
| | - Jeremy D. Osko
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, United States
| | - Margherita Brindisi
- University of Siena, Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, via Aldo Moro 2, 53100 Siena, Italy
| | - Nicola Relitti
- University of Siena, Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, via Aldo Moro 2, 53100 Siena, Italy
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126, Pisa, Italy
| | - A. Prasanth Saraswati
- University of Siena, Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, via Aldo Moro 2, 53100 Siena, Italy
| | - Stefano Federico
- University of Siena, Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, via Aldo Moro 2, 53100 Siena, Italy
| | - Giulia Chemi
- University of Siena, Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, via Aldo Moro 2, 53100 Siena, Italy
| | - Samuele Maramai
- University of Siena, Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, via Aldo Moro 2, 53100 Siena, Italy
| | - Gabriele Carullo
- University of Siena, Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, via Aldo Moro 2, 53100 Siena, Italy
| | - Benedikt Jaeger
- Klinik für Pneumologie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, Hannover, 30625, Germany
| | - Alfonso Carleo
- Klinik für Pneumologie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, Hannover, 30625, Germany
| | - Rosaria Benedetti
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Vico L. de Crecchio 7, 80138, Naples, Italy
| | - Federica Sarno
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Vico L. de Crecchio 7, 80138, Naples, Italy
| | - Stefania Lamponi
- University of Siena, Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, via Aldo Moro 2, 53100 Siena, Italy
| | - Paola Rottoli
- University of Siena, Specialization School of Respiratory Diseases, Department of Medical Sciences, Surgery and Neurosciences, Centro didattico Le Scotte, , 53100, Siena, Italy
| | - Elena Bargagli
- University of Siena, Department of Medical Sciences, Surgery and Neurosciences, Respiratory Diseases Unit, AOUS, Centro didattico Le Scotte, 53100, Siena, Italy
| | - Carlo Bertucci
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro, 6, Bologna 40126, Italy
| | - Daniele Tedesco
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro, 6, Bologna 40126, Italy
| | - Daniel Herp
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstraße 25, 79104, Freiburg, Germany
| | - Johanna Senger
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstraße 25, 79104, Freiburg, Germany
| | - Giovina Ruberti
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), via E. Ramarini 32, 00015 Monterotondo (Rome), Italy
| | - Fulvio Saccoccia
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), via E. Ramarini 32, 00015 Monterotondo (Rome), Italy
| | - Simona Saponara
- Department of Life Sciences, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Beatrice Gorelli
- Department of Life Sciences, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Massimo Valoti
- Department of Life Sciences, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Breándan Kennedy
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, D04 V1W8, Dublin, Ireland
| | - Husvinee Sundaramurthi
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, D04 V1W8, Dublin, Ireland
| | - Stefania Butini
- University of Siena, Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, via Aldo Moro 2, 53100 Siena, Italy
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstraße 25, 79104, Freiburg, Germany
| | - Katy M. Roach
- Department of Respiratory Sciences, University of Leicester, UK, Institute of Lung Health and NIHR Leicester BRC-Respiratory, LE5 4PW, Leicester, UK
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Vico L. de Crecchio 7, 80138, Naples, Italy
| | - Peter Bradding
- Department of Respiratory Sciences, University of Leicester, UK, Institute of Lung Health and NIHR Leicester BRC-Respiratory, LE5 4PW, Leicester, UK
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, United States
| | - Sandra Gemma
- University of Siena, Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, via Aldo Moro 2, 53100 Siena, Italy
| | - Antje Prasse
- Klinik für Pneumologie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, Hannover, 30625, Germany
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13
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Grillo A, Fezza F, Chemi G, Colangeli R, Brogi S, Fazio D, Federico S, Papa A, Relitti N, Di Maio R, Giorgi G, Lamponi S, Valoti M, Gorelli B, Saponara S, Benedusi M, Pecorelli A, Minetti P, Valacchi G, Butini S, Campiani G, Gemma S, Maccarrone M, Di Giovanni G. Selective Fatty Acid Amide Hydrolase Inhibitors as Potential Novel Antiepileptic Agents. ACS Chem Neurosci 2021; 12:1716-1736. [PMID: 33890763 DOI: 10.1021/acschemneuro.1c00192] [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] [Indexed: 12/11/2022] Open
Abstract
Temporal lobe epilepsy is the most common form of epilepsy, and current antiepileptic drugs are ineffective in many patients. The endocannabinoid system has been associated with an on-demand protective response to seizures. Blocking endocannabinoid catabolism would elicit antiepileptic effects, devoid of psychotropic effects. We herein report the discovery of selective anandamide catabolic enzyme fatty acid amide hydrolase (FAAH) inhibitors with promising antiepileptic efficacy, starting from a further investigation of our prototypical inhibitor 2a. When tested in two rodent models of epilepsy, 2a reduced the severity of the pilocarpine-induced status epilepticus and the elongation of the hippocampal maximal dentate activation. Notably, 2a did not affect hippocampal dentate gyrus long-term synaptic plasticity. These data prompted our further endeavor aiming at discovering new antiepileptic agents, developing a new set of FAAH inhibitors (3a-m). Biological studies highlighted 3h and 3m as the best performing analogues to be further investigated. In cell-based studies, using a neuroblastoma cell line, 3h and 3m could reduce the oxinflammation state by decreasing DNA-binding activity of NF-kB p65, devoid of cytotoxic effect. Unwanted cardiac effects were excluded for 3h (Langendorff perfused rat heart). Finally, the new analogue 3h reduced the severity of the pilocarpine-induced status epilepticus as observed for 2a.
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Affiliation(s)
- Alessandro Grillo
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Filomena Fezza
- Department of Experimental Medicine Tor Vergata, University of Rome, Via Montpellier 1, 00121 Rome, Italy
| | - Giulia Chemi
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Roberto Colangeli
- Laboratory of Neurophysiology, Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, MSD2080 Msida, Malta
- Department of Experimental and Clinical Medicine, Section of Neuroscience and Cell Biology, Università Politecnica delle Marche, 60126 Ancona, Italy
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Domenico Fazio
- European Center for Brain Research/IRCCS Santa Lucia Foundation, Via del Fosso di Fiorano 64, 00143 Rome, Italy
| | - Stefano Federico
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Alessandro Papa
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Nicola Relitti
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Roberto Di Maio
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, University of Pittsburgh, Pittsburgh, 15261 Pennsylvania, United States
| | - Gianluca Giorgi
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Stefania Lamponi
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Massimo Valoti
- Department of Life Sciences, University of Siena, Via Aldo Moro, 2, 53100 Siena, Italy
| | - Beatrice Gorelli
- Department of Life Sciences, University of Siena, Via Aldo Moro, 2, 53100 Siena, Italy
| | - Simona Saponara
- Department of Life Sciences, University of Siena, Via Aldo Moro, 2, 53100 Siena, Italy
| | - Mascia Benedusi
- Department of Biomedical and Specialist Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, 44121 Ferrara, Italy
| | - Alessandra Pecorelli
- Plants for Human Health Institute, Animal Science Department, NC Research Campus, NC State University, 600 Laureate Way, Kannapolis, 28081 North Carolina, United States
| | | | - Giuseppe Valacchi
- Department of Biomedical and Specialist Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, 44121 Ferrara, Italy
- Plants for Human Health Institute, Animal Science Department, NC Research Campus, NC State University, 600 Laureate Way, Kannapolis, 28081 North Carolina, United States
- Department of Food and Nutrition, Kyung Hee University, 02447 Seoul, South Korea
| | - Stefania Butini
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Giuseppe Campiani
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Sandra Gemma
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Mauro Maccarrone
- European Center for Brain Research/IRCCS Santa Lucia Foundation, Via del Fosso di Fiorano 64, 00143 Rome, Italy
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio snc, 67100 L’Aquila, Italy
| | - Giuseppe Di Giovanni
- Laboratory of Neurophysiology, Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, MSD2080 Msida, Malta
- Neuroscience Division, School of Biosciences, Cardiff University, CF10 3AT Cardiff, United Kingdom
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14
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Zhang XH, Qin-Ma, Wu HP, Khamis MY, Li YH, Ma LY, Liu HM. A Review of Progress in Histone Deacetylase 6 Inhibitors Research: Structural Specificity and Functional Diversity. J Med Chem 2021; 64:1362-1391. [PMID: 33523672 DOI: 10.1021/acs.jmedchem.0c01782] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Histone deacetylases (HDACs) are essential for maintaining homeostasis by catalyzing histone deacetylation. Aberrant expression of HDACs is associated with various human diseases. Although HDAC inhibitors are used as effective chemotherapeutic agents in clinical practice, their applications remain limited due to associated side effects induced by weak isoform selectivity. HDAC6 displays unique structure and cellular localization as well as diverse substrates and exhibits a wider range of biological functions than other isoforms. HDAC6 inhibitors have been effectively used to treat cancers, neurodegenerative diseases, and autoimmune disorders without exerting significant toxic effects. Progress has been made in defining the crystal structures of HDAC6 catalytic domains which has influenced the structure-based drug design of HDAC6 inhibitors. This review summarizes recent literature on HDAC6 inhibitors with particular reference to structural specificity and functional diversity. It may provide up-to-date guidance for the development of HDAC6 inhibitors and perspectives for optimization of therapeutic applications.
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Affiliation(s)
- Xin-Hui Zhang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Qin-Ma
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Hui-Pan Wu
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Mussa Yussuf Khamis
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Yi-Han Li
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Li-Ying Ma
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China.,China Meheco Topfond Pharmaceutical Co., Ltd., Zhumadian, 463000, PR China
| | - Hong-Min Liu
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
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15
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Saraswati AP, Relitti N, Brindisi M, Osko JD, Chemi G, Federico S, Grillo A, Brogi S, McCabe NH, Turkington RC, Ibrahim O, O’Sullivan J, Lamponi S, Ghanim M, Kelly VP, Zisterer D, Amet R, Hannon Barroeta P, Vanni F, Ulivieri C, Herp D, Sarno F, Di Costanzo A, Saccoccia F, Ruberti G, Jung M, Altucci L, Gemma S, Butini S, Christianson DW, Campiani G. Spiroindoline-Capped Selective HDAC6 Inhibitors: Design, Synthesis, Structural Analysis, and Biological Evaluation. ACS Med Chem Lett 2020; 11:2268-2276. [PMID: 33214839 DOI: 10.1021/acsmedchemlett.0c00395] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/29/2020] [Indexed: 12/12/2022] Open
Abstract
Histone deacetylase inhibitors (HDACi) have emerged as promising therapeutics for the treatment of neurodegeneration, cancer, and rare disorders. Herein, we report the development of a series of spiroindoline-based HDAC6 isoform-selective inhibitors based on the X-ray crystal studies of the hit 6a. We identified compound 6j as the most potent and selective hHDAC6 inhibitor of the series. Biological investigation of compounds 6b, 6h, and 6j demonstrated their antiproliferative activity against several cancer cell lines. Western blotting studies indicated that they were able to increase tubulin acetylation, without significant variation in histone acetylation state, and induced PARP cleavage indicating their apoptotic potential at the molecular level. 6j induced HDAC6-dependent pSTAT3 inhibition.
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Affiliation(s)
- A. Prasanth Saraswati
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Nicola Relitti
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Margherita Brindisi
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Jeremy D. Osko
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Giulia Chemi
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Stefano Federico
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Alessandro Grillo
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126, Pisa, Italy
| | - Niamh H. McCabe
- Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, U.K
| | - Richard C. Turkington
- Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, U.K
| | - Ola Ibrahim
- School of Dental Science, Trinity College Dublin, Lincoln Place, Dublin 2, Ireland
| | - Jeffrey O’Sullivan
- School of Dental Science, Trinity College Dublin, Lincoln Place, Dublin 2, Ireland
| | - Stefania Lamponi
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Magda Ghanim
- School of Biochemistry and Immunology, Trinity Biomedical Science Institute, Trinity College, 152-160, Pearse Street, Dublin 2, Ireland
| | - Vincent P. Kelly
- School of Biochemistry and Immunology, Trinity Biomedical Science Institute, Trinity College, 152-160, Pearse Street, Dublin 2, Ireland
| | - Daniela Zisterer
- School of Biochemistry and Immunology, Trinity Biomedical Science Institute, Trinity College, 152-160, Pearse Street, Dublin 2, Ireland
| | - Rebecca Amet
- School of Biochemistry and Immunology, Trinity Biomedical Science Institute, Trinity College, 152-160, Pearse Street, Dublin 2, Ireland
| | - Patricia Hannon Barroeta
- School of Biochemistry and Immunology, Trinity Biomedical Science Institute, Trinity College, 152-160, Pearse Street, Dublin 2, Ireland
| | - Francesca Vanni
- Department of Life Sciences, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Cristina Ulivieri
- Department of Life Sciences, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Daniel Herp
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstraße 25, 79104, Freiburg, Germany
| | - Federica Sarno
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli″, 80138 Naples, Italy
| | - Antonella Di Costanzo
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli″, 80138 Naples, Italy
| | - Fulvio Saccoccia
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), via E. Ramarini 32, 00015 Monterotondo, Rome, Italy
| | - Giovina Ruberti
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), via E. Ramarini 32, 00015 Monterotondo, Rome, Italy
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstraße 25, 79104, Freiburg, Germany
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli″, 80138 Naples, Italy
| | - Sandra Gemma
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Stefania Butini
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Giuseppe Campiani
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
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16
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Relitti N, Saraswati AP, Chemi G, Brindisi M, Brogi S, Herp D, Schmidtkunz K, Saccoccia F, Ruberti G, Ulivieri C, Vanni F, Sarno F, Altucci L, Lamponi S, Jung M, Gemma S, Butini S, Campiani G. Novel quinolone-based potent and selective HDAC6 inhibitors: Synthesis, molecular modeling studies and biological investigation. Eur J Med Chem 2020; 212:112998. [PMID: 33199154 DOI: 10.1016/j.ejmech.2020.112998] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/03/2020] [Accepted: 11/03/2020] [Indexed: 01/08/2023]
Abstract
In this work we describe the synthesis of potent and selective quinolone-based histone deacetylase 6 (HDAC6) inhibitors. The quinolone moiety has been exploited as an innovative bioactive cap-group for HDAC6 inhibition; its synthesis was achieved by applying a multicomponent reaction. The optimization of potency and selectivity of these products was performed by employing computational studies which led to the discovery of the diethylaminomethyl derivatives 7g and 7k as the most promising hit molecules. These compounds were investigated in cellular studies to evaluate their anticancer effect against colon (HCT-116) and histiocytic lymphoma (U9347) cancer cells, showing good to excellent potency, leading to tumor cell death by apoptosis induction. The small molecules 7a, 7g and 7k were able to strongly inhibit the cytoplasmic and slightly the nuclear HDAC enzymes, increasing the acetylation of tubulin and of the lysine 9 and 14 of histone 3, respectively. Compound 7g was also able to increase Hsp90 acetylation levels in HCT-116 cells, thus further supporting its HDAC6 inhibitory profile. Cytotoxicity and mutagenicity assays of these molecules showed a safe profile; moreover, the HPLC analysis of compound 7k revealed good solubility and stability profile.
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Affiliation(s)
- Nicola Relitti
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - A Prasanth Saraswati
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Giulia Chemi
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Margherita Brindisi
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | - Daniel Herp
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstraße 25, 79104, Freiburg, Germany
| | - Karin Schmidtkunz
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstraße 25, 79104, Freiburg, Germany
| | - Fulvio Saccoccia
- Institute of Biochemistry and Cell Biology, CNR, Campus A. Buzzati-Traverso. Via E. Ramarini 32, 00015, Monterotondo, Rome, Italy
| | - Giovina Ruberti
- Institute of Biochemistry and Cell Biology, CNR, Campus A. Buzzati-Traverso. Via E. Ramarini 32, 00015, Monterotondo, Rome, Italy
| | - Cristina Ulivieri
- Department of Life Sciences, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Francesca Vanni
- Department of Life Sciences, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Federica Sarno
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Vico L. de Crecchio 7, 80138, Naples, Italy
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Vico L. de Crecchio 7, 80138, Naples, Italy
| | - Stefania Lamponi
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstraße 25, 79104, Freiburg, Germany
| | - Sandra Gemma
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Stefania Butini
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Giuseppe Campiani
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy.
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17
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Linciano P, Benedetti R, Pinzi L, Russo F, Chianese U, Sorbi C, Altucci L, Rastelli G, Brasili L, Franchini S. Investigation of the effect of different linker chemotypes on the inhibition of histone deacetylases (HDACs). Bioorg Chem 2020; 106:104462. [PMID: 33213894 DOI: 10.1016/j.bioorg.2020.104462] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 12/14/2022]
Abstract
Histone Deacetylases (HDACs) are among the most attractive and interesting targets in anticancer drug discovery. The clinical relevance of HDAC inhibitors (HDACIs) is testified by four FDA-approved drugs for cancer treatment. However, one of the main drawbacks of these drugs resides in the lack of selectivity against the different HDAC isoforms, resulting in severe side effects. Thus, the identification of selective HDACIs represents an exciting challenge for medicinal chemists. HDACIs are composed of a cap group, a linker region, and a metal-binding group interacting with the catalytic zinc ion. While the cap group has been extensively investigated, less information is available about the effect of the linker on isoform selectivity. To this aim, in this work, we explored novel linker chemotypes to direct isoform selectivity. A small library of 25 hydroxamic acids with hitherto unexplored linker chemotypes was prepared. In vitro tests demonstrated that, depending on the linker type, some candidates selectively inhibit HDAC1 over HDAC6 isoform or vice versa. Docking calculations were performed to rationalize the effect of the novel linker chemotypes on biologic activity. Moreover, four compounds were able to increase the levels of acetylation of histone H3 or tubulin. These compounds were also assayed in breast cancer MCF7 cells to test their antiproliferative effect. Three compounds showed a significant reduction of cancer proliferation, representing valuable starting points for further optimization.
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Affiliation(s)
- Pasquale Linciano
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, via G. Campi 103, 41125 Modena, Italy
| | - Rosaria Benedetti
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "Luigi Vanvitelli", via L. De Crecchio 7, 80138 Napoli, Italy
| | - Luca Pinzi
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, via G. Campi 103, 41125 Modena, Italy
| | - Fabiana Russo
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, via G. Campi 103, 41125 Modena, Italy
| | - Ugo Chianese
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "Luigi Vanvitelli", via L. De Crecchio 7, 80138 Napoli, Italy
| | - Claudia Sorbi
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, via G. Campi 103, 41125 Modena, Italy.
| | - Lucia Altucci
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "Luigi Vanvitelli", via L. De Crecchio 7, 80138 Napoli, Italy
| | - Giulio Rastelli
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, via G. Campi 103, 41125 Modena, Italy
| | - Livio Brasili
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, via G. Campi 103, 41125 Modena, Italy
| | - Silvia Franchini
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, via G. Campi 103, 41125 Modena, Italy.
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18
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Hydroxamic acid hybrids as the potential anticancer agents: An Overview. Eur J Med Chem 2020; 205:112679. [DOI: 10.1016/j.ejmech.2020.112679] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/12/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023]
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19
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Di Capua A, Reale A, Paolino M, Chemi G, Brogi S, Cappelli A, Giorgi G, Grande F, Di Cesare Mannelli L, Ghelardini C, Matucci R, Garofalo A, Anzini M. Design, synthesis and biological evaluation of 7-substituted 4-phenyl-6H-imidazo[1,5-a]thieno[3,2-f] [1,4]diazepines as safe anxiolytic agents. Eur J Med Chem 2020; 200:112405. [PMID: 32492595 DOI: 10.1016/j.ejmech.2020.112405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 11/27/2022]
Abstract
A series of 4-phenyl-6H-imidazo[1,5-a]thieno[3,2-f][1,4]diazepine-7-carboxylate esters were synthesized and tested as central benzodiazepine receptor (CBR) ligands by the ability to displace [3H]flumazenil from rat cortical membranes. All the compounds showed high affinity with IC50 values ranging from 5.19 to 16.22 nM. In particular, compounds 12b (IC50 = 8.66 nM) and 12d (IC50 = 5.19 nM) appeared as the most effective ligands being their affinity values significantly lower than that of diazepam (IC50 = 18.52 nM). Compounds 12a-f were examined in vivo for their pharmacological effects in mice and five potential benzodiazepine (BDZ) actions were thus taken into consideration: anxiolytic, anticonvulsant, anti-amnesic, hypnotic, and locomotor activities. All the new synthesized compounds were able to induce a significant antianxiety effect and, among them, compound 12f protected pentylenetetrazole (PTZ)-induced convulsions in a dose-dependent manner reaching a 40% effect at 30 mg/kg. In addition, all the compounds were able to significantly prevent the memory impairment evoked by scopolamine, while none of them was able to interfere with pentobarbital-evoked sleep and influence motor coordination. Moreover, title compounds did not affect locomotor and exploratory activity at the same time and doses at which the anti-anxiety effect was observed. Finally, molecular docking simulations were carried out in order to assess the binding mode for compounds 12a-f. The obtained results demonstrated that these compounds bind the BDZ binding site in a similar fashion to flumazenil.
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Affiliation(s)
- Angela Di Capua
- Dipartimento di Biotecnologie, Chimica e Farmacia, (Dipartimento d'Eccellenza 2018-2022), Università di Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Annalisa Reale
- Dipartimento di Biotecnologie, Chimica e Farmacia, (Dipartimento d'Eccellenza 2018-2022), Università di Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Marco Paolino
- Dipartimento di Biotecnologie, Chimica e Farmacia, (Dipartimento d'Eccellenza 2018-2022), Università di Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Giulia Chemi
- Dipartimento di Biotecnologie, Chimica e Farmacia, (Dipartimento d'Eccellenza 2018-2022), Università di Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Simone Brogi
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno Pisano 6, 56126, Pisa, Italy
| | - Andrea Cappelli
- Dipartimento di Biotecnologie, Chimica e Farmacia, (Dipartimento d'Eccellenza 2018-2022), Università di Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Gianluca Giorgi
- Dipartimento di Biotecnologie, Chimica e Farmacia, (Dipartimento d'Eccellenza 2018-2022), Università di Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Fedora Grande
- Dipartimento di Farmacia e Scienze della Salute e della Nutrizione (Dipartimento d'Eccellenza 2018-2022), Università della Calabria, Edificio Polifunzionale, 87036, Arcavacata di Rende (CS), Italy
| | - Lorenzo Di Cesare Mannelli
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino - Sezione di Farmacologia e Tossicologia, Università di Firenze, Viale G. Pieraccini 6, I-50139, Firenze, Italy
| | - Carla Ghelardini
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino - Sezione di Farmacologia e Tossicologia, Università di Firenze, Viale G. Pieraccini 6, I-50139, Firenze, Italy
| | - Rosanna Matucci
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino - Sezione di Farmacologia e Tossicologia, Università di Firenze, Viale G. Pieraccini 6, I-50139, Firenze, Italy
| | - Antonio Garofalo
- Dipartimento di Farmacia e Scienze della Salute e della Nutrizione (Dipartimento d'Eccellenza 2018-2022), Università della Calabria, Edificio Polifunzionale, 87036, Arcavacata di Rende (CS), Italy
| | - Maurizio Anzini
- Dipartimento di Biotecnologie, Chimica e Farmacia, (Dipartimento d'Eccellenza 2018-2022), Università di Siena, Via Aldo Moro 2, 53100, Siena, Italy.
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20
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Design, synthesis and biological evaluation of coumarin-based N-hydroxycinnamamide derivatives as novel histone deacetylase inhibitors with anticancer activities. Bioorg Chem 2020; 101:104023. [DOI: 10.1016/j.bioorg.2020.104023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/21/2020] [Accepted: 06/12/2020] [Indexed: 12/14/2022]
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21
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Zou Y, Cao Z, Wang J, Chen X, Chen YQ, Li Y, Liu J, Zhao Y, Wang A, He B. A Series of Novel HDAC Inhibitors with Anthraquinone as a Cap Group. Chem Pharm Bull (Tokyo) 2020; 68:613-617. [PMID: 32611998 DOI: 10.1248/cpb.c20-00206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Although anthraquinone derivatives possess significant antitumor activity, most of them also displayed those side effects like cardiotoxicity, mainly owing to their inhibition of topoisomerase II of DNA repair mechanisms. Our raised design strategy by switching therapeutic target from topoisomerase II to histone deacetylase (HDAC) has been applied to the design of anthraquinone derivatives in current study. Consequently, a series of novel HDAC inhibitors with a tricylic diketone of anthraquinone as a cap group have been synthesized. After screening and evaluation, compounds 4b, 4d, 7b and 7d have displayed the comparable inhibition in enzymatic activity and cell proliferation than that of Vorinostat (SAHA). Notably, compound 4b showed certain selectivity of antiproliferative effects on cancer cell lines over non-cancer cell lines.
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Affiliation(s)
- Yefang Zou
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University.,School of Pharmacy, Guizhou Medical University
| | - Zhuoxian Cao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University.,School of Pharmacy, Guizhou Medical University
| | - Jie Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University.,School of Pharmacy, Guizhou Medical University
| | - Xiaoxue Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University.,School of Pharmacy, Guizhou Medical University
| | - Yan-Qin Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University.,School of Pharmacy, Guizhou Medical University
| | - Yan Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University.,School of Basic Medicine, Guizhou Medical University
| | - Jingzi Liu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University.,School of Pharmacy, Guizhou Medical University
| | - Yonglong Zhao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University.,School of Pharmacy, Guizhou Medical University
| | - Aimin Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University.,School of Pharmacy, Guizhou Medical University
| | - Bin He
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University.,School of Pharmacy, Guizhou Medical University
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22
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Frydenvang K, Pickering DS, Kshirsagar GU, Chemi G, Gemma S, Sprogøe D, Kærn AM, Brogi S, Campiani G, Butini S, Kastrup JS. Ionotropic Glutamate Receptor GluA2 in Complex with Bicyclic Pyrimidinedione-Based Compounds: When Small Compound Modifications Have Distinct Effects on Binding Interactions. ACS Chem Neurosci 2020; 11:1791-1800. [PMID: 32437601 DOI: 10.1021/acschemneuro.0c00195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
(S)-2-Amino-3-(5-methyl-3-hydroxyisoxazol-4-yl)propanoic acid (AMPA) receptors comprise an important class of ionotropic glutamate receptors activated by glutamate in the central nervous system. These receptors have been shown to be involved in brain diseases, for example, Alzheimer's disease and epilepsy. To understand the functional role of AMPA receptors at the molecular level and their potential as targets for drugs, development of tool compounds is essential. We have previously reported the synthesis of six bicyclic pyrimidinedione-based analogues of willardiine with differences limited to the pyrimidinedione-fused five-membered rings. Despite minor molecular differences, we observed >500-fold difference in binding affinity of the compounds at full-length GluA2. Here, we report binding affinities and the binding mode of these compounds at the ligand-binding domain of GluA2 using X-ray crystallography. The structures revealed similar binding modes, with distinct differences in the interaction between GluA2 and the compounds. The methylene (2) and sulfur (3) containing compounds showed the greatest binding affinities. Changing the dihydrothiophene (3) into pyrrolidine (4), N-methyl pyrrolidine (5), or dihydrofuran (6) induced flexibility in the position of a binding-site water molecule and changes in the hydrogen-bonding network between compound, water, and GluA2. This might be essential for explaining the reduced binding affinity of these compounds. The weakest binding affinity was observed when the aliphatic oxygen containing dihydrofuran (6) was changed into an aromatic furan system (7). Molecular docking studies revealed two possible orientations of 7, whereas only one binding mode was observed for the other analogues. This could likely contribute to the weakest binding affinity of 7 at GluA2.
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Affiliation(s)
- Karla Frydenvang
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Darryl S. Pickering
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Giridhar U. Kshirsagar
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
- Department of Biotechnology, Chemistry and Pharmacy (DoE 2018-2022), University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Giulia Chemi
- Department of Biotechnology, Chemistry and Pharmacy (DoE 2018-2022), University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Sandra Gemma
- Department of Biotechnology, Chemistry and Pharmacy (DoE 2018-2022), University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Desiree Sprogøe
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Anne Mette Kærn
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Giuseppe Campiani
- Department of Biotechnology, Chemistry and Pharmacy (DoE 2018-2022), University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Stefania Butini
- Department of Biotechnology, Chemistry and Pharmacy (DoE 2018-2022), University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Jette Sandholm Kastrup
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
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23
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Computer-Driven Development of an in Silico Tool for Finding Selective Histone Deacetylase 1 Inhibitors. Molecules 2020; 25:molecules25081952. [PMID: 32331470 PMCID: PMC7221830 DOI: 10.3390/molecules25081952] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 04/18/2020] [Accepted: 04/20/2020] [Indexed: 12/19/2022] Open
Abstract
Histone deacetylases (HDACs) are a class of epigenetic modulators overexpressed in numerous types of cancers. Consequently, HDAC inhibitors (HDACIs) have emerged as promising antineoplastic agents. Unfortunately, the most developed HDACIs suffer from poor selectivity towards a specific isoform, limiting their clinical applicability. Among the isoforms, HDAC1 represents a crucial target for designing selective HDACIs, being aberrantly expressed in several malignancies. Accordingly, the development of a predictive in silico tool employing a large set of HDACIs (aminophenylbenzamide derivatives) is herein presented for the first time. Software Phase was used to derive a 3D-QSAR model, employing as alignment rule a common-features pharmacophore built on 20 highly active/selective HDAC1 inhibitors. The 3D-QSAR model was generated using 370 benzamide-based HDACIs, which yielded an excellent correlation coefficient value (R2 = 0.958) and a satisfactory predictive power (Q2 = 0.822; Q2F3 = 0.894). The model was validated (r2ext_ts = 0.794) using an external test set (113 compounds not used for generating the model), and by employing a decoys set and the receiver-operating characteristic (ROC) curve analysis, evaluating the Güner-Henry score (GH) and the enrichment factor (EF). The results confirmed a satisfactory predictive power of the 3D-QSAR model. This latter represents a useful filtering tool for screening large chemical databases, finding novel derivatives with improved HDAC1 inhibitory activity.
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24
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Saccoccia F, Brindisi M, Gimmelli R, Relitti N, Guidi A, Saraswati AP, Cavella C, Brogi S, Chemi G, Butini S, Papoff G, Senger J, Herp D, Jung M, Campiani G, Gemma S, Ruberti G. Screening and Phenotypical Characterization of Schistosoma mansoni Histone Deacetylase 8 ( SmHDAC8) Inhibitors as Multistage Antischistosomal Agents. ACS Infect Dis 2020; 6:100-113. [PMID: 31661956 DOI: 10.1021/acsinfecdis.9b00224] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Schistosomiasis (also known as bilharzia) is a neglected tropical disease caused by platyhelminths of the genus Schistosoma. The disease is endemic in tropical and subtropical areas of the world where water is infested by the intermediate parasite host, the snail. More than 800 million people live in endemic areas and more than 200 million are infected and require treatment. Praziquantel (PZQ) is the drug of choice for schistosomiasis treatment and transmission control being safe and very effective against adult worms of all the clinically relevant Schistosoma species. Unfortunately, it is ineffective on immature, juvenile worms; therefore, it does not prevent reinfection. Moreover, the risk of development and spread of drug resistance because of the widespread use of a single drug in such a large population represents a serious threat. Therefore, research aimed at identifying novel drugs to be used alone or in combination with PZQ are needed. Schistosoma mansoni histone deacetylase 8 (SmHDAC8) is a class I zinc-dependent HDAC, which is abundantly expressed in all stages of its life cycle, thus representing an interesting target for drug discovery. Through virtual screening and phenotypical characterization of selected hits, we discovered two main chemical classes of compounds characterized by the presence of a hydroxamate-based metal binding group coupled to a spiroindoline or a tricyclic thieno[3,2-b]indole core as capping groups. Some of the compounds of both classes were deeply investigated and showed to impair viability of larval, juvenile, and adult schistosomes, to impact egg production in vitro and/or to induce morphological alterations of the adult schistosome reproductive systems. Noteworthy, all of them inhibit the recombinant form of SmHDAC8 enzyme in vitro. Overall, we identified very interesting scaffolds, paving the way to the development of effective antischistosomal agents.
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Affiliation(s)
- Fulvio Saccoccia
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Campus A. Buzzati-Traverso, via E. Ramarini 32, 00015 Monterotondo (Rome), Italy
| | - Margherita Brindisi
- Department of Excellence of Pharmacy, University of Napoli Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Roberto Gimmelli
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Campus A. Buzzati-Traverso, via E. Ramarini 32, 00015 Monterotondo (Rome), Italy
| | - Nicola Relitti
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Alessandra Guidi
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Campus A. Buzzati-Traverso, via E. Ramarini 32, 00015 Monterotondo (Rome), Italy
| | - A Prasanth Saraswati
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Caterina Cavella
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Simone Brogi
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126, Pisa, Italy
| | - Giulia Chemi
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Stefania Butini
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Giuliana Papoff
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Campus A. Buzzati-Traverso, via E. Ramarini 32, 00015 Monterotondo (Rome), Italy
| | - Johanna Senger
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Daniel Herp
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Giuseppe Campiani
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Sandra Gemma
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Giovina Ruberti
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Campus A. Buzzati-Traverso, via E. Ramarini 32, 00015 Monterotondo (Rome), Italy
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25
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Thakur A, Singh A, Kaur N, Ojha R, Nepali K. Steering the antitumor drug discovery campaign towards structurally diverse indolines. Bioorg Chem 2020; 94:103436. [DOI: 10.1016/j.bioorg.2019.103436] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/05/2019] [Accepted: 11/11/2019] [Indexed: 12/13/2022]
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26
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Alfano AI, Zampella A, Novellino E, Brindisi M, Lange H. Harnessing interrupted Fischer in continuous flow: sustainable synthesis of (spiro)indolenine and (spiro)indoline privileged scaffolds. REACT CHEM ENG 2020. [DOI: 10.1039/d0re00329h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
3,3-Disubstituted indolenines are obtained via a green and sustainable flow chemistry protocol for interrupted Fischer indolisation reactions.
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Affiliation(s)
- Antonella Ilenia Alfano
- SPOTS-LAB – Sustainable Pharmaceutical and Organic Technology and Synthesis Laboratory
- Department of Pharmacy
- University of Naples ‘Federico II’
- 80131 Naples
- Italy
| | - Angela Zampella
- SPOTS-LAB – Sustainable Pharmaceutical and Organic Technology and Synthesis Laboratory
- Department of Pharmacy
- University of Naples ‘Federico II’
- 80131 Naples
- Italy
| | - Ettore Novellino
- SPOTS-LAB – Sustainable Pharmaceutical and Organic Technology and Synthesis Laboratory
- Department of Pharmacy
- University of Naples ‘Federico II’
- 80131 Naples
- Italy
| | - Margherita Brindisi
- SPOTS-LAB – Sustainable Pharmaceutical and Organic Technology and Synthesis Laboratory
- Department of Pharmacy
- University of Naples ‘Federico II’
- 80131 Naples
- Italy
| | - Heiko Lange
- SPOTS-LAB – Sustainable Pharmaceutical and Organic Technology and Synthesis Laboratory
- Department of Pharmacy
- University of Naples ‘Federico II’
- 80131 Naples
- Italy
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27
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Hamoud MMS, Pulya S, Osman NA, Bobde Y, Hassan AEA, Abdel-Fattah HA, Ghosh B, Ghanim AM. Design, synthesis, and biological evaluation of novel nicotinamide derivatives as potential histone deacetylase-3 inhibitors. NEW J CHEM 2020. [DOI: 10.1039/d0nj01274b] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The selected nicotinamide-based HDACi displayed selectivity towards HDAC3 over pan HDAC and exhibited potent cytotoxicity against the used cell lines.
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Affiliation(s)
- Mohamed M. S. Hamoud
- Department of Pharmaceutical Organic Chemistry
- Faculty of Pharmacy
- Zagazig University
- Zagazig 44519
- Egypt
| | - Sravani Pulya
- Department of Pharmacy, BITS-Pilani
- Hyderabad Campus, Shamirpet
- Hyderabad
- India
| | - Nermine A. Osman
- Department of Pharmaceutical Organic Chemistry
- Faculty of Pharmacy
- Zagazig University
- Zagazig 44519
- Egypt
| | - Yamini Bobde
- Department of Pharmacy, BITS-Pilani
- Hyderabad Campus, Shamirpet
- Hyderabad
- India
| | - Abdalla E. A. Hassan
- Applied Nucleic Acids Research Center
- Zagazig University
- Egypt
- Department of Chemistry
- Faculty of Science
| | - Hanan A. Abdel-Fattah
- Department of Pharmaceutical Organic Chemistry
- Faculty of Pharmacy
- Zagazig University
- Zagazig 44519
- Egypt
| | - Balaram Ghosh
- Department of Pharmacy, BITS-Pilani
- Hyderabad Campus, Shamirpet
- Hyderabad
- India
| | - Amany M. Ghanim
- Department of Pharmaceutical Organic Chemistry
- Faculty of Pharmacy
- Zagazig University
- Zagazig 44519
- Egypt
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28
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Bai Y, Ahmad D, Wang T, Cui G, Li W. Research Advances in the Use of Histone Deacetylase Inhibitors for Epigenetic Targeting of Cancer. Curr Top Med Chem 2019; 19:995-1004. [PMID: 30686256 DOI: 10.2174/1568026619666190125145110] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 11/21/2018] [Accepted: 11/25/2018] [Indexed: 12/11/2022]
Abstract
The causes and progression of cancer are controlled by epigenetic processes. The mechanisms involved in epigenetic regulation of cancer development, gene expression, and signaling pathways have been studied. Histone deacetylases (HDACs) have a major impact on chromatin remodeling and epigenetics, making their inhibitors a very interesting area of cancer research. This review comprehensively summarizes the literature regarding HDAC inhibitors (HDACis) as an anticancer treatment published in the past few years. In addition, we explain the mechanisms of their therapeutic effects on cancer. An analysis of the beneficial characteristics and drawbacks of HDACis also is presented, which will assist preclinical and clinical researchers in the design of future experiments to improve the therapeutic efficacy of these drugs and circumvent the challenges in the path of successful epigenetic therapy. Future therapeutic strategies may include a combination of HDACis and chemotherapy or other inhibitors to target multiple oncogenic signaling pathways.
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Affiliation(s)
- Yu Bai
- School of Pharmacy, Jilin Medical University, Jilin, China.,Center for Biomaterials, Jilin Medical University, Jilin, China
| | - Daid Ahmad
- Department of Nanotechnology Engineering, University of Waterloo, Waterloo, ON, Canada
| | - Ting Wang
- Department of the Gastrointestinal Surgery, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Guihua Cui
- School of Pharmacy, Jilin Medical University, Jilin, China.,Center for Biomaterials, Jilin Medical University, Jilin, China
| | - Wenliang Li
- School of Pharmacy, Jilin Medical University, Jilin, China.,Center for Biomaterials, Jilin Medical University, Jilin, China.,Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
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29
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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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30
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Brindisi M, Saraswati AP, Brogi S, Gemma S, Butini S, Campiani G. Old but Gold: Tracking the New Guise of Histone Deacetylase 6 (HDAC6) Enzyme as a Biomarker and Therapeutic Target in Rare Diseases. J Med Chem 2019; 63:23-39. [PMID: 31415174 DOI: 10.1021/acs.jmedchem.9b00924] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Epigenetic regulation orchestrates many cellular processes and greatly influences key disease mechanisms. Histone deacetylase (HDAC) enzymes play a crucial role either as biomarkers or therapeutic targets owing to their involvement in specific pathophysiological pathways. Beyond their well-characterized role as histone modifiers, HDACs also interact with several nonhistone substrates and their increased expression has been highlighted in specific diseases. The HDAC6 isoform, due to its unique cytoplasmic localization, modulates the acetylation status of tubulin, HSP90, TGF-β, and peroxiredoxins. HDAC6 also exerts noncatalytic activities through its interaction with ubiquitin. Both catalytic and noncatalytic functions of HDACs are being actively studied in the field of specific rare disorders beyond the well-established role in carcinogenesis. This Perspective outlines the application of HDAC(6) inhibitors in rare diseases, such as Rett syndrome, inherited retinal disorders, idiopathic pulmonary fibrosis, and Charcot-Marie-Tooth disease, highlighting their therapeutic potential as innovative and targeted disease-modifying agents.
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Affiliation(s)
- Margherita Brindisi
- Department of Pharmacy, Department of Excellence 2018-2022 , University of Naples Federico II , Via D. Montesano 49 , I-80131 Naples , Italy
| | - A Prasanth Saraswati
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 , University of Siena , via Aldo Moro 2 , 53100 , Siena , Italy
| | - Simone Brogi
- Department of Pharmacy , University of Pisa , via Bonanno 6 , 56126 , Pisa , Italy
| | - Sandra Gemma
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 , University of Siena , via Aldo Moro 2 , 53100 , Siena , Italy
| | - Stefania Butini
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 , University of Siena , via Aldo Moro 2 , 53100 , Siena , Italy
| | - Giuseppe Campiani
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 , University of Siena , via Aldo Moro 2 , 53100 , Siena , Italy
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31
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Computational Approaches for Drug Discovery. Molecules 2019; 24:molecules24173061. [PMID: 31443558 PMCID: PMC6749237 DOI: 10.3390/molecules24173061] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022] Open
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32
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Zhang Y, Ying JB, Hong JJ, Li FC, Fu TT, Yang FY, Zheng GX, Yao XJ, Lou Y, Qiu Y, Xue WW, Zhu F. How Does Chirality Determine the Selective Inhibition of Histone Deacetylase 6? A Lesson from Trichostatin A Enantiomers Based on Molecular Dynamics. ACS Chem Neurosci 2019; 10:2467-2480. [PMID: 30784262 DOI: 10.1021/acschemneuro.8b00729] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Histone deacetylase 6 (HDAC6) plays a key role in a variety of neurological disorders, which makes it attractive drug target for the treatment of Alzheimer's disease, Parkinson's disease, and memory/learning impairment. The selectivity of HDAC6 inhibitors (sHDAC6Is) are widely considered to be susceptible to the sizes of their Cap group and the physicochemical properties of their linker or zinc-binding group, which makes the discovery of new sHDAC6Is extremely difficult. With the discovery of the distinct selectivity between Trichostatin A (TSA) enantiomers, the chirality residing in the connective units between TSA's Cap and linker shows a great impact on its selectivity. However, the mechanism underlining ( S)-TSA's selectivity is still elusive, and the way chirality switches the selective ( S)-TSA to nonselective ( R)-TSA is unknown. In this study, multiple computational approaches were collectively applied to explore, validate, and differentiate the binding modes of two TSA enantiomers in HDACs (especially the HDAC6) at atomic level. First, two nonconservative residues (G200/M205 and Y197/F202 in HDAC1/6) in loop3 and four conservative residues deep inside the hydrophobic binding pocket were discovered as the decisive residues of ( S)-TSA's selectivity toward HDAC6. Then, a novel mechanism underlying the selectivity of ( S)-TSA toward HDAC6 was proposed, which was composed of the trigger by two nonconservative residues F202 and M205 in HDAC6 and a subsequently improved fit of ( S)-TSA deep inside HDAC6's hydrophobic binding pocket. TSA enantiomers were used as a molecular probe to explore the mechanism underlying sHDAC6Is' selectivity in this study. Because of their decisive roles in ( S)-TSA's selectivity to HDAC6, both F202 and M205 in HDAC6 should be especially considered in the discovery of novel sHDAC6Is.
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Affiliation(s)
- Yang Zhang
- Lab of Innovative Drug Research and Bioinformatics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Jun Biao Ying
- Lab of Innovative Drug Research and Bioinformatics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jia Jun Hong
- Lab of Innovative Drug Research and Bioinformatics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Feng Cheng Li
- Lab of Innovative Drug Research and Bioinformatics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ting Ting Fu
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Feng Yuan Yang
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Guo Xun Zheng
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Xiao Jun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Yan Lou
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou 310000, China
| | - Yunqing Qiu
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou 310000, China
| | - Wei Wei Xue
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- Lab of Innovative Drug Research and Bioinformatics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
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33
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Lamponi S, Aloisi AM, Bonechi C, Consumi M, Donati A, Leone G, Rossi C, Tamasi G, Ghiandai L, Ferrini E, Fiorenzani P, Ceccarelli I, Magnani A. Evaluation of in vitro cell and blood compatibility and in vivo analgesic activity of plant-derived dietary supplements. JOURNAL OF INTEGRATIVE MEDICINE-JIM 2019; 17:213-220. [DOI: 10.1016/j.joim.2019.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/29/2018] [Indexed: 12/21/2022]
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34
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Yang Q, Wang Y, Zhang S, Tang J, Li F, Yin J, Li Y, Fu J, Li B, Luo Y, Xue W, Zhu F. Biomarker Discovery for Immunotherapy of Pituitary Adenomas: Enhanced Robustness and Prediction Ability by Modern Computational Tools. Int J Mol Sci 2019; 20:E151. [PMID: 30609812 PMCID: PMC6337483 DOI: 10.3390/ijms20010151] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 12/25/2018] [Accepted: 12/26/2018] [Indexed: 12/15/2022] Open
Abstract
Pituitary adenoma (PA) is prevalent in the general population. Due to its severe complications and aggressive infiltration into the surrounding brain structure, the effective management of PA is required. Till now, no drug has been approved for treating non-functional PA, and the removal of cancerous cells from the pituitary is still under experimental investigation. Due to its superior specificity and safety profile, immunotherapy stands as one of the most promising strategies for dealing with PA refractory to the standard treatment, and various studies have been carried out to discover immune-related gene markers as target candidates. However, the lists of gene markers identified among different studies are reported to be highly inconsistent because of the greatly limited number of samples analyzed in each study. It is thus essential to substantially enlarge the sample size and comprehensively assess the robustness of the identified immune-related gene markers. Herein, a novel strategy of direct data integration (DDI) was proposed to combine available PA microarray datasets, which significantly enlarged the sample size. First, the robustness of the gene markers identified by DDI strategy was found to be substantially enhanced compared with that of previous studies. Then, the DDI of all reported PA-related microarray datasets were conducted to achieve a comprehensive identification of PA gene markers, and 66 immune-related genes were discovered as target candidates for PA immunotherapy. Finally, based on the analysis of human protein⁻protein interaction network, some promising target candidates (GAL, LMO4, STAT3, PD-L1, TGFB and TGFBR3) were proposed for PA immunotherapy. The strategy proposed together with the immune-related markers identified in this study provided a useful guidance for the development of novel immunotherapy for PA.
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Affiliation(s)
- Qingxia Yang
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China.
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Song Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Jing Tang
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China.
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Jiayi Yin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Yi Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Jianbo Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Bo Li
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China.
| | - Yongchao Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Weiwei Xue
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China.
| | - Feng Zhu
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China.
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
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35
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Hanson K, Tian N, Vickers JC, King AE. The HDAC6 Inhibitor Trichostatin A Acetylates Microtubules and Protects Axons From Excitotoxin-Induced Degeneration in a Compartmented Culture Model. Front Neurosci 2018; 12:872. [PMID: 30555293 PMCID: PMC6282003 DOI: 10.3389/fnins.2018.00872] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/08/2018] [Indexed: 12/15/2022] Open
Abstract
Axon degeneration has been implicated as a pathological process in several neurodegenerative diseases and acquired forms of neural injury. We have previously shown that stabilizing microtubules can protect axons against excitotoxin-induced fragmentation, however, the alterations of microtubules following excitotoxicity that results in axon degeneration are currently unknown. Hence, this study investigated whether excitotoxicity affects the post-translational modifications of microtubules and microtubule-associated proteins, and whether reversing these changes has the potential to rescue axons from degeneration. To investigate microtubule alterations, primary mouse cortical neurons at 10 days in vitro were treated with 10 or 25 μM kainic acid to induce excitotoxicity and axon degeneration. Post-translational modifications of microtubules and associated proteins were examined at 6 h following kainic acid exposure, relative to axon degeneration. While there were no changes to tyrosinated tubulin or MAP1B, acetylated tubulin was significantly (p < 0.05) decreased by 40% at 6 h post-treatment. To determine whether increasing microtubule acetylation prior to kainic acid exposure could prevent axon fragmentation, we investigated the effect of reducing microtubule deacetylation with the HDAC6 inhibitor, trichostatin A. We found that trichostatin A prevented kainic acid-induced microtubule deacetylation and significantly (p < 0.05) protected axons from fragmentation. These data suggest that microtubule acetylation is a potential target for axonal protection where excitotoxicity may play a role in neuronal degeneration.
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Affiliation(s)
- Kelsey Hanson
- Wicking Dementia Research and Education Centre, College of Health, University of Tasmania, Hobart, TAS, Australia
| | - Nan Tian
- Wicking Dementia Research and Education Centre, College of Health, University of Tasmania, Hobart, TAS, Australia
| | - James C Vickers
- Wicking Dementia Research and Education Centre, College of Health, University of Tasmania, Hobart, TAS, Australia
| | - Anna E King
- Wicking Dementia Research and Education Centre, College of Health, University of Tasmania, Hobart, TAS, Australia
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