1
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Anand A, Ghosh P, Singh R, Gajanan Bajad N, Kumar A, Singh SK. Identification of potent histone deacetylase 2 (HDAC2) inhibitors through combined structure and ligand-based designs and molecular modelling approach. J Biomol Struct Dyn 2024; 42:4679-4698. [PMID: 37306006 DOI: 10.1080/07391102.2023.2222177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/01/2023] [Indexed: 06/13/2023]
Abstract
Histone deacetylase 2 (HDAC2) is associated with various neuropathic degenerative diseases and is considered a novel target for Alzheimer's disease (AD). Elevated levels of HDAC2 trigger excitatory neurotransmission and reduce synaptic plasticity, synaptic number, and memory formation. In the current study, we identified HDAC2 inhibitors using an integrated structure and ligand-based approaches to drug design. Three pharmacophore models were generated by using different pharmacophoric features and validated using the Enrichment factor (EF), Güner-henry (GH) score, and percentage yield. The model of choice was used to screen a library of Zinc-15 compounds and interfering compounds were eliminated by using drug likeliness and PAINS filtering. Further, docking studies in three stages were carried out to obtain hits with good binding energies and were followed by ADMET studies yielding three virtual hits. The virtual hits, i.e. ZINC000008184553, ZINC0000013641114, and ZINC000032533141, were subjected to molecular dynamics simulation studies. Compound ZINC000008184553, identified as lead, was found to have optimal stability, low toxicity under simulated conditions, and may potentially inhibit HDAC2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Asha Anand
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U), Varanasi, India
| | - Powsali Ghosh
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U), Varanasi, India
| | - Ravi Singh
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U), Varanasi, India
| | - Nilesh Gajanan Bajad
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U), Varanasi, India
| | - Ashok Kumar
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U), Varanasi, India
| | - Sushil Kumar Singh
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U), Varanasi, India
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2
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Drakontaeidi A, Pontiki E. A Review on Molecular Docking on HDAC Isoforms: Novel Tool for Designing Selective Inhibitors. Pharmaceuticals (Basel) 2023; 16:1639. [PMID: 38139766 PMCID: PMC10746130 DOI: 10.3390/ph16121639] [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: 10/08/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 12/24/2023] Open
Abstract
Research into histone deacetylases (HDACs) has experienced a remarkable surge in recent years. These enzymes are key regulators of several fundamental biological processes, often associated with severe and potentially fatal diseases. Inhibition of their activity represents a promising therapeutic approach and a prospective strategy for the development of new therapeutic agents. A critical aspect of their inhibition is to achieve selectivity in terms of enzyme isoforms, which is essential to improve treatment efficacy while reducing undesirable pleiotropic effects. The development of computational chemistry tools, particularly molecular docking, is greatly enhancing the precision of designing molecules with inherent potential for specific activity. Therefore, it was considered necessary to review the molecular docking studies conducted on the major isozymes of the enzyme in order to identify the specific interactions associated with each selective HDAC inhibitor. In particular, the most critical isozymes of HDAC (1, 2, 3, 6, and 8) have been thoroughly investigated within the scope of this review.
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Affiliation(s)
| | - Eleni Pontiki
- Department of Pharmaceutical Chemistry, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
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3
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De Vita S, Meninno S, Capasso L, Colarusso E, Chini MG, Lauro G, Rinaldi R, De Cicco A, Sian V, Terracciano S, Nebbioso A, Lattanzi A, Bifulco G. 2-Substituted 1,5-benzothiazepine-based HDAC inhibitors exert anticancer activities on human solid and acute myeloid leukemia cell lines. Bioorg Med Chem 2023; 93:117444. [PMID: 37611334 DOI: 10.1016/j.bmc.2023.117444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/31/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023]
Abstract
Herein, we report the development of a new series of histone deacetylase inhibitors (HDACi) containing a 2-substituted 1,5-benzothiazepine scaffold. First, a virtual combinatorial library (∼1.6 × 103 items) was built according to a convenient synthetic route, and then it was submitted to molecular docking experiments on seven HDACs isoforms belonging to classes I and II. Integrated computational filters were used to select the most promising ones that were synthesized through an optimized approach, also amenable to generating both racemic and enantioenriched benzothiazepine-based derivatives. The obtained compounds showed potent HDAC inhibitory activity, especially those containing the sulphone moiety, endowed with IC50 in the nanomolar range. In addition, in vitro outcomes of our synthesized compounds demonstrated a cytotoxic effect on U937 and HCT116 cell lines and an arrest in the G2/M phase (13 ≤ IC50 ≤ 18 µM). Finally, Western blot analyses outlined the modulation of the histone acetyl markers such as H3K9/14, acetyl-tubulin, and the apoptotic indicator p21 in both cancer cell lines, disclosing a good HDAC inhibitor activity exerted by the designed items. Given the key role of HDACs in many cellular pathways, which makes these enzymes appealing and "hot" drug targets, our findings highlighted the importance of these 2-substituted 1,5-benzothiazepine-based compounds (both in the reduced and oxidized version) for the development of novel epidrugs.
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Affiliation(s)
- Simona De Vita
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
| | - Sara Meninno
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
| | - Lucia Capasso
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138 Naples, Italy.
| | - Ester Colarusso
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
| | - Maria Giovanna Chini
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, Pesche, Isernia 86090, Italy.
| | - Gianluigi Lauro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
| | - Romolo Rinaldi
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
| | - Annalisa De Cicco
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
| | - Veronica Sian
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138 Naples, Italy.
| | - Stefania Terracciano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
| | - Angela Nebbioso
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138 Naples, Italy.
| | - Alessandra Lattanzi
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
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Amin SA, Khatun S, Gayen S, Das S, Jha T. Are inhibitors of histone deacetylase 8 (HDAC8) effective in hematological cancers especially acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL)? Eur J Med Chem 2023; 258:115594. [PMID: 37429084 DOI: 10.1016/j.ejmech.2023.115594] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/17/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023]
Abstract
Histone deacetylase 8 (HDAC8) aberrantly deacetylates histone and non-histone proteins. These include structural maintenance of chromosome 3 (SMC3) cohesin protein, retinoic acid induced 1 (RAI1), p53, etc and thus, regulating diverse processes such as leukemic stem cell (LSC) transformation and maintenance. HDAC8, one of the crucial HDACs, affects the gene silencing process in solid and hematological cancer progressions especially on acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL). A specific HDAC8 inhibitor PCI-34051 showed promising results against both T-cell lymphoma and AML. Here, we summarize the role of HDAC8 in hematological malignancies, especially in AML and ALL. This article also introduces the structure/function of HDAC8 and a special attention has been paid to address the HDAC8 enzyme selectivity issue in hematological cancer especially against AML and ALL.
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Affiliation(s)
- Sk Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India; Department of Pharmaceutical Technology, JIS University, 81, Nilgunj Road, Agarpara, Kolkata, West Bengal, India.
| | - Samima Khatun
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
| | - Sanjib Das
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
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5
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Kong SJ, Nam G, Boggu PR, Park GM, Kang JE, Park HJ, Jung YH. Synthesis and biological evaluation of novel N-benzyltriazolyl-hydroxamate derivatives as selective histone deacetylase 6 inhibitors. Bioorg Med Chem 2023; 79:117154. [PMID: 36645952 DOI: 10.1016/j.bmc.2023.117154] [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: 10/06/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
Histone deacetylases (HDAC) regulate post-translational acetylation and the inhibition of these enzymes has emerged as an intriguing disease therapeutic. Among them, class IIb HDAC6 has the unique characteristic of mainly deacetylating cytoplasmic proteins, suggesting clinical applications for neurodegenerative diseases, inflammation, and cancer. In this study, we designed a novel N-benzyltriazolyl-hydroxamate scaffold based on the known HDAC6 inhibitors nexturastat A and tubastatin A. Among the 27 derivatives, 3-fluoro-4-((3-(2-fluorophenyl)-1H-1,2,4-triazol-1-yl)methyl)-N-hydroxybenzamide 4u (HDAC6 IC50 = 7.08 nM) showed nanomolar HDAC6 inhibitory activity with 42-fold selectivity over HDAC1. Structure-activity relationship (SAR) and computational docking studies were conducted to optimize the triazole capping group. Docking analysis revealed that the capping group aligned with the conserved L1 pocket of HDAC6 and was associated with subtype selectivity. Overall, our study explored the triazole-based biaryl capping group and its substitution and orientation, suggesting a rationale for the design of HDAC6-selective inhibitors.
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Affiliation(s)
- Sun Ju Kong
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Gibeom Nam
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Pulla Reddy Boggu
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Gi Min Park
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Ji Eun Kang
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hyun-Ju Park
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Young Hoon Jung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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Pavan AR, Lopes JR, Dos Santos JL. The state of the art of fetal hemoglobin-inducing agents. Expert Opin Drug Discov 2022; 17:1279-1293. [PMID: 36302760 DOI: 10.1080/17460441.2022.2141708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
INTRODUCTION Sickle cell anemia (SCA) is a hematological genetic disorder caused by a mutation in the gene of the β-globin. Pharmacological treatments will continue to be an important approach, including the strategy to induce fetal hemoglobin (HbF). AREAS COVERED Here, we analyzed the articles described in the literature regarding the drug discovery of HbF inducers. The main approaches for such strategy will be discussed, highlighting those most promising. EXPERT OPINION The comprehension of the mechanisms involved in the β-globin regulation is the main key to design new drugs to induce HbF. Among the strategies, gamma-globin regulation by epigenetic enzymes seems to be a promising approach to be pursued, although the comprehension of the selectivity role for those new drugs is crucial to reduce adverse effects. The low druggability of transcription factors and their vital role in embryonic human development are critical points that should be taken in account for drug design. The guanylate cyclase and the NO/cGMP signaling pathway seem to be promising not only for HbF induction, but also for the protective effects in the cardiovascular system. The association of drugs acting through different mechanisms to induce HbF seems to be promising for the discovery of new drugs.
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Affiliation(s)
- Aline Renata Pavan
- São Paulo State University (UNESP), Institute of Chemistry, Araraquara, Brazil
| | - Juliana Romano Lopes
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Drugs and Medicine Department, Araraquara, Brazil
| | - Jean Leandro Dos Santos
- São Paulo State University (UNESP), Institute of Chemistry, Araraquara, Brazil.,School of Pharmaceutical Sciences, São Paulo State University (UNESP), Drugs and Medicine Department, Araraquara, Brazil
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Urias BS, Pavan AR, Albuquerque GR, Prokopczyk IM, Alves TMF, de Melo TRF, Sartori GR, da Silva JHM, Chin CM, Santos JLD. Optimization of Resveratrol Used as a Scaffold to Design Histone Deacetylase (HDAC-1 and HDAC-2) Inhibitors. Pharmaceuticals (Basel) 2022; 15:ph15101260. [PMID: 36297372 PMCID: PMC9611521 DOI: 10.3390/ph15101260] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/24/2022] Open
Abstract
Histone deacetylases (HDAC) are epigenetic enzymes responsible for repressing gene expression through the deacetylation of histone lysine residues. Therefore, inhibition of HDACs has become an interesting approach for the treatment of several diseases, including cancer, hematology, neurodegenerative, immune diseases, bacterial infections, and more. Resveratrol (RVT) has pleiotropic effects, including pan-inhibition of HDAC isoforms; however, its ability to interfere with membranes requires additional optimization to eliminate nonspecific and off-target effects. Thus, to explore RVT as a scaffold, we designed a series of novel HDAC-1 and -2 inhibitors containing the 2-aminobenzamide subunit. Using molecular modeling, all compounds, except unsaturated compounds (4) and (7), exhibited a similar mode of interaction at the active sites of HDAC 1 and 2. The docking score values obtained from the study ranged from −12.780 to −10.967 Kcal/mol. All compounds were synthesized, with overall yields ranging from 33% to 67.3%. In an initial screening, compounds (4), (5), (7), and (20)–(26), showed enzymatic inhibitory effects ranging from 1 to 96% and 6 to 93% against HDAC-1 and HDAC-2, respectively. Compound (5), the most promising HDAC inhibitor in this series, was selected for IC50 assays, resulting in IC50 values of 0.44 µM and 0.37 µM against HDAC-1 and HDAC-2, respectively. In a panel of selectivity against HDACs 3–11, compound (5) presented selectivity towards Class I, mainly HDAC-1, 2, and 3. All compounds exhibited suitable physicochemical and ADMET properties as determined using in silico simulations. In conclusion, the optimization of the RVT structure allows the design of selective HDAC inhibitors, mainly targeting HDAC-1 and HDAC-2 isoforms.
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Affiliation(s)
- Beatriz Silva Urias
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara 14800-903, SP, Brazil
| | - Aline Renata Pavan
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara 14800-903, SP, Brazil
- Institute of Chemistry, São Paulo State University (UNESP), Araraquara 14800-060, SP, Brazil
- Correspondence: (A.R.P.); (J.L.D.S.); Tel.: +55-16-3301-6972 (J.L.D.S.)
| | | | - Igor Muccilo Prokopczyk
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara 14800-903, SP, Brazil
| | - Tânia Mara Ferreira Alves
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara 14800-903, SP, Brazil
| | | | - Geraldo Rodrigues Sartori
- Laboratory of Structural and Functional Biology Applied to Biopharmaceuticals, Oswaldo Cruz Foundation (Fiocruz), Eusébio 61773-270, CE, Brazil
- Postgraduate Program in Computational and Systems Biology, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro 21040-222, RJ, Brazil
| | - João Hermínio Martins da Silva
- Laboratory of Structural and Functional Biology Applied to Biopharmaceuticals, Oswaldo Cruz Foundation (Fiocruz), Eusébio 61773-270, CE, Brazil
| | - Chung Man Chin
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara 14800-903, SP, Brazil
| | - Jean Leandro Dos Santos
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara 14800-903, SP, Brazil
- Correspondence: (A.R.P.); (J.L.D.S.); Tel.: +55-16-3301-6972 (J.L.D.S.)
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Wu Y, Zhang B, Dong X, Ma S, Hu S. Discovery of Novel Small Molecule HDAC1, 2, 3 Inhibitors -- Combined
Receptor-Based and Ligand-Based Virtual Screening Strategy. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180819666211220124300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aims:
This study aims to investigate and validate the potential drug target to HDAC1.
Background:
Human histone deacetylase 1 (HDAC1) can catalyze the deacetylation of histones belonging
to the family of human histone deacetylases (HDACs). Amide hydrolase HDAC1 plays a key role in
the development of many serious cancers such as prostate cancer, gastric cancer, lung cancer, esophageal
cancer, colon cancer, and breast cancer. Therefore, HDAC1 inhibitors, promoting the transcription of a
series of key genes such as the p53 gene and inhibiting the development of cancer through various downstream
mechanisms, have great potential for the treatment of cancer.
Objective:
The objective of this study is to discover new skeleton HDAC1 inhibitors efficiently and conveniently
with therapeutic potential for cancer.
Method:
Based on the crystal structure of HDAC1, through the combination of receptor-based and ligand-
based virtual screening from the commercial compound library, the top-ranked compounds are selected
for purchase through binding modes analysis, and their activities were verified through in vitro
HDAC1 inhibitory biological experiments.
Results:
Based on LeDock, 5ICN showed good distinguishing ability and was used as the receptor. According
to the results of the LeDock docking scoring from receptor-based virtual screening, 69 compounds
with binding energy less than -7.5 kcal/mol were obtained and used for ligand-based virtual
screening. A total of 21 novel compounds with high potential HDAC1 inhibitory activity were collected
by combining the similarity searching (NN) and the multinomial Naive Bayes machine learning model
(NB) methods. Through binding modes analysis, 10 compounds with different structures with potential
HDAC1 inhibitory activity were selected and screened HDAC1 inhibitory in vitro. May267 showed moderate
HDAC1 inhibitory activity, and the inhibition rate was 48% at a concentration of 20 μM.
Conclusion:
This study discovers novel small molecule HDAC1 inhibitors by combined receptor-based
and ligand-based virtual screening strategy, which provides an efficient method for the discovery of other
small molecule drugs. May267 shows moderate HDAC1 inhibitory activity, which can be further optimized
as a lead compound. However, it still has the problem of poor kinase selectivity to be solved.
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Affiliation(s)
- Yi Wu
- Department of General Surgery, Nanjing Medical University, Hangzhou First People’s Hospital, Hangzhou, Zhejiang
310006, P.R. China
| | - Bo Zhang
- Department of Clinical Pharmacology, Key Laboratory of Clinical Cancer Pharmacology
and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People\'s Hospital, Cancer Center,
Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Xiaowu Dong
- Hangzhou Institute of Innovative
Medicine, Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang
University, Hangzhou, Zhejiang 310058, P.R. China
| | - Shenglin Ma
- Department of Oncology, Nanjing Medical University, Hangzhou First People’s Hospital, Hangzhou,
Zhejiang 310006, P.R. China
| | - Shengquan Hu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou,
Zhejiang 310058, P.R. China
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9
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Dihydropyrazole-Carbohydrazide Derivatives with Dual Activity as Antioxidant and Anti-Proliferative Drugs on Breast Cancer Targeting the HDAC6. Pharmaceuticals (Basel) 2022; 15:ph15060690. [PMID: 35745608 PMCID: PMC9230091 DOI: 10.3390/ph15060690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/20/2022] [Accepted: 05/26/2022] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BC) is the most frequently diagnosed cancer and is the second-most common cause of death in women worldwide. Because of this, the search for new drugs and targeted therapy to treat BC is an urgent and global need. Histone deacetylase 6 (HDAC6) is a promising anti-BC drug target associated with its development and progression. In the present work, the design and synthesis of a new family of dihydropyrazole-carbohydrazide derivatives (DPCH) derivatives focused on HDAC6 inhibitory activity is presented. Computational chemistry approaches were employed to rationalize the design and evaluate their physicochemical and toxic-biological properties. The new family of nine DPCH was synthesized and characterized. Compounds exhibited optimal physicochemical and toxicobiological properties for potential application as drugs to be used in humans. The in silico studies showed that compounds with –Br, –Cl, and –OH substituents had good affinity with the catalytic domain 2 of HDAC6 like the reference compounds. Nine DPCH derivatives were assayed on MCF-7 and MDA-MB-231 BC cell lines, showing antiproliferative activity with IC50 at μM range. Compound 2b showed, in vitro, an IC50 value of 12 ± 3 µM on human HDAC6. The antioxidant activity of DPCH derivatives showed that all the compounds exhibit antioxidant activity similar to that of ascorbic acid. In conclusion, the DPCH derivatives are promising drugs with therapeutic potential for the epigenetic treatment of BC, with low cytotoxicity towards healthy cells and important antioxidant activity.
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10
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Pan A, Sun XM, Huang FQ, Liu JF, Cai YY, Wu X, Alolga RN, Li P, Liu BL, Liu Q, Qi LW. The mitochondrial β-oxidation enzyme HADHA restrains hepatic glucagon response by promoting β-hydroxybutyrate production. Nat Commun 2022; 13:386. [PMID: 35046401 PMCID: PMC8770464 DOI: 10.1038/s41467-022-28044-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 01/06/2022] [Indexed: 11/09/2022] Open
Abstract
Disordered hepatic glucagon response contributes to hyperglycemia in diabetes. The regulators involved in glucagon response are less understood. This work aims to investigate the roles of mitochondrial β-oxidation enzyme HADHA and its downstream ketone bodies in hepatic glucagon response. Here we show that glucagon challenge impairs expression of HADHA. Liver-specific HADHA overexpression reversed hepatic gluconeogenesis in mice, while HADHA knockdown augmented glucagon response. Stable isotope tracing shows that HADHA promotes ketone body production via β-oxidation. The ketone body β-hydroxybutyrate (BHB) but not acetoacetate suppresses gluconeogenesis by selectively inhibiting HDAC7 activity via interaction with Glu543 site to facilitate FOXO1 nuclear exclusion. In HFD-fed mice, HADHA overexpression improved metabolic disorders, and these effects are abrogated by knockdown of BHB-producing enzyme. In conclusion, BHB is responsible for the inhibitory effect of HADHA on hepatic glucagon response, suggesting that HADHA activation or BHB elevation by pharmacological intervention hold promise in treating diabetes.
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Affiliation(s)
- An Pan
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xiao-Meng Sun
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Feng-Qing Huang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Jin-Feng Liu
- Clinical Metabolomics Center, China Pharmaceutical University, Nanjing, 211198, China
| | - Yuan-Yuan Cai
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xin Wu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Raphael N Alolga
- Clinical Metabolomics Center, China Pharmaceutical University, Nanjing, 211198, China
| | - Ping Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Bao-Lin Liu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qun Liu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
- Clinical Metabolomics Center, China Pharmaceutical University, Nanjing, 211198, China.
| | - Lian-Wen Qi
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
- Clinical Metabolomics Center, China Pharmaceutical University, Nanjing, 211198, China.
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11
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Ukey S, Choudhury C, Sharma P. Identification of unique subtype-specific interaction features in Class II zinc-dependent HDAC subtype binding pockets: A computational study. J Biosci 2021. [DOI: 10.1007/s12038-021-00197-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Hu P, Sun M, Lu F, Wang S, Hou L, Yu Y, Zhang Y, Sun L, Yao J, Yang F, Wang C, Ma Z. Polymerized vorinostat mediated photodynamic therapy using lysosomal spatiotemporal synchronized drug release complex. Colloids Surf B Biointerfaces 2021; 205:111903. [PMID: 34144323 DOI: 10.1016/j.colsurfb.2021.111903] [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: 04/07/2021] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 01/16/2023]
Abstract
A combination of photodynamic therapy (PDT) and histone deacetylase inhibitor (HDACis) could potentiate single-mode anti-tumor activity of HDACis or PDT to inhibit tumor relapse and metastasis. However, poor solubility and heterogeneity in cellular uptake and tissue distribution hamper the dual mode antitumor effect. For a controlled drug release of photosensitizers and HDACis in cytoplasm, photosensitizer pyropheophorbide-a (Pyro) encapsulated in polymer polyethylene glycol-b-poly (asparaginyl-vorinostat) (simplified as Pyro@FPPS) are fabricated to achieve their lysosomal spatiotemporal synchronized release. With HDACis modeling PDT in vitro and in vivo, it seems that polymerized Vorinostat encapsulated photosensitizers significantly inhibited the tumor proliferation and metastasis by spatiotemporal synchronized drugs release, and Pyro@FPPS reported here reveals a promising prospect to exert drugs' synergistic effect in a spatiotemporal synchronized manner and can be an effective strategy to inhibit tumor growth, recurrence and metastasis in clinic.
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Affiliation(s)
- Pengwei Hu
- School of Pharmacy, Second Military Medical University, Shanghai, People's Republic of China; Harbin Institute of Technology (Shenzhen), School of Science, Shenzhen, People's Republic of China; Department of Pharmacy, Hebei North University, Zhangjiakou, People's Republic of China
| | - Miao Sun
- School of Pharmacy, Second Military Medical University, Shanghai, People's Republic of China
| | - Fengkun Lu
- Department of Pharmacy, Hebei North University, Zhangjiakou, People's Republic of China
| | - Sizhen Wang
- School of Pharmacy, Second Military Medical University, Shanghai, People's Republic of China
| | - Lei Hou
- School of Pharmacy, Second Military Medical University, Shanghai, People's Republic of China; Department of Pharmacy, Hebei North University, Zhangjiakou, People's Republic of China
| | - Yingjie Yu
- School of Pharmacy, Second Military Medical University, Shanghai, People's Republic of China
| | - Yunchang Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, People's Republic of China
| | - Linhong Sun
- School of Pharmacy, Second Military Medical University, Shanghai, People's Republic of China
| | - Jianzhong Yao
- School of Pharmacy, Second Military Medical University, Shanghai, People's Republic of China
| | - Feng Yang
- School of Pharmacy, Second Military Medical University, Shanghai, People's Republic of China.
| | - Chen Wang
- Department of Oncology, Ruijin North Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.
| | - Zhiqiang Ma
- School of Pharmacy, Second Military Medical University, Shanghai, People's Republic of China.
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13
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Shetty MG, Pai P, Deaver RE, Satyamoorthy K, Babitha KS. Histone deacetylase 2 selective inhibitors: A versatile therapeutic strategy as next generation drug target in cancer therapy. Pharmacol Res 2021; 170:105695. [PMID: 34082029 DOI: 10.1016/j.phrs.2021.105695] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/04/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023]
Abstract
Acetylation and deacetylation of histone and several non-histone proteins are the two important processes amongst the different modes of epigenetic modulation that are involved in regulating cancer initiation and development. Abnormal expression of histone deacetylases (HDACs) is often reported in various types of cancers. Few pan HDAC inhibitors have been approved for use as therapeutic interventions for cancer treatment including vorinostat, belinostat and panobinostat. However, not all the HDAC isoforms are abnormally expressed in certain cancers, such as in the case of, ovarian cancer where overexpression of HDAC1-3, lung cancer where overexpression of HDAC 1 and 3 and gastric cancer where overexpression of HDAC2 is seen. Therefore, pan-inhibition of HDAC is not an efficient way to combat cancer via HDAC inhibition. Hence, isoform-selective HDAC inhibition can be one of the best therapeutic strategies in the treatment of cancer. In this context since aberrant expression of HDAC2 largely contributes to cancer progression by silencing pro-apoptotic protein expressions such as NOXA and APAF1 (caspase 9-activating proteins) and inactivation of tumor suppressor p53, HDAC2 specific inhibitors may help to develop not only the direct targets but also indirect targets that are crucial for tumor development. However, to develop a HDAC2 specific and potent inhibitor, extensive knowledge of its structure and specific functions is essential. The present review updates details on the structural features, physiological functions, and roles of HDAC2 in different types of cancer, emphasizing the challenges and status of the development of HDAC2 selective inhibitors against various types of cancer.
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Affiliation(s)
| | - Padmini Pai
- Department of Biophysics, Manipal School of Life Sciences, MAHE, Manipal, India
| | - Renita Esther Deaver
- Department of Biotechnology, Manipal School of Life Sciences, MAHE, Manipal, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, MAHE, Manipal, India
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14
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Gediya P, Parikh PK, Vyas VK, Ghate MD. Histone deacetylase 2: A potential therapeutic target for cancer and neurodegenerative disorders. Eur J Med Chem 2021; 216:113332. [PMID: 33714914 DOI: 10.1016/j.ejmech.2021.113332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 02/20/2021] [Accepted: 02/21/2021] [Indexed: 10/22/2022]
Abstract
Histone deacetylases (HDACs) have been implicated in a number of diseases including cancer, cardiovascular disorders, diabetes mellitus, neurodegenerative disorders and inflammation. For the treatment of epigenetically altered diseases such as cancer, HDAC inhibitors have made a significant progress in terms of development of isoform selective inhibitiors. Isoform specific HDAC inhibitors have less adverse events and better safety profile. A HDAC isoform i.e., HDAC2 demonstrated significant role in the development of variety of diseases, mainly involved in the cancer and neurodegenerative disorders. Discovery and development of selective HDAC2 inhibitors have a great potential for the treatment of target diseases. In the present compilation, we have reviewed the role of HDAC2 in progression of cancer and neurodegenerative disorders, and information on the drug development opportunities for selective HDAC2 inhibition.
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Affiliation(s)
- Piyush Gediya
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, 382481, Gujarat, India
| | - Palak K Parikh
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, 382481, Gujarat, India; Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Navrangpura, Ahmedabad, 380009, Gujarat, India
| | - Vivek K Vyas
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, 382481, Gujarat, India
| | - Manjunath D Ghate
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, 382481, Gujarat, India.
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15
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Overcome the tumor immunotherapy resistance by combination of the HDAC6 inhibitors with antitumor immunomodulatory agents. Bioorg Chem 2021; 109:104754. [PMID: 33677416 DOI: 10.1016/j.bioorg.2021.104754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/10/2021] [Accepted: 02/16/2021] [Indexed: 11/21/2022]
Abstract
Tumor immunotherapy is currently subject of intense scientific and clinical developments. In previous decade, therapists used natural immune system from the human body to treat several diseases. Although tumor immune disease is a big challenge, combinatorial therapeutic strategy has been succeeded to show the clinical significance. In this context, we discuss the HDAC6 and tumor immune diseases relationship. Also, we summarized the current state of knowledge that based on the combination treatments of the HDAC6 inhibitors (HDAC6is) with antitumor immunomodulatory agents. We observed that, the combination therapies slow down the tumor immune diseases by blocking the aggresome and proteasome pathway. The combination therapy was able to reduce M2 macrophage and increasing PD-L1 blockade sensitivity. Most importantly, multiple combinations of HDAC6is with other agents may consider as potential strategies to treat tumor immune diseases, by reducing the side effects and improve efficacy for the future clinical development.
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16
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Lourenço de Freitas N, Deberaldini MG, Gomes D, Pavan AR, Sousa Â, Dos Santos JL, Soares CP. Histone Deacetylase Inhibitors as Therapeutic Interventions on Cervical Cancer Induced by Human Papillomavirus. Front Cell Dev Biol 2021; 8:592868. [PMID: 33634093 PMCID: PMC7901962 DOI: 10.3389/fcell.2020.592868] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022] Open
Abstract
The role of epigenetic modifications on the carcinogenesis process has received a lot of attention in the last years. Among those, histone acetylation is a process regulated by histone deacetylases (HDAC) and histone acetyltransferases (HAT), and it plays an important role in epigenetic regulation, allowing the control of the gene expression. HDAC inhibitors (HDACi) induce cancer cell cycle arrest, differentiation, and cell death and reduce angiogenesis and other cellular events. Human papillomaviruses (HPVs) are small, non-enveloped double-stranded DNA viruses. They are major human carcinogens, being intricately linked to the development of cancer in 4.5% of the patients diagnosed with cancer worldwide. Long-term infection of high-risk (HR) HPV types, mainly HPV16 and HPV18, is one of the major risk factors responsible for promoting cervical cancer development. In vitro and in vivo assays have demonstrated that HDACi could be a promising therapy to HPV-related cervical cancer. Regardless of some controversial studies, the therapy with HDACi could target several cellular targets which HR-HPV oncoproteins could be able to deregulate. This review article describes the role of HDACi as a possible intervention in cervical cancer treatment induced by HPV, highlighting the main advances reached in the last years and providing insights for further investigations regarding those agents against cervical cancer.
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Affiliation(s)
- Natália Lourenço de Freitas
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
| | - Maria Gabriela Deberaldini
- Drugs and Medicines Department, School of Pharmaceutical Science, São Paulo State University (UNESP), Araraquara, Brazil
- Institute of Chemistry, São Paulo State University (UNESP), Araraquara, Brazil
| | - Diana Gomes
- CICS-UBI – Health Science Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Aline Renata Pavan
- Drugs and Medicines Department, School of Pharmaceutical Science, São Paulo State University (UNESP), Araraquara, Brazil
- Institute of Chemistry, São Paulo State University (UNESP), Araraquara, Brazil
| | - Ângela Sousa
- CICS-UBI – Health Science Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Jean Leandro Dos Santos
- Drugs and Medicines Department, School of Pharmaceutical Science, São Paulo State University (UNESP), Araraquara, Brazil
| | - Christiane P. Soares
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
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17
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De Vita S, Terracciano S, Bruno I, Chini MG. From Natural Compounds to Bioactive Molecules through NMR and
In Silico
Methodologies. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000469] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Simona De Vita
- Department of Pharmacy University of Salerno Via Giovanni Paolo II, n°132 84084 Fisciano (SA) Italy
| | - Stefania Terracciano
- Department of Pharmacy University of Salerno Via Giovanni Paolo II, n°132 84084 Fisciano (SA) Italy
| | - Ines Bruno
- Department of Pharmacy University of Salerno Via Giovanni Paolo II, n°132 84084 Fisciano (SA) Italy
| | - Maria Giovanna Chini
- Department of Biosciences and Territory University of Molise C.da Fonte Lappone‐ 86090 Pesche (IS) Italy
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18
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ElHady AK, Shih SP, Chen YC, Liu YC, Ahmed NS, Keeton AB, Piazza GA, Engel M, Abadi AH, Abdel-Halim M. Extending the use of tadalafil scaffold: Development of novel selective phosphodiesterase 5 inhibitors and histone deacetylase inhibitors. Bioorg Chem 2020; 98:103742. [PMID: 32199305 DOI: 10.1016/j.bioorg.2020.103742] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/27/2020] [Accepted: 03/07/2020] [Indexed: 12/17/2022]
Abstract
Herein we present the synthesis and characterization of a novel chemical series of tadalafil analogues that display different pharmacological profiles. Compounds that have the 6R, 12aR configuration and terminal carboxylic acid group at the side chain arising from the piperazinedione nitrogen were potent PDE5 inhibitors, with compound 11 having almost equal potency to tadalafil and superior selectivity over PDE11, the most common off-target for tadalafil. Modifying the stereochemistry into 6S, 12aS configuration and adopting the hydroxamic acid moiety as a terminal group gave rise to compounds that only inhibited HDAC. Dual PDE5/HDAC inhibition could be achieved with compounds having 6R, 12aR configuration and hydroxamic acid moiety as a terminal group. The anticancer activity of the synthesized compounds was evaluated against a diverse number of cell lines of different origin. The compounds elicited anticancer activity against cell lines belonging to lymphoproliferative cancer as well as solid tumors. Despite the previous reports suggesting anticancer activity of PDE5 inhibitors, the growth inhibitory activity of the compounds seemed to be solely dependent on HDAC inhibition. Compound 26 (pan HDAC IC50 = 14 nM, PDE5 IC50 = 46 nM) displayed the most potent anticancer activity in the present series and was shown to induce apoptosis in Molt-4 cells. HDAC isoform selectivity testing for compound 26 showed that it is more selective for HDAC6 and 8 over HDAC1 by more than 20-fold.
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Affiliation(s)
- Ahmed K ElHady
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Shou-Ping Shih
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, 70 Lien-Hai Road, Kaohsiung 804, Taiwan; Doctoral Degree Program in Marine Biotechnology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan
| | - Yu-Cheng Chen
- The Ph.D. Program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taichung 40402, Taiwan
| | - Yi-Chang Liu
- Division of Hematology-Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan; Department of Internal Medicine, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Nermin S Ahmed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Adam B Keeton
- Department of Oncologic Sciences and Pharmacology, Drug Discovery Research Center, Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36608, USA
| | - Gary A Piazza
- Department of Oncologic Sciences and Pharmacology, Drug Discovery Research Center, Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36608, USA
| | - Matthias Engel
- Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123 Saarbrücken, Germany
| | - Ashraf H Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt.
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19
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Balasubramaniam S, Vijayan S, Goldman LV, May XA, Dodson K, Adhikari S, Rivas F, Watkins DL, Stoddard SV. Design and synthesis of diazine-based panobinostat analogues for HDAC8 inhibition. Beilstein J Org Chem 2020; 16:628-637. [PMID: 32318119 PMCID: PMC7155894 DOI: 10.3762/bjoc.16.59] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/24/2020] [Indexed: 12/13/2022] Open
Abstract
Guided by computational analysis, herein we report the design, synthesis and evaluation of four novel diazine-based histone deacetylase inhibitors (HDACis). The targets of interest (TOI) are analogues of panobinostat, one of the most potent and versatile HDACi reported. By simply replacing the phenyl core of panobinostat with that of a diazine derivative, docking studies against HDAC2 and HDAC8 revealed that the four analogues exhibit inhibition activities comparable to that of panobinostat. Multistep syntheses afforded the visualized targets TOI1, TOI2, TOI3-rev and TOI4 whose biological evaluation confirmed the strength of HDAC8 inhibition with TOI4 displaying the greatest efficacy at varying concentrations. The results of this study lay the foundation for future design strategies toward more potent HDACis for HDAC8 isozymes and further therapeutic applications for neuroblastoma.
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Affiliation(s)
| | - Sajith Vijayan
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677-1848, USA
| | - Liam V Goldman
- Department of Chemistry, Rhodes College, Memphis, TN 38112, USA
| | - Xavier A May
- Department of Chemistry, Rhodes College, Memphis, TN 38112, USA
| | - Kyra Dodson
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677-1848, USA
| | - Sweta Adhikari
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677-1848, USA
| | - Fatima Rivas
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Davita L Watkins
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677-1848, USA
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20
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In silico Design of Novel Histone Deacetylase 4 Inhibitors: Design Guidelines for Improved Binding Affinity. Int J Mol Sci 2019; 21:ijms21010219. [PMID: 31905609 PMCID: PMC6981887 DOI: 10.3390/ijms21010219] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/19/2019] [Accepted: 12/25/2019] [Indexed: 02/02/2023] Open
Abstract
Histone deacetylases (HDAC) are being targeted for a number of diseases such as cancer, inflammatory disease, and neurological disorders. Within this family of 18 isozymes, HDAC4 is a prime target for glioma, one of the most aggressive brain tumors reported. Thus, the development of HDAC4 inhibitors could present a novel therapeutic route for glioma. In this work, molecular docking studies on cyclopropane hydroxamic acid derivatives identified five novel molecular interactions to the HDAC4 receptor that could be harnessed to enhance inhibitor binding. Thus, design guidelines for the optimization of potent HDAC4 inhibitors were developed which can be utilized to further the development of HDAC4 inhibitors. Using the developed guidelines, eleven novel cyclopropane hydroxamic acid derivatives were designed that outcompeted all original cyclopropane hydroxamic acids HDAC4 inhibitors studied in silico. The results of this work will be an asset to paving the way for further design and optimization of novel potent HDAC4 inhibitors for gliomas.
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21
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Daniel L, Gotsbacher MP, Richardson-Sanchez T, Tieu W, Codd R. Exploring hydroxamic acid inhibitors of HDAC1 and HDAC2 using small molecule tools and molecular or homology modelling. Bioorg Med Chem Lett 2019; 29:2581-2586. [PMID: 31400937 DOI: 10.1016/j.bmcl.2019.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/25/2019] [Accepted: 08/01/2019] [Indexed: 10/26/2022]
Abstract
Hydroxamic acid compounds 1-10 containing a N-hydroxycinnamamide scaffold and a 4-(benzylamino)methyl cap group that was either unsubstituted (1) or substituted with one (2-4) or two (5-10) methoxy groups in variable positions were prepared as inhibitors of Zn(II)-containing histone deacetylases (HDACs). The 3,4- (9) and 3,5- (10) bis-methoxy-substituted compounds were the least potent against HeLa nuclear extract, HDAC1 and HDAC2. Molecular modelling showed methoxy groups in the 3-, 4- and 5-position, but not the 2-position, had unfavourable steric interactions with the G32-H33-P34 triad on a loop at the surface of the HDAC2 active site cavity. An HDAC1 homology model showed potential ionic (E243..K288) and cation-pi (K247..F292) interactions between helix 10 and helix 11 that were absent in HDAC2 ((G243..K288) and (K247..V292)). This surface-located interhelical constraint could inform the design of bitopic HDAC1 and HDAC2 selective ligands using an allosteric approach, and/or protein-protein interaction (PPI) inhibitors.
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Affiliation(s)
- Lydia Daniel
- School of Medical Sciences (Pharmacology), The University of Sydney, New South Wales 2006, Australia
| | - Michael P Gotsbacher
- School of Medical Sciences (Pharmacology), The University of Sydney, New South Wales 2006, Australia
| | - Tomas Richardson-Sanchez
- School of Medical Sciences (Pharmacology), The University of Sydney, New South Wales 2006, Australia
| | - William Tieu
- School of Medical Sciences (Pharmacology), The University of Sydney, New South Wales 2006, Australia
| | - Rachel Codd
- School of Medical Sciences (Pharmacology), The University of Sydney, New South Wales 2006, Australia.
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22
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Structure-activity relationship study of thiazolyl-hydroxamate derivatives as selective histone deacetylase 6 inhibitors. Bioorg Med Chem 2019; 27:3408-3420. [DOI: 10.1016/j.bmc.2019.06.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/18/2019] [Accepted: 06/20/2019] [Indexed: 11/19/2022]
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23
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How could histone deacetylase activators be useful leads in the search for new therapeutics? Future Med Chem 2019; 11:1241-1243. [DOI: 10.4155/fmc-2019-0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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24
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Liu J, Zhu Y, He Y, Zhu H, Gao Y, Li Z, Zhu J, Sun X, Fang F, Wen H, Li W. Combined pharmacophore modeling, 3D-QSAR and docking studies to identify novel HDAC inhibitors using drug repurposing. J Biomol Struct Dyn 2019; 38:533-547. [PMID: 30938574 DOI: 10.1080/07391102.2019.1590241] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Histone deacetylases (HDACs), a critical family of epigenetic enzymes, has emerged as a promising target for antitumor drugs. Here, we describe our protocol of virtual screening in identification of novel potential HDAC inhibitors through pharmacophore modeling, 3D-QSAR, molecular docking and molecular dynamics (MD) simulation. Considering the limitation of current virtual screening works, drug repurposing strategy was applied to discover druggable HDAC inhibitor. The ligand-based pharmacophore and 3D-QSAR models were established, and their reliability was validated by different methods. Then, the DrugBank database was screened, followed by molecular docking. MD simulation (100 ns) was performed to further study the stability of ligand binding modes. Finally, results indicated the hit DB03889 with high in silico inhibitory potency was suitable for further experimental analysis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jian Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, Jiangsu, China.,Jiangsu Key Laboratory for Functional Substances of Chinese Medicine Stake Key Laboratory Cultivation Base for TCM Quality and Efficacy School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yehua Zhu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yufang He
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Haohao Zhu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yi Gao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhi Li
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Junru Zhu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xinjie Sun
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Fang Fang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hongmei Wen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, Jiangsu, China.,Jiangsu Key Laboratory for Functional Substances of Chinese Medicine Stake Key Laboratory Cultivation Base for TCM Quality and Efficacy School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wei Li
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, Jiangsu, China.,Jiangsu Key Laboratory for Functional Substances of Chinese Medicine Stake Key Laboratory Cultivation Base for TCM Quality and Efficacy School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
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25
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Zhang Q, Lv J, He F, Yu C, Qu Y, Zhang X, Xu A, Wu J. Design, synthesis and activity evaluation of indole-based double – Branched HDAC1 inhibitors. Bioorg Med Chem 2019; 27:1595-1604. [DOI: 10.1016/j.bmc.2019.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/19/2019] [Accepted: 03/02/2019] [Indexed: 11/28/2022]
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26
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Umamaheswari A, Puratchikody A, Hari N. Synthesis and Investigation of Therapeutic Potential of Isoform-Specific HDAC8 Inhibitors for the Treatment of Cutaneous T Cell Lymphoma. Anticancer Agents Med Chem 2019; 19:916-934. [PMID: 30836926 DOI: 10.2174/1871520619666190301150254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/08/2018] [Accepted: 02/07/2019] [Indexed: 01/28/2023]
Abstract
BACKGROUND The available treatment option for any type of cancer including CTCL is chemotherapy and radiation therapy which indiscriminately persuade on the normal cells. One way out for selective destruction of CTCL cells without damaging normal cells is the use of histone deacetylase inhibitors (HDACi). Despite promising results in the treatment of CTCL, these HDACi have shown a broadband inhibition profile, moderately selective for one HDAC class but not for a particular isotype. The prevalence of drug-induced side effects leaves open a narrow window of speculation that the decreased therapeutic efficacy and observed side effects may be most likely due to non specific HDAC isoform inhibition. The aim of this paper is to synthesis and evaluates HDAC8 isoform specific inhibitors. METHODS Based on the preliminary report on the design and in silico studies of 52 hydroxamic acid derivatives bearing multi-substituent heteroaromatic rings with chiral amine linker, five compounds were shortlisted and synthesized by microwave assisted approach and high yielding synthetic protocol. A series of in vitro assays in addition to HDAC8 inhibitory activity was used to evaluate the synthesised compounds. RESULTS Inhibitors 1e, 2e, 3e, 4e and 5e exerted the anti-proliferative activities against CTCL cell lines at 20- 100 µM concentrations. Both the pyrimidine- and pyridine-based probes exhibited μM inhibitory activity against HDAC8. The pyrimidine-based probe 1e displayed remarkable HDAC8 selectivity superior to that of the standard drug, SAHA with an IC50 at 0.1µM. CONCLUSION Our study demonstrated that simple modifications at different portions of pharmacophore in the hydroxamic acid analogues are effective for improving both HDAC8 inhibitory activity and isoform selectivity. Potent and highly isoform-selective HDAC8 inhibitors were identified. These findings would be expedient for further development of HDAC8-selective inhibitors.
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Affiliation(s)
- Appavoo Umamaheswari
- D-3 Research Group, Department of Pharmaceutical Technology, University College of Engineering (BIT Campus), Anna University Tiruchirappalli, Tamilnadu, India
| | - Ayarivan Puratchikody
- D-3 Research Group, Department of Pharmaceutical Technology, University College of Engineering (BIT Campus), Anna University Tiruchirappalli, Tamilnadu, India
| | - Natarajan Hari
- Nuclear Magnetic Resonance Laboratory, School of Chemical & Biotechnology, SASTRA University, Thirumalaisamudram, Thanjavur, Tamilnadu, India
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27
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Anti-Cancer Activity of Derivatives of 1,3,4-Oxadiazole. Molecules 2018; 23:molecules23123361. [PMID: 30567416 PMCID: PMC6320996 DOI: 10.3390/molecules23123361] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 12/14/2022] Open
Abstract
Compounds containing 1,3,4-oxadiazole ring in their structure are characterised by multidirectional biological activity. Their anti-proliferative effects associated with various mechanisms, such as inhibition of growth factors, enzymes, kinases and others, deserve attention. The activity of these compounds was tested on cell lines of various cancers. In most publications, the most active derivatives of 1,3,4-oxadiazole exceeded the effect of reference drugs, so they may become the main new anti-cancer drugs in the future.
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28
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Zhang L, Chen Y, Jiang Q, Song W, Zhang L. Therapeutic potential of selective histone deacetylase 3 inhibition. Eur J Med Chem 2018; 162:534-542. [PMID: 30472601 DOI: 10.1016/j.ejmech.2018.10.072] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 02/06/2023]
Abstract
Histone deacetylases (HDACs) are closely related to the occurrence and development of a variety of diseases, such as tumor, inflammation, diabetes mellitus, cardiovascular and neurodegenerative diseases. Inhibition of HDACs by developing HDAC inhibitors has achieved significant progress in the treatment of diseases caused by epigenetic abnormalities, and especially in the cancer therapy. Isoform selective HDAC inhibitors are emphasized to be disease specific and have less off-target effects and better safety performances. HDAC3 has been illustrated to play specific role in the development of several diseases, and the discovery of HDAC3 selective inhibitors has exhibited potential in the targeted disease treatment. Herein, we summarize the current knowledge about the prospects of selective inhibition of HDAC3 for the drug development.
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Affiliation(s)
- Lihui Zhang
- School of Stomatology, Weifang Medical University, Weifang, Shandong, China
| | - Yiming Chen
- Department of Medicinal Chemistry, School of Pharmacy, Weifang Medical University, Weifang, Shandong, China
| | - Qixiao Jiang
- School of Pharmacy, Qingdao University, Qingdao, Shandong, China
| | - Weiguo Song
- Department of Medicinal Chemistry, School of Pharmacy, Weifang Medical University, Weifang, Shandong, China
| | - Lei Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Weifang Medical University, Weifang, Shandong, China.
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29
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Stoddard SV, May XA, Rivas F, Dodson K, Vijayan S, Adhika S, Parker K, Watkins DL. Design of Potent Panobinostat Histone Deacetylase Inhibitor Derivatives: Molecular Considerations for Enhanced Isozyme Selectivity between HDAC2 and HDAC8. Mol Inform 2018; 38:e1800080. [PMID: 30369061 DOI: 10.1002/minf.201800080] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/29/2018] [Indexed: 11/07/2022]
Abstract
Histone Deacetylases (HDACs) are an important family of 18 isozymes, which are being pursued as drug targets for many types of disorders. HDAC2 and HDAC8 are two of the isozymes, which have been identified as drug targets for the design of anti-cancer, neurodegenerative, immunological, and anti-parasitic agents. Design of potent HDAC2 and HDAC8 inhibitors will be useful for the therapeutic advances in many disorders. This work was undertaken to develop potent HDAC2 and HDAC8 inhibitors. A docking study was performed comparing panobinostat derivatives in both HDAC2 and HDAC8. Six of our derivatives showed stronger binding to HDAC2 than panobinostat, and two of our derivatives showed stronger binding to HDAC8 than panobinostat. We evaluated the molecular features, which improved potency of our inhibitors over panobinostat and also identified another molecular consideration, which could be used to enhance histone deacetylase inhibitor (HDACi) selectivity towards either the HDAC2 or HDAC8 isozymes. The results of this work can be used to assist future design of more potent and selective HDACi for HDAC2 and HDAC8.
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Affiliation(s)
- Shana V Stoddard
- Rhodes College, Department of Chemistry, 2000 North Parkway, Memphis, TN, 38112, USA
| | - Xavier A May
- Rhodes College, Department of Chemistry, 2000 North Parkway, Memphis, TN, 38112, USA
| | - Fatima Rivas
- St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105-3678, USA
| | - Kyra Dodson
- University of Mississippi, Department of Chemistry and Biochemistry P.O. Box 1848, Oxford, MS, 38677, USA
| | - Sajith Vijayan
- University of Mississippi, Department of Chemistry and Biochemistry P.O. Box 1848, Oxford, MS, 38677, USA
| | - Swetha Adhika
- University of Mississippi, Department of Chemistry and Biochemistry P.O. Box 1848, Oxford, MS, 38677, USA
| | - Kordarius Parker
- University of Mississippi, Department of Chemistry and Biochemistry P.O. Box 1848, Oxford, MS, 38677, USA
| | - Davita L Watkins
- University of Mississippi, Department of Chemistry and Biochemistry P.O. Box 1848, Oxford, MS, 38677, USA
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30
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Létévé M, Gonzalez C, Moroy G, Martinez A, Jeanblanc J, Legastelois R, Naassila M, Sapi J, Bourguet E. Unexpected effect of cyclodepsipeptides bearing a sulfonylhydrazide moiety towards histone deacetylase activity. Bioorg Chem 2018; 81:222-233. [PMID: 30153587 DOI: 10.1016/j.bioorg.2018.08.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/08/2018] [Accepted: 08/09/2018] [Indexed: 12/01/2022]
Affiliation(s)
- Mathieu Létévé
- Institut de Chimie Moléculaire de Reims, UMR 7312-CNRS, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096 Reims Cedex, France; Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé), France
| | - Céline Gonzalez
- INSERM U1247, Groupe de Recherche sur l'Alcool et les Pharmacodépendances (GRAP), Université de Picardie Jules Verne, C.U.R.S. (Centre Universitaire de Recherche en Santé), Chemin du Thil, 80000 Amiens, France; Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé), France
| | - Gautier Moroy
- INSERM UMR-S 973, Molécules Thérapeutiques In Silico, Université de Paris Diderot, Sorbonne Paris Cité, 35 rue Hélène Brion, 75013 Paris Cedex, France
| | - Agathe Martinez
- Institut de Chimie Moléculaire de Reims, UMR 7312-CNRS, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096 Reims Cedex, France
| | - Jérôme Jeanblanc
- INSERM U1247, Groupe de Recherche sur l'Alcool et les Pharmacodépendances (GRAP), Université de Picardie Jules Verne, C.U.R.S. (Centre Universitaire de Recherche en Santé), Chemin du Thil, 80000 Amiens, France; Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé), France
| | - Rémi Legastelois
- INSERM U1247, Groupe de Recherche sur l'Alcool et les Pharmacodépendances (GRAP), Université de Picardie Jules Verne, C.U.R.S. (Centre Universitaire de Recherche en Santé), Chemin du Thil, 80000 Amiens, France; Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé), France
| | - Mickaël Naassila
- INSERM U1247, Groupe de Recherche sur l'Alcool et les Pharmacodépendances (GRAP), Université de Picardie Jules Verne, C.U.R.S. (Centre Universitaire de Recherche en Santé), Chemin du Thil, 80000 Amiens, France; Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé), France
| | - Janos Sapi
- Institut de Chimie Moléculaire de Reims, UMR 7312-CNRS, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096 Reims Cedex, France; Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé), France
| | - Erika Bourguet
- Institut de Chimie Moléculaire de Reims, UMR 7312-CNRS, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096 Reims Cedex, France; Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé), France.
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31
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Identification by Inverse Virtual Screening of magnolol-based scaffold as new tankyrase-2 inhibitors. Bioorg Med Chem 2018; 26:3953-3957. [DOI: 10.1016/j.bmc.2018.06.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 12/27/2022]
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32
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Giordano A, del Gaudio F, Johansson C, Riccio R, Oppermann U, Di Micco S. Virtual Fragment Screening Identification of a Quinoline-5,8-dicarboxylic Acid Derivative as a Selective JMJD3 Inhibitor. ChemMedChem 2018; 13:1160-1164. [PMID: 29633584 PMCID: PMC6055880 DOI: 10.1002/cmdc.201800198] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Indexed: 11/08/2022]
Abstract
The quinoline-5,8 dicarboxylic acid scaffold has been identified by a fragment-based approach as new potential lead compound for the development of JMJD3 inhibitors. Among them, 3-(2,4-dimethoxypyrimidin-5-yl)quinoline-5,8-dicarboxylic acid (compound 3) shows low micromolar inhibitory activity against Jumonji domain-containing protein 3 (JMJD3). The experimental evaluation of inhibitory activity against seven related isoforms of JMJD3 highlighted an unprecedented selectivity toward the biological target of interest.
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Affiliation(s)
- Assunta Giordano
- Institute of Biomolecular Chemistry (ICB)Consiglio Nazionale delle Ricerche (CNR)Via Campi Flegrei 3480078Pozzuoli (Napoli)Italy
- Department of PharmacyUniversity of SalernoVia Giovanni Paolo II, 13284084Fisciano (Salerno)Italy
| | - Federica del Gaudio
- Department of PharmacyUniversity of SalernoVia Giovanni Paolo II, 13284084Fisciano (Salerno)Italy
- PhD Program in Drug Discovery and DevelopmentUniversity of SalernoVia Giovanni Paolo II, 13284084Fisciano (Salerno)Italy
- Farmaceutici Damor S.p.AVia E. Scaglione 2780145NaplesItaly
| | - Catrine Johansson
- Botnar Research Centre, Oxford NIHR BRUOxford University, Oxford Centre for Translational Myeloma ResearchOxfordOX3 7LDUK
| | - Raffaele Riccio
- Department of PharmacyUniversity of SalernoVia Giovanni Paolo II, 13284084Fisciano (Salerno)Italy
| | - Udo Oppermann
- Botnar Research Centre, Oxford NIHR BRUOxford University, Oxford Centre for Translational Myeloma ResearchOxfordOX3 7LDUK
- Freiburg Institute for Advanced Studies (FRIAS)University of FreiburgAlbertstraße 1979104FreiburgGermany
| | - Simone Di Micco
- Department of PharmacyUniversity of SalernoVia Giovanni Paolo II, 13284084Fisciano (Salerno)Italy
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33
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Giordano A, Forte G, Massimo L, Riccio R, Bifulco G, Di Micco S. Discovery of new erbB4 inhibitors: Repositioning an orphan chemical library by inverse virtual screening. Eur J Med Chem 2018; 152:253-263. [PMID: 29730188 DOI: 10.1016/j.ejmech.2018.04.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/05/2018] [Accepted: 04/09/2018] [Indexed: 01/20/2023]
Abstract
Inverse Virtual Screening (IVS) is a docking based approach aimed to the evaluation of the virtual ability of a single compound to interact with a library of proteins. For the first time, we applied this methodology to a library of synthetic compounds, which proved to be inactive towards the target they were initially designed for. Trifluoromethyl-benzenesulfonamides 3-21 were repositioned by means of IVS identifying new lead compounds (14-16, 19 and 20) for the inhibition of erbB4 in the low micromolar range. Among these, compound 20 exhibited an interesting value of IC50 on MCF7 cell lines, thus validating IVS in lead repurposing.
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Affiliation(s)
- Assunta Giordano
- Institute of Biomolecular Chemistry (ICB), Consiglio Nazionale delle Ricerche (CNR), Via Campi Flegrei 34, I-80078, Pozzuoli, Napoli, Italy; Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy
| | - Giovanni Forte
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy
| | - Luigia Massimo
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy; PhD Program in Drug Discovery and Development, University of Salerno, Via Giovanni Paolo II 132, I-84084, Fisciano, SA, Italy
| | - Raffaele Riccio
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.
| | - Simone Di Micco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.
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34
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Amin SA, Adhikari N, Jha T. Structure-activity relationships of HDAC8 inhibitors: Non-hydroxamates as anticancer agents. Pharmacol Res 2018. [DOI: 10.1016/j.phrs.2018.03.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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35
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Leonhardt M, Sellmer A, Krämer OH, Dove S, Elz S, Kraus B, Beyer M, Mahboobi S. Design and biological evaluation of tetrahydro-β-carboline derivatives as highly potent histone deacetylase 6 (HDAC6) inhibitors. Eur J Med Chem 2018; 152:329-357. [PMID: 29738953 DOI: 10.1016/j.ejmech.2018.04.046] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/09/2018] [Accepted: 04/21/2018] [Indexed: 10/17/2022]
Abstract
Various diseases are related to epigenetic modifications. Histone deacetylases (HDACs) and histone acetyl transferases (HATs) determine the pattern of histone acetylation, and thus are involved in the regulation of gene expression. First generation histone deacetylase inhibitors (HDACi) are unselective, hinder all different kinds of zinc dependent HDACs and additionally cause several side effects. Subsequently, selective HDACi are gaining more and more interest. Especially, selective histone deacetylase 6 inhibitors (HDAC6i) are supposed to be less toxic. Here we present a successful optimization study of tubastatin A, the synthesis and biological evaluation of new inhibitors based on hydroxamic acids linked to various tetrahydro-β-carboline derivatives. The potency of our selective HDAC6 inhibitors, exhibiting IC50 values in a range of 1-10 nM towards HDAC6, was evaluated with the help of a recombinant human HDAC6 enzyme assay. Selectivity was proofed in cellular assays by the hyperacetylation of surrogate parameter α-tubulin in the absence of acetylated histone H3 analyzed by Western Blot. We show that all synthesized compounds, with varies modifications of the rigid cap group, were selective and potent HDAC6 inhibitors.
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Affiliation(s)
- Michel Leonhardt
- Institute of Pharmacy, Department of Pharmaceutical/Medicinal Chemistry I, University of Regensburg, 93040, Regensburg, Germany
| | - Andreas Sellmer
- Institute of Pharmacy, Department of Pharmaceutical/Medicinal Chemistry I, University of Regensburg, 93040, Regensburg, Germany
| | - Oliver H Krämer
- Institute of Toxicology, University Medical Center Mainz, 55131, Mainz, Germany
| | - Stefan Dove
- Institute of Pharmacy, Department of Pharmaceutical/Medicinal Chemistry II, University of Regensburg, 93040, Regensburg, Germany
| | - Sigurd Elz
- Institute of Pharmacy, Department of Pharmaceutical/Medicinal Chemistry I, University of Regensburg, 93040, Regensburg, Germany
| | - Birgit Kraus
- Institute of Pharmacy, Department of Pharmaceutical Biology, University of Regensburg, 93040, Regensburg, Germany
| | - Mandy Beyer
- Institute of Toxicology, University Medical Center Mainz, 55131, Mainz, Germany
| | - Siavosh Mahboobi
- Institute of Pharmacy, Department of Pharmaceutical/Medicinal Chemistry I, University of Regensburg, 93040, Regensburg, Germany.
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36
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Heimburg T, Kolbinger FR, Zeyen P, Ghazy E, Herp D, Schmidtkunz K, Melesina J, Shaik TB, Erdmann F, Schmidt M, Romier C, Robaa D, Witt O, Oehme I, Jung M, Sippl W. Structure-Based Design and Biological Characterization of Selective Histone Deacetylase 8 (HDAC8) Inhibitors with Anti-Neuroblastoma Activity. J Med Chem 2017; 60:10188-10204. [DOI: 10.1021/acs.jmedchem.7b01447] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Tino Heimburg
- Institute
of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle/Saale, Germany
| | - Fiona R. Kolbinger
- Clinical
Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), INF 280, 69120 Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), 69120 Heidelberg, Germany
- Preclinical Program, Hopp Children’s Cancer Center at NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany
| | - Patrik Zeyen
- Institute
of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle/Saale, Germany
| | - Ehab Ghazy
- Institute
of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle/Saale, Germany
| | - Daniel Herp
- Institute
of Pharmaceutical Sciences, University of Freiburg, 79104 Freiburg, Germany
| | - Karin Schmidtkunz
- Institute
of Pharmaceutical Sciences, University of Freiburg, 79104 Freiburg, Germany
| | - Jelena Melesina
- Institute
of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle/Saale, Germany
| | - Tajith Baba Shaik
- Département
de Biologie Structurale Intégrative, Institut de Génétique
et Biologie Moléculaire et Cellulaire (IGBMC), Université
de Strasbourg (UDS), CNRS, INSERM, 67404 Illkirch Cedex, France
| | - Frank Erdmann
- Institute
of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle/Saale, Germany
| | - Matthias Schmidt
- Institute
of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle/Saale, Germany
| | - Christophe Romier
- Département
de Biologie Structurale Intégrative, Institut de Génétique
et Biologie Moléculaire et Cellulaire (IGBMC), Université
de Strasbourg (UDS), CNRS, INSERM, 67404 Illkirch Cedex, France
| | - Dina Robaa
- Institute
of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle/Saale, Germany
| | - Olaf Witt
- Clinical
Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), INF 280, 69120 Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), 69120 Heidelberg, Germany
- Preclinical Program, Hopp Children’s Cancer Center at NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany
- Department
of Pediatric Oncology, Hematology and Immunology, University of Heidelberg Medical Center, 69120 Heidelberg, Germany
| | - Ina Oehme
- Clinical
Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), INF 280, 69120 Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), 69120 Heidelberg, Germany
- Preclinical Program, Hopp Children’s Cancer Center at NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany
| | - Manfred Jung
- Institute
of Pharmaceutical Sciences, University of Freiburg, 79104 Freiburg, Germany
| | - Wolfgang Sippl
- Institute
of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle/Saale, Germany
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37
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Gabr MT, El-Gohary NS, El-Bendary ER, El-Kerdawy MM, Ni N. Microwave-assisted synthesis and antitumor evaluation of a new series of thiazolylcoumarin derivatives. EXCLI JOURNAL 2017; 16:1114-1131. [PMID: 29285008 PMCID: PMC5735336 DOI: 10.17179/excli2017-208] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 07/31/2017] [Indexed: 12/22/2022]
Abstract
A new series of thiazolylcoumarin derivatives was synthesized. The designed strategy embraced a molecular hybridization approach which involves the combination of the thiazole and coumarin pharmacophores together. The new hybrid compounds were tested for in vitro antitumor efficacy over cervical (Hela) and kidney fibroblast (COS-7) cancer cells. Compounds 5f, 5h, 5m and 5r displayed promising efficacy toward Hela cell line. In addition, 5h and 5r were found to be the most active candidates toward COS-7 cell line. The four active analogs, 5f, 5h, 5m and 5r were screened for in vivo antitumor activity over EAC cells in mice, as well as in vitro cytotoxicity toward W138 normal cells. Results illustrated that 5r has the highest in vivo activity, and that the four analogs are less cytotoxic than 5-FU toward W138 normal cells. In this study, 3D pharmacophore analysis was performed to investigate the matching pharmacophoric features of the synthesized compounds with trichostatin A. In silico studies showed that the investigated compounds meet the optimal needs for good oral absorption with no expected toxicity hazards.
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Affiliation(s)
- Moustafa T Gabr
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt.,Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
| | - Nadia S El-Gohary
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Eman R El-Bendary
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Mohamed M El-Kerdawy
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Nanting Ni
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
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38
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Bourguet E, Ozdarska K, Moroy G, Jeanblanc J, Naassila M. Class I HDAC Inhibitors: Potential New Epigenetic Therapeutics for Alcohol Use Disorder (AUD). J Med Chem 2017; 61:1745-1766. [PMID: 28771357 DOI: 10.1021/acs.jmedchem.7b00115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Alcohol use disorder (AUD) represents a serious public health issue, and discovery of new therapies is a pressing necessity. Alcohol exposure has been widely demonstrated to modulate epigenetic mechanisms, such as histone acetylation/deacetylation balance, in part via histone deacetylase (HDAC) inhibition. Epigenetic factors have been suggested to play a key role in AUD. To date, 18 different mammalian HDAC isoforms have been identified, and these have been divided into four classes. Since recent studies have suggested that both epigenetic mechanisms underlying AUD and the efficacy of HDAC inhibitors (HDACIs) in different animal models of AUD may involve class I HDACs, we herein report the development of class I HDACIs, including information regarding their structure, potency, and selectivity. More effort is required to improve the selectivity, pharmacokinetics, and toxicity profiles of HDACIs to achieve a better understanding of their efficacy in reducing addictive behavior.
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Affiliation(s)
- Erika Bourguet
- Institut de Chimie Moléculaire de Reims, UMR 7312-CNRS, UFR Pharmacie , Université de Reims Champagne-Ardenne , 51 rue Cognacq-Jay , 51096 Reims Cedex , France.,Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé) , 51095 Reims Cedex , France
| | - Katarzyna Ozdarska
- Institut de Chimie Moléculaire de Reims, UMR 7312-CNRS, UFR Pharmacie , Université de Reims Champagne-Ardenne , 51 rue Cognacq-Jay , 51096 Reims Cedex , France.,Department of Bioanalysis and Drugs Analysis , Medical University of Warsaw , S. Banacha 1 , 02-097 Warsaw , Poland
| | - Gautier Moroy
- Sorbonne Paris Cité, Molécules Thérapeutiques In Silico (MTi), INSERM UMR-S 973 , Université Paris Diderot , 35 rue Hélène Brion , 75013 Paris , France
| | - Jérôme Jeanblanc
- INSERM ERi 24, Groupe de Recherche sur l'Alcool et les Pharmacodépendances (GRAP) , Université de Picardie Jules Verne, C.U.R.S. (Centre Universitaire de Recherche en Santé) , Chemin du Thil , 80000 Amiens , France.,Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé) , 51095 Reims Cedex , France
| | - Mickaël Naassila
- INSERM ERi 24, Groupe de Recherche sur l'Alcool et les Pharmacodépendances (GRAP) , Université de Picardie Jules Verne, C.U.R.S. (Centre Universitaire de Recherche en Santé) , Chemin du Thil , 80000 Amiens , France.,Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé) , 51095 Reims Cedex , France
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39
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Traoré MM, Zwick V, Simões-Pires CA, Nurisso A, Issa M, Cuendet M, Maynadier M, Wein S, Vial H, Jamet H, Wong YS. Hydroxyl Ketone-Based Histone Deacetylase Inhibitors To Gain Insight into Class I HDAC Selectivity versus That of HDAC6. ACS OMEGA 2017; 2:1550-1562. [PMID: 30023639 PMCID: PMC6044785 DOI: 10.1021/acsomega.6b00481] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/29/2017] [Indexed: 06/07/2023]
Abstract
Little is known about the biological and structural features that govern the isoform selectivity for class I histone deacetylases (HDACs) over HDAC6. In addition to that for known inhibitors, like benzamides, psammaplin A, and cyclodepsipeptide-derived thiols, selectivity was also observed for naturally occurring cyclopeptide HDAC inhibitors with an aliphatic flexible linker and ketonelike zinc-binding group (ZBG). The present study reports that this isoform selectivity is mainly due to the linker and ZBG, as replacement of the cyclopeptide cap region by a simple aniline retained class I HDAC isoform selectivity toward HDAC6 in enzymatic assays. The best cyclopeptide-free analogues preserved efficacy against Plasmodium falciparum and cancer cell lines. Molecular modeling provided hypotheses to explain this selectivity and suggests different behaviors of the flexible linker on HDAC1 and HDAC6 pockets, which may influence, on the basis of the strength of the ZBG, its coordination with the zinc ion.
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Affiliation(s)
- Mohamed
D. M. Traoré
- Département
de Pharmacochimie Moléculaire, CNRS
UMR 5063, ICMG FR 2607, Univ. Grenoble Alpes, 470 rue de la chimie, 38041 Grenoble cedex 9, France
- Département
de Chimie Moléculaire, CNRS UMR 5250,
ICMG FR 2607, Univ. Grenoble Alpes, 301 rue de la chimie, 38041 Grenoble cedex 9, France
| | - Vincent Zwick
- School
of Pharmaceutical Sciences, University of
Geneva, University of Lausanne, rue Michel Servet 1, 1211 Geneva, Switzerland
| | - Claudia A. Simões-Pires
- School
of Pharmaceutical Sciences, University of
Geneva, University of Lausanne, rue Michel Servet 1, 1211 Geneva, Switzerland
| | - Alessandra Nurisso
- School
of Pharmaceutical Sciences, University of
Geneva, University of Lausanne, rue Michel Servet 1, 1211 Geneva, Switzerland
- Laboratoire
Dynamique des Interactions Membranaires Normales et Pathologiques, UMR 5235, CNRS, University of Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
| | - Mark Issa
- School
of Pharmaceutical Sciences, University of
Geneva, University of Lausanne, rue Michel Servet 1, 1211 Geneva, Switzerland
| | - Muriel Cuendet
- School
of Pharmaceutical Sciences, University of
Geneva, University of Lausanne, rue Michel Servet 1, 1211 Geneva, Switzerland
| | - Marjorie Maynadier
- Département
de Biochimie, Université de Montréal, Montréal, Québec, Canada H3C 3J7
| | - Sharon Wein
- Département
de Biochimie, Université de Montréal, Montréal, Québec, Canada H3C 3J7
| | - Henri Vial
- Département
de Biochimie, Université de Montréal, Montréal, Québec, Canada H3C 3J7
| | - Helene Jamet
- Département
de Chimie Moléculaire, CNRS UMR 5250,
ICMG FR 2607, Univ. Grenoble Alpes, 301 rue de la chimie, 38041 Grenoble cedex 9, France
| | - Yung-Sing Wong
- Département
de Pharmacochimie Moléculaire, CNRS
UMR 5063, ICMG FR 2607, Univ. Grenoble Alpes, 470 rue de la chimie, 38041 Grenoble cedex 9, France
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40
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Ahmad M, Aga MA, Bhat JA, Kumar B, Rouf A, Capalash N, Mintoo MJ, Kumar A, Mahajan P, Mondhe DM, Nargotra A, Sharma PR, Zargar MA, Vishwakarma RA, Shah BA, Taneja SC, Hamid A. Exploring Derivatives of Quinazoline Alkaloid l-Vasicine as Cap Groups in the Design and Biological Mechanistic Evaluation of Novel Antitumor Histone Deacetylase Inhibitors. J Med Chem 2017; 60:3484-3497. [DOI: 10.1021/acs.jmedchem.7b00322] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Mudassier Ahmad
- Cancer Pharmacology
Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu-180001, India
| | | | - Javeed Ahmad Bhat
- Cancer Pharmacology
Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu-180001, India
- Department of Biotechnology, Panjab University, Chandigarh-160014, India
| | | | | | - Neena Capalash
- Department of Biotechnology, Panjab University, Chandigarh-160014, India
| | - Mubashir Javeed Mintoo
- Cancer Pharmacology
Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu-180001, India
- CSIR-Academy of Scientific & Innovative Research, New Delhi, India
| | | | - Priya Mahajan
- Discovery Informatics Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu-180001, India
| | - Dilip Manikrao Mondhe
- Cancer Pharmacology
Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu-180001, India
- CSIR-Academy of Scientific & Innovative Research, New Delhi, India
| | - Amit Nargotra
- Discovery Informatics Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu-180001, India
| | | | - Mohmmad Afzal Zargar
- Department of Biochemistry, University of Kashmir, Srinagar, Jammu and Kashmir-190006, India
| | | | - Bhahwal Ali Shah
- CSIR-Academy of Scientific & Innovative Research, New Delhi, India
| | | | - Abid Hamid
- Cancer Pharmacology
Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu-180001, India
- CSIR-Academy of Scientific & Innovative Research, New Delhi, India
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41
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Manal M, Chandrasekar M, Gomathi Priya J, Nanjan M. Inhibitors of histone deacetylase as antitumor agents: A critical review. Bioorg Chem 2016; 67:18-42. [DOI: 10.1016/j.bioorg.2016.05.005] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/29/2016] [Accepted: 05/15/2016] [Indexed: 12/11/2022]
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42
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Roche J, Bertrand P. Inside HDACs with more selective HDAC inhibitors. Eur J Med Chem 2016; 121:451-483. [PMID: 27318122 DOI: 10.1016/j.ejmech.2016.05.047] [Citation(s) in RCA: 234] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 05/20/2016] [Accepted: 05/21/2016] [Indexed: 01/08/2023]
Abstract
Inhibitors of histone deacetylases (HDACs) are nowadays part of the therapeutic arsenal mainly against cancers, with four compounds approved by the Food and Drug Administration. During the last five years, several groups have made continuous efforts to improve this class of compounds, designing more selective compounds or compounds with multiple capacities. After a survey of the HDAC biology and structures, this review summarizes the results of the chemists working in this field, and highlights when possible the behavior of the molecules inside their targets.
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Affiliation(s)
- Joëlle Roche
- Laboratoire Ecologie et Biologie des Interactions, Equipe « SEVE Sucres & Echanges Végétaux-Environnement », Université de Poitiers, UMR CNRS 7267, F-86073 Poitiers Cedex 09, France; Réseau Epigénétique du Cancéropôle Grand Ouest, France
| | - Philippe Bertrand
- Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, 4 rue Michel Brunet, TSA 51106, B28, F-86073 Poitiers Cedex 09, France; Réseau Epigénétique du Cancéropôle Grand Ouest, France.
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43
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Bieliauskas AV, Weerasinghe SVW, Negmeldin AT, Pflum MKH. Structural Requirements of Histone Deacetylase Inhibitors: SAHA Analogs Modified on the Hydroxamic Acid. Arch Pharm (Weinheim) 2016; 349:373-82. [PMID: 27062198 DOI: 10.1002/ardp.201500472] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/15/2016] [Accepted: 03/18/2016] [Indexed: 11/09/2022]
Abstract
Histone deacetylase (HDAC) proteins have emerged as targets for anti-cancer therapeutics, with several inhibitors used in the clinic, including suberoylanilide hydroxamic acid (SAHA, vorinostat). Because SAHA and many other inhibitors target all or most of the 11 human HDAC proteins, the creation of selective inhibitors has been studied intensely. Recently, inhibitors selective for HDAC1 and HDAC2 were reported where selectivity was attributed to interactions between substituents on the metal binding moiety of the inhibitor and residues in the 14-Å internal cavity of the HDAC enzyme structure. Based on this earlier work, we synthesized and tested SAHA analogs with substituents on the hydroxamic acid metal binding moiety. The N-substituted SAHA analogs displayed reduced potency and solubility, but greater selectivity, compared to SAHA. Docking studies suggested that the N-substituent accesses the 14-Å internal cavity to impart preferential inhibition of HDAC1. These studies with N-substituted SAHA analogs are consistent with the strategy exploiting the 14-Å internal cavity of HDAC proteins to create HDAC1/2 selective inhibitors.
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Affiliation(s)
| | | | | | - Mary Kay H Pflum
- Department of Chemistry, Wayne State University, Detroit, MI, USA
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44
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Ballante F, Marshall GR. An Automated Strategy for Binding-Pose Selection and Docking Assessment in Structure-Based Drug Design. J Chem Inf Model 2016; 56:54-72. [PMID: 26682916 DOI: 10.1021/acs.jcim.5b00603] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Molecular docking is a widely used technique in drug design to predict the binding pose of a candidate compound in a defined therapeutic target. Numerous docking protocols are available, each characterized by different search methods and scoring functions, thus providing variable predictive capability on a same ligand-protein system. To validate a docking protocol, it is necessary to determine a priori the ability to reproduce the experimental binding pose (i.e., by determining the docking accuracy (DA)) in order to select the most appropriate docking procedure and thus estimate the rate of success in docking novel compounds. As common docking programs use generally different root-mean-square deviation (RMSD) formulas, scoring functions, and format results, it is both difficult and time-consuming to consistently determine and compare their predictive capabilities in order to identify the best protocol to use for the target of interest and to extrapolate the binding poses (i.e., best-docked (BD), best-cluster (BC), and best-fit (BF) poses) when applying a given docking program over thousands/millions of molecules during virtual screening. To reduce this difficulty, two new procedures called Clusterizer and DockAccessor have been developed and implemented for use with some common and "free-for-academics" programs such as AutoDock4, AutoDock4(Zn), AutoDock Vina, DOCK, MpSDockZn, PLANTS, and Surflex-Dock to automatically extrapolate BD, BC, and BF poses as well as to perform consistent cluster and DA analyses. Clusterizer and DockAccessor (code available over the Internet) represent two novel tools to collect computationally determined poses and detect the most predictive docking approach. Herein an application to human lysine deacetylase (hKDAC) inhibitors is illustrated.
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Affiliation(s)
- Flavio Ballante
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, Missouri 63110, United States
| | - Garland R Marshall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, Missouri 63110, United States
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45
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Zhou J, Yang Z, Zhang F, Luo HB, Li M, Wu R. A salt bridge turns off the foot-pocket in class-II HDACs. Phys Chem Chem Phys 2016; 18:21246-50. [DOI: 10.1039/c6cp03144g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It is for the first time revealed that a conserved R–E salt bridge turns off the foot-pocket in class-II HDACs.
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Affiliation(s)
- Jingwei Zhou
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006
- P. R. China
| | - Zuolong Yang
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006
- P. R. China
| | - Fan Zhang
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006
- P. R. China
| | - Hai-Bin Luo
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006
- P. R. China
| | - Min Li
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006
- P. R. China
| | - Ruibo Wu
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006
- P. R. China
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46
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Iranshahi M, Chini MG, Masullo M, Sahebkar A, Javidnia A, Chitsazian Yazdi M, Pergola C, Koeberle A, Werz O, Pizza C, Terracciano S, Piacente S, Bifulco G. Can Small Chemical Modifications of Natural Pan-inhibitors Modulate the Biological Selectivity? The Case of Curcumin Prenylated Derivatives Acting as HDAC or mPGES-1 Inhibitors. JOURNAL OF NATURAL PRODUCTS 2015; 78:2867-2879. [PMID: 26588603 DOI: 10.1021/acs.jnatprod.5b00700] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Curcumin, or diferuloylmethane, a polyphenolic molecule isolated from the rhizome of Curcuma longa, is reported to modulate multiple molecular targets involved in cancer and inflammatory processes. On the basis of its pan-inhibitory characteristics, here we show that simple chemical modifications of the curcumin scaffold can regulate its biological selectivity. In particular, the curcumin scaffold was modified with three types of substituents at positions C-1, C-8, and/or C-8' [C5 (isopentenyl, 5-8), C10 (geranyl, 9-12), and C15 (farnesyl, 13, 14)] in order to make these molecules more selective than the parent compound toward two specific targets: histone deacetylase (HDAC) and microsomal prostaglandin E2 synthase-1 (mPGES-1). From combined in silico and in vitro analyses, three selective inhibitors by proper substitution at position 8 were revealed. Compound 13 has improved HDAC inhibitory activity and selectivity with respect to the parent compound, while 5 and 9 block the mPGES-1 enzyme. We hypothesize about the covalent interaction of curcumin, 5, and 9 with the mPGES-1 binding site.
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Affiliation(s)
- Mehrdad Iranshahi
- Biotechnology Research Center and School of Pharmacy, Mashhad University of Medical Sciences , Vakil Abad Boulevard, Opposite Mellat Park, 91775-1365 Mashhad, Iran
| | - Maria Giovanna Chini
- Department of Pharmacy, University of Salerno , Via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy
| | - Milena Masullo
- Department of Pharmacy, University of Salerno , Via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy
| | - Amirhossein Sahebkar
- Biotechnology Research Center and School of Pharmacy, Mashhad University of Medical Sciences , Vakil Abad Boulevard, Opposite Mellat Park, 91775-1365 Mashhad, Iran
| | - Azita Javidnia
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences , Enghlab Street, 14155-6559 Tehran, Iran
| | - Mahsa Chitsazian Yazdi
- Biotechnology Research Center and School of Pharmacy, Mashhad University of Medical Sciences , Vakil Abad Boulevard, Opposite Mellat Park, 91775-1365 Mashhad, Iran
| | - Carlo Pergola
- Institute of Pharmacy, Friedrich Schiller University Jena , Philosophenweg 14, 07743 Jena, Germany
| | - Andreas Koeberle
- Institute of Pharmacy, Friedrich Schiller University Jena , Philosophenweg 14, 07743 Jena, Germany
| | - Oliver Werz
- Institute of Pharmacy, Friedrich Schiller University Jena , Philosophenweg 14, 07743 Jena, Germany
| | - Cosimo Pizza
- Department of Pharmacy, University of Salerno , Via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy
| | - Stefania Terracciano
- Department of Pharmacy, University of Salerno , Via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy
| | - Sonia Piacente
- Department of Pharmacy, University of Salerno , Via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno , Via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy
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Target engagement and drug residence time can be observed in living cells with BRET. Nat Commun 2015; 6:10091. [PMID: 26631872 PMCID: PMC4686764 DOI: 10.1038/ncomms10091] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 10/30/2015] [Indexed: 12/18/2022] Open
Abstract
The therapeutic action of drugs is predicated on their physical engagement with cellular targets. Here we describe a broadly applicable method using bioluminescence resonance energy transfer (BRET) to reveal the binding characteristics of a drug with selected targets within intact cells. Cell-permeable fluorescent tracers are used in a competitive binding format to quantify drug engagement with the target proteins fused to Nanoluc luciferase. The approach enabled us to profile isozyme-specific engagement and binding kinetics for a panel of histone deacetylase (HDAC) inhibitors. Our analysis was directed particularly to the clinically approved prodrug FK228 (Istodax/Romidepsin) because of its unique and largely unexplained mechanism of sustained intracellular action. Analysis of the binding kinetics by BRET revealed remarkably long intracellular residence times for FK228 at HDAC1, explaining the protracted intracellular behaviour of this prodrug. Our results demonstrate a novel application of BRET for assessing target engagement within the complex milieu of the intracellular environment.
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Murugan K, Sangeetha S, Ranjitha S, Vimala A, Al-Sohaibani S, Rameshkumar G. HDACiDB: a database for histone deacetylase inhibitors. DRUG DESIGN DEVELOPMENT AND THERAPY 2015; 9:2257-64. [PMID: 25945037 PMCID: PMC4408954 DOI: 10.2147/dddt.s78276] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
An histone deacetylase (HDAC) inhibitor database (HDACiDB) was constructed to enable rapid access to data relevant to the development of epigenetic modulators (HDAC inhibitors [HDACi]), helping bring precision cancer medicine a step closer. Thousands of HDACi targeting HDACs are in various stages of development and are being tested in clinical trials as monotherapy and in combination with other cancer agents. Despite the abundance of HDACi, information resources are limited. Tools for in silico experiments on specific HDACi prediction, for designing and analyzing the generated data, as well as custom-made specific tools and interactive databases, are needed. We have developed an HDACiDB that is a composite collection of HDACi and currently comprises 1,445 chemical compounds, including 419 natural and 1,026 synthetic ones having the potential to inhibit histone deacetylation. Most importantly, it will allow application of Lipinski’s rule of five drug-likeness and other physicochemical property-based screening of the inhibitors. It also provides easy access to information on their source of origin, molecular properties, drug likeness, as well as bioavailability with relevant references cited. Being the first comprehensive database on HDACi that contains all known natural and synthetic HDACi, the HDACiDB may help to improve our knowledge concerning the mechanisms of actions of available HDACi and enable us to selectively target individual HDAC isoforms and establish a new paradigm for intelligent epigenetic cancer drug design. The database is freely available on the http://hdacidb.bioinfo.au-kbc.org.in/hdacidb/website.
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Affiliation(s)
- Kasi Murugan
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Shanmugasamy Sangeetha
- Bioinformatics Laboratory, Anna University K. Balachander Research Centre, MIT Campus of Anna University Chennai, Chennai, India
| | - Shanmugasamy Ranjitha
- Bioinformatics Laboratory, Anna University K. Balachander Research Centre, MIT Campus of Anna University Chennai, Chennai, India
| | - Antony Vimala
- Bioinformatics Laboratory, Anna University K. Balachander Research Centre, MIT Campus of Anna University Chennai, Chennai, India
| | - Saleh Al-Sohaibani
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Gopal Rameshkumar
- Bioinformatics Laboratory, Anna University K. Balachander Research Centre, MIT Campus of Anna University Chennai, Chennai, India
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Deschamps N, Simões-Pires CA, Carrupt PA, Nurisso A. How the flexibility of human histone deacetylases influences ligand binding: an overview. Drug Discov Today 2015; 20:736-42. [PMID: 25597521 DOI: 10.1016/j.drudis.2015.01.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 12/12/2014] [Accepted: 01/09/2015] [Indexed: 12/17/2022]
Abstract
Over the past decade, human histone deacetylases (HDACs) have become interesting as therapeutic targets because of the benefits that their modulation might provide in aging-related disorders. Recently, studies using crystallography and computational chemistry have provided information on the structure and conformational changes related to HDAC-mediated recognition events. Through the description of the key mass and one-off movements observed in metal-dependent HDACs, here we highlight the impact of flexibility on drug-binding affinity and specificity. The collected information will be useful for not only a better understanding of the biological functions of HDACs, but also the conception of new selective binders.
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Affiliation(s)
- Nathalie Deschamps
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Quai Ernest Ansermet, 30, CH-1211 Geneva 4, Switzerland
| | - Claudia Avello Simões-Pires
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Quai Ernest Ansermet, 30, CH-1211 Geneva 4, Switzerland
| | - Pierre-Alain Carrupt
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Quai Ernest Ansermet, 30, CH-1211 Geneva 4, Switzerland
| | - Alessandra Nurisso
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Quai Ernest Ansermet, 30, CH-1211 Geneva 4, Switzerland.
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50
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Halder AK, Mallick S, Shikha D, Saha A, Saha KD, Jha T. Design of dual MMP-2/HDAC-8 inhibitors by pharmacophore mapping, molecular docking, synthesis and biological activity. RSC Adv 2015. [DOI: 10.1039/c5ra12606a] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Recent analyses have highlighted the promotion of cancer migration and invasion, mediated through HDAC via MMP-2 and MMP-9.
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Affiliation(s)
- Amit K. Halder
- Natural Science Laboratory
- Division of Medicinal and Pharmaceutical Chemistry
- Department of Pharmaceutical Technology
- Jadavpur University
- Kolkata 700032
| | - Sumana Mallick
- Cancer Biology & Inflammatory Disorder Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Deep Shikha
- Natural Science Laboratory
- Division of Medicinal and Pharmaceutical Chemistry
- Department of Pharmaceutical Technology
- Jadavpur University
- Kolkata 700032
| | - Achintya Saha
- Department of Chemical Technology
- University of Calcutta
- Kolkata 700009
- India
| | - Krishna D. Saha
- Cancer Biology & Inflammatory Disorder Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Tarun Jha
- Natural Science Laboratory
- Division of Medicinal and Pharmaceutical Chemistry
- Department of Pharmaceutical Technology
- Jadavpur University
- Kolkata 700032
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