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Khatun S, Bhagat RP, Amin SA, Jha T, Gayen S. Density functional theory (DFT) studies in HDAC-based chemotherapeutics: Current findings, case studies and future perspectives. Comput Biol Med 2024; 175:108468. [PMID: 38657469 DOI: 10.1016/j.compbiomed.2024.108468] [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: 11/02/2023] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024]
Abstract
Density Functional Theory (DFT) is a quantum chemical computational method used to predict and analyze the electronic properties of atoms, molecules, and solids based on the density of electrons rather than wavefunctions. It provides insights into the structure, bonding, and behavior of different molecules, including those involved in the development of chemotherapeutic agents, such as histone deacetylase inhibitors (HDACis). HDACs are a wide group of metalloenzymes that facilitate the removal of acetyl groups from acetyl-lysine residues situated in the N-terminal tail of histones. Abnormal HDAC recruitment has been linked to several human diseases, especially cancer. Therefore, it has been recognized as a prospective target for accelerating the development of anticancer therapies. Researchers have studied HDACs and its inhibitors extensively using a combination of experimental methods and diverse in-silico approaches such as machine learning and quantitative structure-activity relationship (QSAR) methods, molecular docking, molecular dynamics, pharmacophore mapping, and more. In this context, DFT studies can make significant contribution by shedding light on the molecular properties, interactions, reaction pathways, transition states, reactivity and mechanisms involved in the development of HDACis. This review attempted to elucidate the scope in which DFT methodologies may be used to enhance our comprehension of the molecular aspects of HDAC inhibitors, aiding in the rational design and optimization of these compounds for therapeutic applications in cancer and other ailments. The insights gained can guide experimental efforts toward developing more potent and selective HDAC inhibitors.
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Affiliation(s)
- Samima Khatun
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Rinki Prasad Bhagat
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Sk Abdul Amin
- Department of Pharmaceutical Technology, JIS University, 81, Nilgunj Road, Agarpara, Kolkata, West Bengal, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, 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.
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Geurs S, Clarisse D, De Bosscher K, D'hooghe M. The Zinc-Binding Group Effect: Lessons from Non-Hydroxamic Acid Vorinostat Analogs. J Med Chem 2023. [PMID: 37276138 DOI: 10.1021/acs.jmedchem.3c00226] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Histone deacetylases (HDACs) are enzymes pursued as drug targets in various cancers and several non-oncological conditions, such as inflammation and neurodegenerative disorders. In the past decade, HDAC inhibitors (HDACi) have emerged as relevant pharmaceuticals, with many efforts devoted to the development of new representatives. However, the growing safety concerns regarding the established hydroxamic acid-based HDAC inhibitors tend to drive current research more toward the design of inhibitors bearing alternative zinc-binding groups (ZBGs). This Perspective presents an overview of all non-hydroxamic acid ZBGs that have been incorporated into the clinically approved prototypical HDACi, suberoylanilide hydroxamic acid (vorinostat). This provides the unique opportunity to compare the inhibition potential and biological effects of different ZBGs in a direct way, as the compounds selected for this Perspective differ only in their ZBG. To that end, different strategies used to select a ZBG, its properties, activity, and liabilities are discussed.
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Affiliation(s)
- Silke Geurs
- SynBioC Research Group, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
- Translational Nuclear Receptor Research, VIB-UGent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B-9052 Ghent, Belgium
| | - Dorien Clarisse
- Translational Nuclear Receptor Research, VIB-UGent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B-9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B-9052 Ghent, Belgium
| | - Karolien De Bosscher
- Translational Nuclear Receptor Research, VIB-UGent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B-9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B-9052 Ghent, Belgium
| | - Matthias D'hooghe
- SynBioC Research Group, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
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Jakubkiene V, Valiulis GE, Schweipert M, Zubriene A, Matulis D, Meyer-Almes FJ, Tumkevicius S. Synthesis and HDAC inhibitory activity of pyrimidine-based hydroxamic acids. Beilstein J Org Chem 2022; 18:837-844. [PMID: 35923158 PMCID: PMC9296983 DOI: 10.3762/bjoc.18.84] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/27/2022] [Indexed: 11/23/2022] Open
Abstract
Histone deacetylases (HDACs) play an essential role in the transcriptional regulation of cells through the deacetylation of nuclear histone and non-histone proteins and are promising therapeutic targets for the treatment of various diseases. Here, the synthesis of new compounds in which a hydroxamic acid residue is attached to differently substituted pyrimidine rings via a methylene group bridge of varying length as potential HDAC inhibitors is described. The target compounds were obtained by alkylation of 2-(alkylthio)pyrimidin-4(3H)-ones with ethyl 2-bromoethanoate, ethyl 4-bromobutanoate, or methyl 6-bromohexanoate followed by aminolysis of the obtained esters with hydroxylamine. Oxidation of the 2-methylthio group to the methylsulfonyl group and following treatment with amines resulted in the formation of the corresponding 2-amino-substituted derivatives, the ester group of which reacted with hydroxylamine to give the corresponding hydroxamic acids. The synthesized hydroxamic acids were tested as inhibitors of the HDAC4 and HDAC8 isoforms. Among the synthesized pyrimidine-based hydroxamic acids N-hydroxy-6-[6-methyl-2-(methylthio)-5-propylpyrimidin-4-yloxy]hexanamide was found to be the most potent inhibitor of both the HDAC4 and HDAC8 isoforms, with an IC50 of 16.6 µM and 1.2 µM, respectively.
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Affiliation(s)
- Virginija Jakubkiene
- Department of Organic Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko 24, 03225 Vilnius, Lithuania
| | - Gabrielius Ernis Valiulis
- Department of Organic Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko 24, 03225 Vilnius, Lithuania
| | - Markus Schweipert
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences, Stephanstr. 7, 64295 Darmstadt, Germany
| | - Asta Zubriene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257 Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257 Vilnius, Lithuania
| | - Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences, Stephanstr. 7, 64295 Darmstadt, Germany
| | - Sigitas Tumkevicius
- Department of Organic Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko 24, 03225 Vilnius, Lithuania
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Adimulam T, Arumugam T, Foolchand A, Ghazi T, Chuturgoon AA. The Effect of Organoselenium Compounds on Histone Deacetylase Inhibition and Their Potential for Cancer Therapy. Int J Mol Sci 2021; 22:ijms222312952. [PMID: 34884764 PMCID: PMC8657714 DOI: 10.3390/ijms222312952] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 12/20/2022] Open
Abstract
Genetic and epigenetic changes alter gene expression, contributing to cancer. Epigenetic changes in cancer arise from alterations in DNA and histone modifications that lead to tumour suppressor gene silencing and the activation of oncogenes. The acetylation status of histones and non-histone proteins are determined by the histone deacetylases and histone acetyltransferases that control gene transcription. Organoselenium compounds have become promising contenders in cancer therapeutics. Apart from their anti-oxidative effects, several natural and synthetic organoselenium compounds and metabolites act as histone deacetylase inhibitors, which influence the acetylation status of histones and non-histone proteins, altering gene transcription. This review aims to summarise the effect of natural and synthetic organoselenium compounds on histone and non-histone protein acetylation/deacetylation in cancer therapy.
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Toshev N, Cheshmedzhieva D, Dudev T. Factors governing the affinity and selectivity of histone deacetylase inhibitors for the HDAC8 enzyme active site: Implications for anticancer therapy. J PHYS ORG CHEM 2021. [DOI: 10.1002/poc.4268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Nikolay Toshev
- Faculty of Chemistry and Pharmacy University of Sofia Sofia Bulgaria
- Faculty of Trade Economics and Commodity Science Plekhanov Russian University of Economics Moscow Russia
| | | | - Todor Dudev
- Faculty of Chemistry and Pharmacy University of Sofia Sofia Bulgaria
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Song H, Hwang YJ, Ha JW, Boo YC. Screening of an Epigenetic Drug Library Identifies 4-((hydroxyamino)carbonyl)- N-(2-hydroxyethyl)- N-Phenyl-Benzeneacetamide that Reduces Melanin Synthesis by Inhibiting Tyrosinase Activity Independently of Epigenetic Mechanisms. Int J Mol Sci 2020; 21:ijms21134589. [PMID: 32605171 PMCID: PMC7370187 DOI: 10.3390/ijms21134589] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/17/2020] [Accepted: 06/27/2020] [Indexed: 12/16/2022] Open
Abstract
The aim of this study was to identify novel antimelanogenic drugs from an epigenetic screening library containing various modulators targeting DNA methyltransferases, histone deacetylases, and other related enzymes/proteins. Of 141 drugs tested, K8 (4-((hydroxyamino)carbonyl)-N-(2-hydroxyethyl)-N-phenyl-benzeneacetamide; HPOB) was found to effectively inhibit the α-melanocyte-stimulating hormone (α-MSH)-induced melanin synthesis in B16-F10 murine melanoma cells without accompanying cytotoxicity. Additional experiments showed that K8 did not significantly reduce the mRNA and protein level of tyrosinase (TYR) or microphthalmia-associated transcription factor (MITF) in cells, but it potently inhibited the catalytic activity TYR in vitro (IC50, 1.1-1.5 µM) as compared to β-arbutin (IC50, 500-700 µM) or kojic acid (IC50, 63 µM). K8 showed copper chelating activity similar to kojic acid. Therefore, these data suggest that K8 inhibits cellular melanin synthesis not by downregulation of TYR protein expression through an epigenetic mechanism, but by direct inhibition of TYR catalytic activity through copper chelation. Metal chelating activity of K8 is not surprising because it is known to inhibit histone deacetylase (HDAC) 6 through zinc chelation. This study identified K8 as a potent inhibitor of cellular melanin synthesis, which may be useful for the treatment of hyperpigmentation disorders.
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Affiliation(s)
- Hyerim Song
- Department of Molecular Medicine, School of Medicine, Kyungpook National University, Daegu 41944, Korea; (H.S.); (Y.J.H.); (J.W.H.)
- Brain Korea (BK) 21 Plus Kyungpook National University (KNU) Biomedical Convergence Program, Kyungpook National University, Daegu 41944, Korea
| | - Yun Jeong Hwang
- Department of Molecular Medicine, School of Medicine, Kyungpook National University, Daegu 41944, Korea; (H.S.); (Y.J.H.); (J.W.H.)
- Brain Korea (BK) 21 Plus Kyungpook National University (KNU) Biomedical Convergence Program, Kyungpook National University, Daegu 41944, Korea
| | - Jae Won Ha
- Department of Molecular Medicine, School of Medicine, Kyungpook National University, Daegu 41944, Korea; (H.S.); (Y.J.H.); (J.W.H.)
- Brain Korea (BK) 21 Plus Kyungpook National University (KNU) Biomedical Convergence Program, Kyungpook National University, Daegu 41944, Korea
| | - Yong Chool Boo
- Department of Molecular Medicine, School of Medicine, Kyungpook National University, Daegu 41944, Korea; (H.S.); (Y.J.H.); (J.W.H.)
- Brain Korea (BK) 21 Plus Kyungpook National University (KNU) Biomedical Convergence Program, Kyungpook National University, Daegu 41944, Korea
- Cell and Matrix Research Institute, Kyungpook National University, Daegu 41944, Korea
- Correspondence: ; Tel.: +82-53-420-4946
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Uba AI, Yelekçi K. Pharmacophore-based virtual screening for identification of potential selective inhibitors of human histone deacetylase 6. Comput Biol Chem 2018; 77:318-330. [PMID: 30463049 DOI: 10.1016/j.compbiolchem.2018.10.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/29/2018] [Accepted: 10/31/2018] [Indexed: 01/07/2023]
Abstract
Histone deacetylase (HDAC) 6 plays a role in oncogenic transformation and cancer metastasis via tubulin deacetylation, making it a critical target for anticancer drug design. However, lack of selectivity shown by many of the current HDAC6 inhibitors in clinical use and trials prompts the continuous search for selective inhibitors. Here, 10 pharmacophore hypotheses were developed based on the 3D common features of training set of 20 HDAC inhibitors in clinical use and trials. The hypotheses were validated using a test set of another 20 HDAC inhibitors along with 400 inactive (decoys) molecules based on Güner-Henry pharmacophore scoring method. Hypothesis 1 consisting of 1 H-bond donor, 1 H-bond acceptor and 2 hydrophobic features, was used to screen "DruglikeDiverse" database using Biovia Discovery Studio 4.5. The top 10 hit compounds were selected based on the pharmacophore fit values (>3.00). Their binding affinity against HDAC6 compared to class I HDACs (1, 2, 3 & 8) and a class IIa member (HDAC7), was calculated by molecular docking using AutoDock4. The stability of binding modes of 2 potential HDAC6-selective inhibitors (ENA501965 and IBS399024) was examined by 30 ns-molecular dynamics (MD) simulation using nanoscale MD (NAMD) software. Both ligands showed potential stability in HDAC6 active site over time. Therefore, these may provide additional scaffolds for further optimization towards the design of safe, potent and selective HDAC6 inhibitors.
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Affiliation(s)
- Abdullahi Ibrahim Uba
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083 Fatih, Istanbul, Turkey; Centre for Biotechnology Research, Bayero University, P.M.B 3011, B.U.K road, Kano, Nigeria
| | - Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083 Fatih, Istanbul, Turkey.
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