1
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Hitoshio K, Maeda H, Teranishi K, Shimokawa J, Yorimitsu H. Synthesis of unsymmetrical dialkoxydiarylsilanes and diarylsilanediols from tetraalkoxysilane having a dioxasilepane unit. Chem Commun (Camb) 2024; 60:7339-7342. [PMID: 38916043 DOI: 10.1039/d4cc02051k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The tetraalkoxysilane carrying a stable seven-membered dioxasilepane moiety and two trifluoroethoxy groups undergoes reliable iterative substitution of the two trifluoroethoxy groups by sequential treatment with different aryl Grignard reagents while keeping the seven-membered structure intact. The process results in the synthesis of unsymmetrical dialkoxydiarylsilanes and eventually diarylsilanediols after proper hydrolysis.
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Affiliation(s)
- Kenshiro Hitoshio
- Department of Chemistry Graduate School of Science, Kyoto University Sakyo-ku, Kyoto 606-8502, Japan.
| | - Hiroki Maeda
- Department of Chemistry Graduate School of Science, Kyoto University Sakyo-ku, Kyoto 606-8502, Japan.
| | - Kento Teranishi
- Department of Chemistry Graduate School of Science, Kyoto University Sakyo-ku, Kyoto 606-8502, Japan.
| | - Jun Shimokawa
- Department of Chemistry Graduate School of Science, Kyoto University Sakyo-ku, Kyoto 606-8502, Japan.
| | - Hideki Yorimitsu
- Department of Chemistry Graduate School of Science, Kyoto University Sakyo-ku, Kyoto 606-8502, Japan.
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2
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Fotie J, Matherne CM, Wroblewski JE. Silicon switch: Carbon-silicon Bioisosteric replacement as a strategy to modulate the selectivity, physicochemical, and drug-like properties in anticancer pharmacophores. Chem Biol Drug Des 2023; 102:235-254. [PMID: 37029092 DOI: 10.1111/cbdd.14239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/19/2023] [Accepted: 03/21/2023] [Indexed: 04/09/2023]
Abstract
Bioisosterism is one of the leading strategies in medicinal chemistry for the design and modification of drugs, consisting in replacing an atom or a substituent with a different atom or a group with similar chemical properties and an inherent biocompatibility. The objective of such an exercise is to produce a diversity of molecules with similar behavior while enhancing the desire biological and pharmacological properties, without inducing significant changes to the chemical framework. In drug discovery and development, the optimization of the absorption, distribution, metabolism, elimination, and toxicity (ADMETox) profile is of paramount importance. Silicon appears to be the right choice as a carbon isostere because they possess very similar intrinsic properties. However, the replacement of a carbon by a silicon atom in pharmaceuticals has proven to result in improved efficacy and selectivity, while enhancing physicochemical properties and bioavailability. The current review discusses how silicon has been strategically introduced to modulate drug-like properties of anticancer agents, from a molecular design strategy, biological activity, computational modeling, and structure-activity relationships perspectives.
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Affiliation(s)
- Jean Fotie
- Department of Chemistry and Physics, Southeastern Louisiana University, Hammond, Louisiana, USA
| | - Caitlyn M Matherne
- Department of Chemistry and Physics, Southeastern Louisiana University, Hammond, Louisiana, USA
| | - Jordan E Wroblewski
- Department of Chemistry and Physics, Southeastern Louisiana University, Hammond, Louisiana, USA
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3
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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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4
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Aging Effects on Optic Nerve Neurodegeneration. Int J Mol Sci 2023; 24:ijms24032573. [PMID: 36768896 PMCID: PMC9917079 DOI: 10.3390/ijms24032573] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 02/03/2023] Open
Abstract
Common risk factors for many ocular pathologies involve non-pathologic, age-related damage to the optic nerve. Understanding the mechanisms of age-related changes can facilitate targeted treatments for ocular pathologies that arise at any point in life. In this review, we examine these age-related, neurodegenerative changes in the optic nerve, contextualize these changes from the anatomic to the molecular level, and appreciate their relationship with ocular pathophysiology. From simple structural and mechanical changes at the optic nerve head (ONH), to epigenetic and biochemical alterations of tissue and the environment, multiple age-dependent mechanisms drive extracellular matrix (ECM) remodeling, retinal ganglion cell (RGC) loss, and lowered regenerative ability of respective axons. In conjunction, aging decreases the ability of myelin to preserve maximal conductivity, even with "successfully" regenerated axons. Glial cells, however, regeneratively overcompensate and result in a microenvironment that promotes RGC axonal death. Better elucidating optic nerve neurodegeneration remains of interest, specifically investigating human ECM, RGCs, axons, oligodendrocytes, and astrocytes; clarifying the exact processes of aged ocular connective tissue alterations and their ultrastructural impacts; and developing novel technologies and pharmacotherapies that target known genetic, biochemical, matrisome, and neuroinflammatory markers. Management models should account for age-related changes when addressing glaucoma, diabetic retinopathy, and other blinding diseases.
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5
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Tinkov OV, Grigorev VY, Grigoreva LD, Osipov VN. HDAC1 PREDICTOR: a simple and transparent application for virtual screening of histone deacetylase 1 inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:915-931. [PMID: 36548122 DOI: 10.1080/1062936x.2022.2147996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
Histone deacetylases play an important role in regulating gene expression by modifying histones and changing chromatin conformation. HDAC dysregulation is involved in many diseases, such as cancer, autoimmune and neurodegenerative diseases. Histone deacetylase 1 (HDAC1) inhibitors represent an important class of drugs. Quantitative Structure-Activity Relationship (QSAR) classification models were developed using 2D RDKit molecular descriptors; ECPF4 (Extended Connectivity Fingerprint) circular fingerprints; and the Random Forest, Gradient Boosting, and Support Vector Machine methods. The developed models were integrated into the HDAC1 PREDICTOR application, which is freely available at the link https://ovttiras-hdac1-inhibitors-hdac1-predictor-app-z3mrbr.streamlitapp.com. The HDAC1 PREDICTOR web application allows one to reveal the compounds for which the predicted activity to inhibit HDAC1 is higher than that of the reference Vorinostat compound (IC50 = 11.08 nM). The algorithm implemented in HDAC1 PREDICTOR for determining the contributions of molecular fragments to the inhibitory activity can be used to find the molecule segments that increase or decrease the activity, enabling the researcher to conduct a rational molecular design of new highly active HDAC1 inhibitors. The developed QSAR models and the code for their construction in the Python programming language are freely available on the GitHub platform at https://github.com/ovttiras/HDAC1-inhibitors.
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Affiliation(s)
- O V Tinkov
- Department of Pharmacology and Pharmaceutical Chemistry, Medical Faculty, Shevchenko Transnistria State University, Tiraspol, Moldova
| | - V Y Grigorev
- Department of Computer-aided Molecular Design, Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences (IPAC RAS), Chernogolovka, Russia
| | - L D Grigoreva
- Department of Fundamental Physicochemical Engineering, Moscow State University, Moscow, Russia
| | - V N Osipov
- Department of Chemical Synthesis, Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, Russia
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6
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Ashok A, Pooranawattanakul S, Tai WL, Cho KS, Utheim TP, Cestari DM, Chen DF. Epigenetic Regulation of Optic Nerve Development, Protection, and Repair. Int J Mol Sci 2022; 23:ijms23168927. [PMID: 36012190 PMCID: PMC9408916 DOI: 10.3390/ijms23168927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/07/2022] [Accepted: 08/08/2022] [Indexed: 11/16/2022] Open
Abstract
Epigenetic factors are known to influence tissue development, functionality, and their response to pathophysiology. This review will focus on different types of epigenetic regulators and their associated molecular apparatus that affect the optic nerve. A comprehensive understanding of epigenetic regulation in optic nerve development and homeostasis will help us unravel novel molecular pathways and pave the way to design blueprints for effective therapeutics to address optic nerve protection, repair, and regeneration.
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Affiliation(s)
- Ajay Ashok
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Sarita Pooranawattanakul
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Wai Lydia Tai
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Kin-Sang Cho
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Tor P. Utheim
- Department of Medical Biochemistry, Oslo University Hospital, 0372 Oslo, Norway
- Department of Ophthalmology, Oslo University Hospital, 0372 Oslo, Norway
| | - Dean M. Cestari
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Dong Feng Chen
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
- Correspondence:
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7
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Geurs S, Clarisse D, Baele F, Franceus J, Desmet T, De Bosscher K, D'hooghe M. Identification of mercaptoacetamide-based HDAC6 inhibitors via a lean inhibitor strategy: screening, synthesis, and biological evaluation. Chem Commun (Camb) 2022; 58:6239-6242. [PMID: 35510683 DOI: 10.1039/d2cc01550a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Non-selective inhibition of different histone deacetylase enzymes by hydroxamic acid-based drugs causes severe side effects when used as a (long-term) cancer treatment. In this work, we searched for a potent zinc-binding group able to replace the contested hydroxamic acid by employing a lean inhibitor strategy. This instructed the synthesis of a set of HDAC6-selective inhibitors containing the more desirable mercaptoacetamide moiety. Biological evaluation of these new compounds showed an IC50 in the nanomolar range, dose-dependent HDAC6 inhibition in MM1.S cells and improved genotoxicity results, rendering these new inhibitors valuable hits for applications even beyond oncology.
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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, FSVMII, Zwijnaarde, Belgium
| | - Dorien Clarisse
- Translational Nuclear Receptor Research, VIB-UGent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, FSVMII, Zwijnaarde, Belgium.,Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, FSVMII, Zwijnaarde, Belgium
| | - Freya Baele
- SynBioC Research Group, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
| | - Jorick Franceus
- Center for Synthetic Biology (CSB), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Tom Desmet
- Center for Synthetic Biology (CSB), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Karolien De Bosscher
- Translational Nuclear Receptor Research, VIB-UGent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, FSVMII, Zwijnaarde, Belgium.,Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, FSVMII, Zwijnaarde, 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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8
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Oikawa T, Fujii S, Mori S, Masuno H, Kawachi E, Kagechika H. Structural development of silicon-containing retinoids: structure-activity relationship study of the hydrophobic pharmacophore of retinobenzoic acids using silyl functionalities. ChemMedChem 2022; 17:e202200176. [PMID: 35451569 DOI: 10.1002/cmdc.202200176] [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: 03/31/2022] [Revised: 04/18/2022] [Indexed: 11/09/2022]
Abstract
We designed and synthesized a series of retinobenzoic acids bearing various silyl functionalities in order to explore in detail the structure-activity relationship (SAR) at the hydrophobic moiety of retinoids. Among the synthesized compounds, 24c bearing a t -butyldimethylsilyl (TBS) group at the hydrophobic site exhibited potent retinoid activity comparable to that of the lead compound Am555S ( 4 ). Compound 24c exhibited transcription-promoting activity towards all three subtypes of retinoic acid receptor (RAR), but showed the highest activity towards RARγ, in contrast to the high RARα-selectivity of Am80 ( 3 ) and Am555S ( 4 ). The SARs presented here should be helpful in the development of subtype-selective retinoids, and in particular 24c might be a promising lead compound for new RARγ ligands.
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Affiliation(s)
- Tsuyoshi Oikawa
- Tokyo Medical and Dental University: Tokyo Ika Shika Daigaku, Institute of Biomaterials and Bioengineering, JAPAN
| | - Shinya Fujii
- Tokyo Medical and Dental University: Tokyo Ika Shika Daigaku, Institute of Biomaterials and Bioengineering, JAPAN
| | - Shuichi Mori
- Tokyo Medical and Dental University: Tokyo Ika Shika Daigaku, Institute of Biomaterials and Bioengineering, JAPAN
| | - Hiroyuki Masuno
- Tokyo Medical and Dental University: Tokyo Ika Shika Daigaku, Institute of Biomaterials and Bioengineering, JAPAN
| | - Emiko Kawachi
- Tokyo Medical and Dental University: Tokyo Ika Shika Daigaku, Institute of Biomaterials and Bioengineering, JAPAN
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9
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Ruzic D, Djoković N, Srdić-Rajić T, Echeverria C, Nikolic K, Santibanez JF. Targeting Histone Deacetylases: Opportunities for Cancer Treatment and Chemoprevention. Pharmaceutics 2022; 14:pharmaceutics14010209. [PMID: 35057104 PMCID: PMC8778744 DOI: 10.3390/pharmaceutics14010209] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/06/2022] [Accepted: 01/12/2022] [Indexed: 02/06/2023] Open
Abstract
The dysregulation of gene expression is a critical event involved in all steps of tumorigenesis. Aberrant histone and non-histone acetylation modifications of gene expression due to the abnormal activation of histone deacetylases (HDAC) have been reported in hematologic and solid types of cancer. In this sense, the cancer-associated epigenetic alterations are promising targets for anticancer therapy and chemoprevention. HDAC inhibitors (HDACi) induce histone hyperacetylation within target proteins, altering cell cycle and proliferation, cell differentiation, and the regulation of cell death programs. Over the last three decades, an increasing number of synthetic and naturally derived compounds, such as dietary-derived products, have been demonstrated to act as HDACi and have provided biological and molecular insights with regard to the role of HDAC in cancer. The first part of this review is focused on the biological roles of the Zinc-dependent HDAC family in malignant diseases. Accordingly, the small-molecules and natural products such as HDACi are described in terms of cancer therapy and chemoprevention. Furthermore, structural considerations are included to improve the HDACi selectivity and combinatory potential with other specific targeting agents in bifunctional inhibitors and proteolysis targeting chimeras. Additionally, clinical trials that combine HDACi with current therapies are discussed, which may open new avenues in terms of the feasibility of HDACi’s future clinical applications in precision cancer therapies.
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Affiliation(s)
- Dusan Ruzic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (D.R.); (N.D.); (K.N.)
| | - Nemanja Djoković
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (D.R.); (N.D.); (K.N.)
| | - Tatjana Srdić-Rajić
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia;
| | - Cesar Echeverria
- Facultad de Medicina, Universidad de Atacama, Copayapu 485, Copiapo 1531772, Chile;
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (D.R.); (N.D.); (K.N.)
| | - Juan F. Santibanez
- Group for Molecular Oncology, Institute for Medical Research, National Institute of the Republic of Serbia, University of Belgrade, Dr. Subotica 4, POB 102, 11129 Belgrade, Serbia
- Centro Integrativo de Biología y Química Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago 8370854, Chile
- Correspondence: ; Tel.: +381-11-2685-788; Fax: +381-11-2643-691
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10
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Singh A, Patel VK, Rajak H. Appraisal of pyrrole as connecting unit in hydroxamic acid based histone deacetylase inhibitors: Synthesis, anticancer evaluation and molecular docking studies. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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Frühauf A, Meyer-Almes FJ. Non-Hydroxamate Zinc-Binding Groups as Warheads for Histone Deacetylases. Molecules 2021; 26:5151. [PMID: 34500583 PMCID: PMC8434074 DOI: 10.3390/molecules26175151] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/22/2021] [Accepted: 08/24/2021] [Indexed: 12/11/2022] Open
Abstract
Histone deacetylases (HDACs) remove acetyl groups from acetylated lysine residues and have a large variety of substrates and interaction partners. Therefore, it is not surprising that HDACs are involved in many diseases. Most inhibitors of zinc-dependent HDACs (HDACis) including approved drugs contain a hydroxamate as a zinc-binding group (ZBG), which is by far the biggest contributor to affinity, while chemical variation of the residual molecule is exploited to create more or less selectivity against HDAC isozymes or other metalloproteins. Hydroxamates have a propensity for nonspecificity and have recently come under considerable suspicion because of potential mutagenicity. Therefore, there are significant concerns when applying hydroxamate-containing compounds as therapeutics in chronic diseases beyond oncology due to unwanted toxic side effects. In the last years, several alternative ZBGs have been developed, which can replace the critical hydroxamate group in HDACis, while preserving high potency. Moreover, these compounds can be developed into highly selective inhibitors. This review aims at providing an overview of the progress in the field of non-hydroxamic HDACis in the time period from 2015 to present. Formally, ZBGs are clustered according to their binding mode and structural similarity to provide qualitative assessments and predictions based on available structural information.
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Affiliation(s)
| | - Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany;
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12
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Melesina J, Simoben CV, Praetorius L, Bülbül EF, Robaa D, Sippl W. Strategies To Design Selective Histone Deacetylase Inhibitors. ChemMedChem 2021; 16:1336-1359. [PMID: 33428327 DOI: 10.1002/cmdc.202000934] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Indexed: 12/15/2022]
Abstract
This review classifies drug-design strategies successfully implemented in the development of histone deacetylase (HDAC) inhibitors, which have many applications including cancer treatment. Our focus is on especially demanded selective HDAC inhibitors and their structure-activity relationships in relation to corresponding protein structures. The main part of the paper is divided into six subsections each narrating how optimization of one of six structural features can influence inhibitor selectivity. It starts with the impact of the zinc binding group on selectivity, continues with the optimization of the linker placed in the substrate binding tunnel as well as the adjustment of the cap group interacting with the surface of the protein, and ends with the addition of groups targeting class-specific sub-pockets: the side-pocket-, lower-pocket- and foot-pocket-targeting groups. The review is rounded off with a conclusion and an outlook on the future of HDAC inhibitor design.
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Affiliation(s)
- Jelena Melesina
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
| | - Conrad V Simoben
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
| | - Lucas Praetorius
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
| | - Emre F Bülbül
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
| | - Dina Robaa
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
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13
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Peptidyl Fluoromethyl Ketones and Their Applications in Medicinal Chemistry. Molecules 2020; 25:molecules25174031. [PMID: 32899354 PMCID: PMC7504820 DOI: 10.3390/molecules25174031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 12/29/2022] Open
Abstract
Peptidyl fluoromethyl ketones occupy a pivotal role in the current scenario of synthetic chemistry, thanks to their numerous applications as inhibitors of hydrolytic enzymes. The insertion of one or more fluorine atoms adjacent to a C-terminal ketone moiety greatly modifies the physicochemical properties of the overall substrate, especially by increasing the reactivity of this functionalized carbonyl group toward nucleophiles. The main application of these peptidyl α-fluorinated ketones in medicinal chemistry relies in their ability to strongly and selectively inhibit serine and cysteine proteases. These compounds can be used as probes to study the proteolytic activity of the aforementioned proteases and to elucidate their role in the insurgence and progress on several diseases. Likewise, if the fluorinated methyl ketone moiety is suitably connected to a peptidic backbone, it may confer to the resulting structure an excellent substrate peculiarity and the possibility of being recognized by a specific subclass of human or pathogenic proteases. Therefore, peptidyl fluoromethyl ketones are also currently highly exploited for the target-based design of compounds for the treatment of topical diseases such as various types of cancer and viral infections.
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14
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Kumari S, Carmona AV, Tiwari AK, Trippier PC. Amide Bond Bioisosteres: Strategies, Synthesis, and Successes. J Med Chem 2020; 63:12290-12358. [PMID: 32686940 DOI: 10.1021/acs.jmedchem.0c00530] [Citation(s) in RCA: 219] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The amide functional group plays a key role in the composition of biomolecules, including many clinically approved drugs. Bioisosterism is widely employed in the rational modification of lead compounds, being used to increase potency, enhance selectivity, improve pharmacokinetic properties, eliminate toxicity, and acquire novel chemical space to secure intellectual property. The introduction of a bioisostere leads to structural changes in molecular size, shape, electronic distribution, polarity, pKa, dipole or polarizability, which can be either favorable or detrimental to biological activity. This approach has opened up new avenues in drug design and development resulting in more efficient drug candidates introduced onto the market as well as in the clinical pipeline. Herein, we review the strategic decisions in selecting an amide bioisostere (the why), synthetic routes to each (the how), and success stories of each bioisostere (the implementation) to provide a comprehensive overview of this important toolbox for medicinal chemists.
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Affiliation(s)
- Shikha Kumari
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Angelica V Carmona
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Amit K Tiwari
- Department of Pharmacology and Experimental Therapeutics, College of Pharmacy and Pharmaceutical Sciences, The University of Toledo, Toledo, Ohio 43614, United States
| | - Paul C Trippier
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States.,Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States.,UNMC Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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15
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Cappellacci L, Perinelli DR, Maggi F, Grifantini M, Petrelli R. Recent Progress in Histone Deacetylase Inhibitors as Anticancer Agents. Curr Med Chem 2020; 27:2449-2493. [PMID: 30332940 DOI: 10.2174/0929867325666181016163110] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/29/2018] [Accepted: 10/09/2018] [Indexed: 12/13/2022]
Abstract
Histone Deacetylase (HDAC) inhibitors are a relatively new class of anti-cancer agents that play important roles in epigenetic or non-epigenetic regulation, inducing death, apoptosis, and cell cycle arrest in cancer cells. Recently, their use has been clinically validated in cancer patients resulting in the approval by the FDA of four HDAC inhibitors, vorinostat, romidepsin, belinostat and panobinostat, used for the treatment of cutaneous/peripheral T-cell lymphoma and multiple myeloma. Many more HDAC inhibitors are at different stages of clinical development for the treatment of hematological malignancies as well as solid tumors. Also, clinical trials of several HDAC inhibitors for use as anti-cancer drugs (alone or in combination with other anti-cancer therapeutics) are ongoing. In the intensifying efforts to discover new, hopefully, more therapeutically efficacious HDAC inhibitors, molecular modelingbased rational drug design has played an important role. In this review, we summarize four major structural classes of HDAC inhibitors (hydroxamic acid derivatives, aminobenzamide, cyclic peptide and short-chain fatty acids) that are in clinical trials and different computer modeling tools available for their structural modifications as a guide to discover additional HDAC inhibitors with greater therapeutic utility.
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Affiliation(s)
- Loredana Cappellacci
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
| | - Diego R Perinelli
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
| | - Filippo Maggi
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
| | - Mario Grifantini
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
| | - Riccardo Petrelli
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
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16
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Konarzewska Z, Śliwińska-Wilczewska S, Felpeto AB, Vasconcelos V, Latała A. Assessment of the Allelochemical Activity and Biochemical Profile of Different Phenotypes of Picocyanobacteria from the Genus Synechococcus. Mar Drugs 2020; 18:md18040179. [PMID: 32230878 PMCID: PMC7230558 DOI: 10.3390/md18040179] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/20/2020] [Accepted: 03/25/2020] [Indexed: 11/17/2022] Open
Abstract
Organisms belonging to Synechococcus sp. genera are observed in all freshwater, brackish, and marine waters of the world. They play a relevant role in these ecosystems, since they are one of the main primary producers, especially in open ocean. Eventually, they form mass blooms in coastal areas, which are potentially dangerous for the functioning of marine ecosystems. Allelopathy could be an important factor promoting the proliferation of these organisms. According to the authors’ best knowledge, there is no information on the allelopathic activity and allelopathic compounds exhibited by different Synechococcus sp. phenotypes. Therefore, the research conducted here aimed to study the bioactivity of compounds produced by three phenotypes of Synechococcus sp. by studying their influence on the growth, chlorophyll fluorescence, and photosynthetic pigments of eighteen cyanobacteria and microalgae species. We demonstrated that three different Synechococcus sp. phenotypes, including a phycocyanin (PC)-rich strain (Type 1; green strain) and phycoerythrin (PE)-rich strains containing phycoerythrobilin (PEB) and phycocyanobilin (PCB) (Type 2; red strain and Type 3a; brown strain), had a significant allelopathic effect on the selected species of cyanobacteria, diatoms, and green algae. For all green algae, a decrease in cell abundance under the influence of phenotypes of donor cyanobacteria was shown, whereas, among some target cyanobacteria and diatom species, the cell-free filtrate was observed to have a stimulatory effect. Our estimates of the stress on photosystem II (Fv/Fm) showed a similar pattern, although for some diatoms, there was an effect of stress on photosynthesis, while a stimulatory effect on growth was also displayed. The pigment content was affected by allelopathy in most cases, particularly for chlorophyll a, whilst it was a bit less significant for carotenoids. Our results showed that Synechococcus sp. Type 3a had the strongest effect on target species, while Synechococcus sp. Type 1 had the weakest allelopathic effect. Furthermore, GC-MS analysis produced different biochemical profiles for the Synechococcus strains. For every phenotype, the most abundant compound was different, with oxime-, methoxy-phenyl- being the most abundant substance for Synechococcus Type 1, eicosane for Synechococcus Type 2, and silanediol for Synechococcus Type 3a.
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Affiliation(s)
- Zofia Konarzewska
- Division of Marine Ecosystems Functioning, Institute of Oceanography, University of Gdańsk, Av. Piłsudskiego 46, 81-378 Gdynia, Poland; (S.Ś.-W.); (A.L.)
- Correspondence:
| | - Sylwia Śliwińska-Wilczewska
- Division of Marine Ecosystems Functioning, Institute of Oceanography, University of Gdańsk, Av. Piłsudskiego 46, 81-378 Gdynia, Poland; (S.Ś.-W.); (A.L.)
| | - Aldo Barreiro Felpeto
- Interdisciplinary Center of Marine and Environmental Research–CIMAR/CIIMAR, University of Porto, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; (A.B.F.); (V.V.)
| | - Vitor Vasconcelos
- Interdisciplinary Center of Marine and Environmental Research–CIMAR/CIIMAR, University of Porto, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; (A.B.F.); (V.V.)
- Department of Biology, Faculty of Sciences, Porto University, Rua do Campo Alegre, 4069-007 Porto, Portugal
| | - Adam Latała
- Division of Marine Ecosystems Functioning, Institute of Oceanography, University of Gdańsk, Av. Piłsudskiego 46, 81-378 Gdynia, Poland; (S.Ś.-W.); (A.L.)
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17
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Lucas EL, Hewitt KA, Chen PP, Castro AJ, Hong X, Jarvo ER. Engaging Sulfonamides: Intramolecular Cross-Electrophile Coupling Reaction of Sulfonamides with Alkyl Chlorides. J Org Chem 2020; 85:1775-1793. [PMID: 31840511 DOI: 10.1021/acs.joc.9b02603] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The application of amine derivatives as coupling partners is rare due to the inherent strength of the C-N bond. Herein, we report the first cross-electrophile coupling reaction of unstrained benzylic sulfonamides. Nickel-catalyzed intramolecular cross-electrophile coupling reactions of acyclic and cyclic benzylic sulfonamides with pendant alkyl chlorides generate cyclopropane products. Mechanistic experiments and DFT calculations are consistent with initiation of the reaction by magnesium iodide accelerated oxidative addition of the benzylic sulfonamide. This work establishes neutral and unstrained amine derivatives as XEC partners, furnishes structural rearrangement of benzylic sulfonamides, and provides valuable information regarding catalyst design for the development of new cross-electrophile coupling reactions of carbon-heteroatom bonds.
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Affiliation(s)
- Erika L Lucas
- Department of Chemistry , University of California , Irvine , California 92697-2025 , United States
| | - Kirsten A Hewitt
- Department of Chemistry , University of California , Irvine , California 92697-2025 , United States
| | - Pan-Pan Chen
- Department of Chemistry , Zhejiang University , Hangzhou 310027 , China
| | - Anthony J Castro
- Department of Chemistry , University of California , Irvine , California 92697-2025 , United States
| | - Xin Hong
- Department of Chemistry , Zhejiang University , Hangzhou 310027 , China
| | - Elizabeth R Jarvo
- Department of Chemistry , University of California , Irvine , California 92697-2025 , United States
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18
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Schweipert M, Jänsch N, Sugiarto WO, Meyer-Almes FJ. Kinetically selective and potent inhibitors of HDAC8. Biol Chem 2020; 400:733-743. [PMID: 30521473 DOI: 10.1515/hsz-2018-0363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/25/2018] [Indexed: 11/15/2022]
Abstract
Histone deacetylase 8 (HDAC8) is an established and validated target for T-cell lymphoma and childhood neuroblastoma. The active site binding pocket of HDAC8 is highly conserved among all zinc-containing representatives of the histone deacetylase (HDAC) family. This explains that most HDACs are unselectively recognized by similar inhibitors featuring a zinc binding group (ZBG), a hydrophobic linker and a head group. In the light of this difficulty, the creation of isoenzyme-selectivity is one of the major challenges in the development of HDAC inhibitors. In a series of trifluoromethylketone inhibitors of HDAC8 compound 10 shows a distinct binding mechanism and a dramatically increased residence time (RT) providing kinetic selectivity against HDAC4. Combining the binding kinetics results with computational docking and binding site flexibility analysis suggests that 10 occupies the conserved catalytic site as well as an adjacent transient sub-pocket of HDAC8.
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Affiliation(s)
- Markus Schweipert
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Stephanstr. 7, 64295 Darmstadt, Germany
| | - Niklas Jänsch
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Stephanstr. 7, 64295 Darmstadt, Germany
| | - Wisely Oki Sugiarto
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Stephanstr. 7, 64295 Darmstadt, Germany
| | - Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Stephanstr. 7, 64295 Darmstadt, Germany
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19
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Galster M, Löppenberg M, Galla F, Börgel F, Agoglitta O, Kirchmair J, Holl R. Phenylethylene glycol-derived LpxC inhibitors with diverse Zn2+-binding groups. Tetrahedron 2019. [DOI: 10.1016/j.tet.2018.12.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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20
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Yadav R, Mishra P, Yadav D. Histone Deacetylase Inhibitors: A Prospect in Drug Discovery. Turk J Pharm Sci 2018; 16:101-114. [PMID: 32454703 DOI: 10.4274/tjps.75047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 01/25/2018] [Indexed: 12/15/2022]
Abstract
Cancer is a provocative issue across the globe and treatment of uncontrolled cell growth follows a deep investigation in the field of drug discovery. Therefore, there is a crucial requirement for discovering an ingenious medicinally active agent that can amend idle drug targets. Increasing pragmatic evidence implies that histone deacetylases (HDACs) are trapped during cancer progression, which increases deacetylation and triggers changes in malignancy. They provide a ground-breaking scaffold and an attainable key for investigating chemical entity pertinent to HDAC biology as a therapeutic target in the drug discovery context. Due to gene expression, an impending requirement to prudently transfer cytotoxicity to cancerous cells, HDAC inhibitors may be developed as anticancer agents. The present review focuses on the basics of HDAC enzymes, their inhibitors, and therapeutic outcomes.
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Affiliation(s)
- Rakesh Yadav
- Banasthali University, Faculty of Pharmacy, Department of Pharmacy, Banasthali, India
| | - Pooja Mishra
- Banasthali University, Faculty of Pharmacy, Department of Pharmacy, Banasthali, India
| | - Divya Yadav
- Banasthali University, Faculty of Pharmacy, Department of Pharmacy, Banasthali, India
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21
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Beus M, Rajić Z, Maysinger D, Mlinarić Z, Antunović M, Marijanović I, Fontinha D, Prudêncio M, Held J, Olgen S, Zorc B. SAHAquines, Novel Hybrids Based on SAHA and Primaquine Motifs, as Potential Cytostatic and Antiplasmodial Agents. ChemistryOpen 2018; 7:624-638. [PMID: 30151334 PMCID: PMC6104433 DOI: 10.1002/open.201800117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Indexed: 12/19/2022] Open
Abstract
We report the synthesis of SAHAquines and related primaquine (PQ) derivatives. SAHAquines are novel hybrid compounds that combine moieties of suberoylanilide hydroxamic acid (SAHA), an anticancer agent with weak antiplasmodial activity, and PQ, an antimalarial drug with low antiproliferative activity. The preparation of SAHAquines is simple, cheap, and high yielding. It includes the following steps: coupling reaction between primaquine and a dicarboxylic acid monoester, hydrolysis, a new coupling reaction with O-protected hydroxylamine, and deprotection. SAHAquines 5 a-d showed significant reduction in cell viability. Among the three human cancer cell lines (U2OS, HepG2, and MCF-7), the most responsive were the MCF-7 cells. The antibodies against acetylated histone H3K9/H3K14 in MCF-7 cells revealed a significant enhancement following treatment with N-hydroxy-N'-{4-[(6-methoxyquinolin-8-yl)amino]pentyl}pentanediamide (5 b). Ethyl (2E)-3-({4-[(6-methoxyquinolin-8-yl)amino]pentyl}carbamoyl)prop-2-enoate (2 b) and SAHAquines were the most active compounds against both the hepatic and erythrocytic stages of Plasmodium parasites, some of them at sub-micromolar concentrations. The results of our research suggest that SAHAquines are promising leads for new anticancer and antimalarial agents.
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Affiliation(s)
- Maja Beus
- Faculty of Pharmacy and BiochemistryUniversity of ZagrebA. Kovačića 110 000ZagrebCroatia
| | - Zrinka Rajić
- Faculty of Pharmacy and BiochemistryUniversity of ZagrebA. Kovačića 110 000ZagrebCroatia
| | - Dusica Maysinger
- Department of Pharmacology and TherapeuticsMcGill University23655 Promenade Sir-William-Osler, McIntyre Medical Sciences BuildingMontrealQuebecH3G 1Y6Canada
| | - Zvonimir Mlinarić
- Faculty of Pharmacy and BiochemistryUniversity of ZagrebA. Kovačića 110 000ZagrebCroatia
| | - Maja Antunović
- Faculty of ScienceUniversity of ZagrebHorvatovac 102A10 000ZagrebCroatia
| | - Inga Marijanović
- Faculty of ScienceUniversity of ZagrebHorvatovac 102A10 000ZagrebCroatia
| | - Diana Fontinha
- Instituto de Medicina Molecular, Faculdade de MedicinaUniversidade de LisboaAv. Prof. Egas Moniz1649-028LisboaPortugal
| | - Miguel Prudêncio
- Instituto de Medicina Molecular, Faculdade de MedicinaUniversidade de LisboaAv. Prof. Egas Moniz1649-028LisboaPortugal
| | - Jana Held
- Institute of Tropical MedicineUniversity of TübingenWilhelmstraße 2772074TübingenGermany
| | - Sureyya Olgen
- Faculty of PharmacyBiruni University10th street No: 4534010 TopkapiIstanbulTurkey
| | - Branka Zorc
- Faculty of Pharmacy and BiochemistryUniversity of ZagrebA. Kovačića 110 000ZagrebCroatia
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22
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Prakash A, Garcia-Moreno JF, Brown JAL, Bourke E. Clinically Applicable Inhibitors Impacting Genome Stability. Molecules 2018; 23:E1166. [PMID: 29757235 PMCID: PMC6100577 DOI: 10.3390/molecules23051166] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/27/2018] [Accepted: 05/01/2018] [Indexed: 12/14/2022] Open
Abstract
Advances in technology have facilitated the molecular profiling (genomic and transcriptomic) of tumours, and has led to improved stratification of patients and the individualisation of treatment regimes. To fully realize the potential of truly personalised treatment options, we need targeted therapies that precisely disrupt the compensatory pathways identified by profiling which allow tumours to survive or gain resistance to treatments. Here, we discuss recent advances in novel therapies that impact the genome (chromosomes and chromatin), pathways targeted and the stage of the pathways targeted. The current state of research will be discussed, with a focus on compounds that have advanced into trials (clinical and pre-clinical). We will discuss inhibitors of specific DNA damage responses and other genome stability pathways, including those in development, which are likely to synergistically combine with current therapeutic options. Tumour profiling data, combined with the knowledge of new treatments that affect the regulation of essential tumour signalling pathways, is revealing fundamental insights into cancer progression and resistance mechanisms. This is the forefront of the next evolution of advanced oncology medicine that will ultimately lead to improved survival and may, one day, result in many cancers becoming chronic conditions, rather than fatal diseases.
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Affiliation(s)
- Anu Prakash
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway, H91 YR71 Galway, Ireland.
| | - Juan F Garcia-Moreno
- Discipline of Surgery, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway, H91 YR71 Galway, Ireland.
| | - James A L Brown
- Discipline of Surgery, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway, H91 YR71 Galway, Ireland.
| | - Emer Bourke
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway, H91 YR71 Galway, Ireland.
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23
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Histone Deacetylase 11 Is an ε-N-Myristoyllysine Hydrolase. Cell Chem Biol 2018; 25:849-856.e8. [PMID: 29731425 DOI: 10.1016/j.chembiol.2018.04.007] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/26/2018] [Accepted: 04/06/2018] [Indexed: 10/17/2022]
Abstract
Histone deacetylase (HDAC) enzymes regulate diverse biological function, including gene expression, rendering them potential targets for intervention in a number of diseases, with a handful of compounds approved for treatment of certain hematologic cancers. Among the human zinc-dependent HDACs, the most recently discovered member, HDAC11, is the only member assigned to subclass IV. It is the smallest protein and has the least well understood biological function. Here, we show that HDAC11 cleaves long-chain acyl modifications on lysine side chains with remarkable efficiency. We further show that several common types of HDAC inhibitors, including the approved drugs romidepsin and vorinostat, do not inhibit this enzymatic activity. Macrocyclic hydroxamic acid-containing peptides, on the other hand, potently inhibit HDAC11 demyristoylation activity. These findings should be taken carefully into consideration in future investigations of the biological function of HDAC11 and will serve as a foundation for the development of selective chemical probes targeting HDAC11.
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24
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Funabiki K, Hayakawa A, Inuzuka T. Convenient, functional group-tolerant, transition metal-free synthesis of aryl and heteroaryl trifluoromethyl ketones with the use of methyl trifluoroacetate. Org Biomol Chem 2018; 16:913-918. [DOI: 10.1039/c7ob02862h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new convenient, functional group-tolerant, transition metal-free route to aryl trifluoromethyl ketones under mild conditions is described.
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Affiliation(s)
- Kazumasa Funabiki
- Department of Chemistry and Biomolecular Science
- Gifu University
- Gifu 501-1193
- Japan
| | - Ayaka Hayakawa
- Department of Chemistry and Biomolecular Science
- Gifu University
- Gifu 501-1193
- Japan
| | - Toshiyasu Inuzuka
- Division of Instrumental Analysis
- Life Science Research Center
- Gifu University
- Gifu 501-1193
- Japan
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25
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Ramesh R, Reddy DS. Quest for Novel Chemical Entities through Incorporation of Silicon in Drug Scaffolds. J Med Chem 2017; 61:3779-3798. [DOI: 10.1021/acs.jmedchem.7b00718] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Remya Ramesh
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110 025, India
| | - D. Srinivasa Reddy
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110 025, India
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26
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Kitir B, Maolanon AR, Ohm RG, Colaço AR, Fristrup P, Madsen AS, Olsen CA. Chemical Editing of Macrocyclic Natural Products and Kinetic Profiling Reveal Slow, Tight-Binding Histone Deacetylase Inhibitors with Picomolar Affinities. Biochemistry 2017; 56:5134-5146. [DOI: 10.1021/acs.biochem.7b00725] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Betül Kitir
- Center
for Biopharmaceuticals and Department for Drug Design and Pharmacology,
Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Alex R. Maolanon
- Center
for Biopharmaceuticals and Department for Drug Design and Pharmacology,
Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Ragnhild G. Ohm
- Center
for Biopharmaceuticals and Department for Drug Design and Pharmacology,
Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Ana R. Colaço
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
| | - Peter Fristrup
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
| | - Andreas S. Madsen
- Center
for Biopharmaceuticals and Department for Drug Design and Pharmacology,
Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Christian A. Olsen
- Center
for Biopharmaceuticals and Department for Drug Design and Pharmacology,
Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
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27
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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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28
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Shyamsunder A, Beichel W, Klose P, Pang Q, Scherer H, Hoffmann A, Murphy GK, Krossing I, Nazar LF. Inhibiting Polysulfide Shuttle in Lithium-Sulfur Batteries through Low-Ion-Pairing Salts and a Triflamide Solvent. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701026] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Abhinandan Shyamsunder
- Department of Chemistry and Waterloo Institute of Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
| | - Witali Beichel
- Freiburger Materialforschungszentrum (FMF); Albert-Ludwigs-Universität Freiburg; Stefan-Meier-Strasse 21 79104 Freiburg im Breisgau Germany
| | - Petra Klose
- Freiburger Materialforschungszentrum (FMF); Albert-Ludwigs-Universität Freiburg; Stefan-Meier-Strasse 21 79104 Freiburg im Breisgau Germany
| | - Quan Pang
- Department of Chemistry and Waterloo Institute of Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
| | - Harald Scherer
- Institut für Anorganische und Analytische Chemie; Albert-Ludwigs-Universität Freiburg; Albertstrasse 21 79104 Freiburg im Breisgau Germany
| | - Anke Hoffmann
- Institut für Anorganische und Analytische Chemie; Albert-Ludwigs-Universität Freiburg; Albertstrasse 21 79104 Freiburg im Breisgau Germany
| | - Graham K. Murphy
- Department of Chemistry and Waterloo Institute of Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
| | - Ingo Krossing
- Freiburger Materialforschungszentrum (FMF); Albert-Ludwigs-Universität Freiburg; Stefan-Meier-Strasse 21 79104 Freiburg im Breisgau Germany
- Institut für Anorganische und Analytische Chemie; Albert-Ludwigs-Universität Freiburg; Albertstrasse 21 79104 Freiburg im Breisgau Germany
| | - Linda F. Nazar
- Department of Chemistry and Waterloo Institute of Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
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29
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Shyamsunder A, Beichel W, Klose P, Pang Q, Scherer H, Hoffmann A, Murphy GK, Krossing I, Nazar LF. Inhibiting Polysulfide Shuttle in Lithium-Sulfur Batteries through Low-Ion-Pairing Salts and a Triflamide Solvent. Angew Chem Int Ed Engl 2017; 56:6192-6197. [DOI: 10.1002/anie.201701026] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 03/12/2017] [Indexed: 01/24/2023]
Affiliation(s)
- Abhinandan Shyamsunder
- Department of Chemistry and Waterloo Institute of Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
| | - Witali Beichel
- Freiburger Materialforschungszentrum (FMF); Albert-Ludwigs-Universität Freiburg; Stefan-Meier-Strasse 21 79104 Freiburg im Breisgau Germany
| | - Petra Klose
- Freiburger Materialforschungszentrum (FMF); Albert-Ludwigs-Universität Freiburg; Stefan-Meier-Strasse 21 79104 Freiburg im Breisgau Germany
| | - Quan Pang
- Department of Chemistry and Waterloo Institute of Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
| | - Harald Scherer
- Institut für Anorganische und Analytische Chemie; Albert-Ludwigs-Universität Freiburg; Albertstrasse 21 79104 Freiburg im Breisgau Germany
| | - Anke Hoffmann
- Institut für Anorganische und Analytische Chemie; Albert-Ludwigs-Universität Freiburg; Albertstrasse 21 79104 Freiburg im Breisgau Germany
| | - Graham K. Murphy
- Department of Chemistry and Waterloo Institute of Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
| | - Ingo Krossing
- Freiburger Materialforschungszentrum (FMF); Albert-Ludwigs-Universität Freiburg; Stefan-Meier-Strasse 21 79104 Freiburg im Breisgau Germany
- Institut für Anorganische und Analytische Chemie; Albert-Ludwigs-Universität Freiburg; Albertstrasse 21 79104 Freiburg im Breisgau Germany
| | - Linda F. Nazar
- Department of Chemistry and Waterloo Institute of Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
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Abstract
Application of silyl functionalities is one of the most promising strategies among various ‘elements chemistry’ approaches for the development of novel and distinctive drug candidates. Replacement of one or more carbon atoms of various biologically active compounds with silicon (so-called sila-substitution) has been intensively studied for decades, and is often effective for alteration of activity profile and improvement of metabolic profile. In addition to simple C/Si exchange, several novel approaches for utilizing silicon in medicinal chemistry have been suggested in recent years, focusing on the intrinsic differences between silicon and carbon. Sila-substitution offers great potential for enlarging the chemical space of medicinal chemistry, and provides many options for structural development of drug candidates.
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Meyners C, Mertens M, Wessig P, Meyer-Almes FJ. A Fluorescence-Lifetime-Based Binding Assay for Class IIa Histone Deacetylases. Chemistry 2017; 23:3107-3116. [DOI: 10.1002/chem.201605140] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Christian Meyners
- Fachbereich Chemie- und Biotechnologie; Hochschule Darmstadt; Haardtring 100 64295 Darmstadt Germany
| | - Monique Mertens
- Institut für Chemie; Universität Potsdam; Karl-Liebknecht-Str. 24-25 14476 Potsdam Germany
| | - Pablo Wessig
- Institut für Chemie; Universität Potsdam; Karl-Liebknecht-Str. 24-25 14476 Potsdam Germany
| | - Franz-Josef Meyer-Almes
- Fachbereich Chemie- und Biotechnologie; Hochschule Darmstadt; Haardtring 100 64295 Darmstadt Germany
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32
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Weekley CM, He C. Developing drugs targeting transition metal homeostasis. Curr Opin Chem Biol 2016; 37:26-32. [PMID: 28040658 DOI: 10.1016/j.cbpa.2016.12.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/23/2016] [Accepted: 12/08/2016] [Indexed: 01/06/2023]
Abstract
Metal dyshomeostasis is involved in the pathogenesis and progression of diseases including cancer and neurodegenerative diseases. Metal chelators and ionophores are well known modulators of transition metal homeostasis, and a number of these molecules are in clinical trials. Metal-binding compounds are not the only drugs capable of targeting transition metal homeostasis. This review presents recent highlights in the development of chelators and ionophores for the treatment of cancer and neurodegenerative disease. Moreover, we discuss the development of small molecules that alter copper and iron homeostasis by inhibiting metal transport proteins. Finally, we consider the emergence of metal regulatory factor 1 as a drug target in diseases where it mediates zinc-induced signalling cascades leading to pathogenesis.
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Affiliation(s)
- Claire M Weekley
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA.
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33
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Al-Balas QA, Hassan MA, Al-Shar'i NA, Mhaidat NM, Almaaytah AM, Al-Mahasneh FM, Isawi IH. Novel glyoxalase-I inhibitors possessing a "zinc-binding feature" as potential anticancer agents. Drug Des Devel Ther 2016; 10:2623-9. [PMID: 27574401 PMCID: PMC4993257 DOI: 10.2147/dddt.s110997] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background The glyoxalase system including two thiol-dependent enzymes, glyoxalase I (Glo-I) and glyoxalase II, plays an important role in a ubiquitous metabolic pathway involved in cellular detoxification of cytotoxic 2-oxoaldehydes. Tumor cells have high glycolytic activity, leading to increased cellular levels of these toxic metabolites. The increased activity of the detoxification system in cancerous cells makes this pathway a viable target for developing novel anticancer agents. In this study, we examined the potential utility of non-glutathione-based inhibitors of the Glo-I enzyme as novel anticancer drugs. Methods Computer-aided drug design techniques, such as customized pharmacophoric features, virtual screening, and flexible docking, were used to achieve the project goals. Retrieved hits were extensively filtered and subsequently docked into the active site of the enzyme. The biological activities of retrieved hits were assessed using an in vitro assay against Glo-I. Results Since Glo-I is a zinc metalloenzyme, a customized Zn-binding pharmacophoric feature was used to search for selective inhibitors via virtual screening of a small-molecule database. Seven hits were selected, purchased, and biologically evaluated. Three of the seven hits inhibited Glo-I activity, the most effective of which exerted 76.4% inhibition at a concentration of 25 µM. Conclusion We successfully identified a potential Glo-I inhibitor that can serve as a lead compound for further optimization. Moreover, our in silico and experimental results were highly correlated. Hence, the docking protocol adopted in this study may be efficiently employed in future optimization steps.
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Affiliation(s)
| | | | | | | | - Ammar M Almaaytah
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
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34
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Tian Y, Jin J, Wang C, Lv W, Li X, Che X, Gong Y, Li Y, Li Q, Hou J, Wang PG, Shen J. A sub-milligram-synthesis protocol for in vitro screening of HDAC11 inhibitors. Bioorg Med Chem Lett 2016; 26:2434-2437. [PMID: 27055940 DOI: 10.1016/j.bmcl.2016.03.116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/25/2016] [Accepted: 03/31/2016] [Indexed: 02/05/2023]
Abstract
This work demonstrated the high efficiency of a sub-milligram-synthesis based medicinal chemistry method. Totally 72 compounds, consisting a tri-substituted pyrrolidine core, were prepared. Around 0.1mg of each compound was solid-phase synthesized. Based on the additive property of UV absorptions of unconjugated chromophores of a molecule, these compounds were quantified by UV measurement. A hit, whose IC50 value was 1.2μM in HDAC11 inhibition assays, highlights the applicability of the approach reported here in future optimization works.
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Affiliation(s)
- Yinping Tian
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, People's Republic of China
| | - Jin Jin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, People's Republic of China
| | - Congying Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, People's Republic of China
| | - Wenhui Lv
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, People's Republic of China
| | - Xuewei Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, People's Republic of China
| | - Xiaona Che
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, People's Republic of China
| | - Yanchao Gong
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, People's Republic of China
| | - Yanjun Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, People's Republic of China
| | - Quanli Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, People's Republic of China
| | - Jingli Hou
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, People's Republic of China
| | - Peng G Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, People's Republic of China.
| | - Jie Shen
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, People's Republic of China.
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Gong CJ, Gao AH, Zhang YM, Su MB, Chen F, Sheng L, Zhou YB, Li JY, Li J, Nan FJ. Design, synthesis and biological evaluation of bisthiazole-based trifluoromethyl ketone derivatives as potent HDAC inhibitors with improved cellular efficacy. Eur J Med Chem 2016; 112:81-90. [PMID: 26890114 DOI: 10.1016/j.ejmech.2016.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 01/04/2016] [Accepted: 02/02/2016] [Indexed: 01/09/2023]
Abstract
Histone deacetylases (HDACs) are a class of epigenetic modulators with complex functions in histone post-translational modifications and are well known targets for antineoplastic drugs. We have previously developed a series of bisthiazole-based hydroxamic acids as novel potent HDAC inhibitors. In the present work, a new series of bisthiazole-based compounds with different zinc binding groups (ZBGs) have been designed and synthesized. Among them is compound 7, containing a trifluoromethyl ketone as the ZBG, which displays potent inhibitory activity towards human HDACs and improved antiproliferative activity in several cancer cell lines.
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Affiliation(s)
- Chao-Jun Gong
- Chinese National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guoshoujing Road, Zhangjiang Hi-Tech Park, Shanghai, 201203, PR China
| | - An-Hui Gao
- Chinese National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guoshoujing Road, Zhangjiang Hi-Tech Park, Shanghai, 201203, PR China
| | - Yang-Ming Zhang
- Chinese National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guoshoujing Road, Zhangjiang Hi-Tech Park, Shanghai, 201203, PR China
| | - Ming-Bo Su
- Chinese National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guoshoujing Road, Zhangjiang Hi-Tech Park, Shanghai, 201203, PR China
| | - Fei Chen
- Chinese National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guoshoujing Road, Zhangjiang Hi-Tech Park, Shanghai, 201203, PR China
| | - Li Sheng
- Chinese National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guoshoujing Road, Zhangjiang Hi-Tech Park, Shanghai, 201203, PR China
| | - Yu-Bo Zhou
- Chinese National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guoshoujing Road, Zhangjiang Hi-Tech Park, Shanghai, 201203, PR China
| | - Jing-Ya Li
- Chinese National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guoshoujing Road, Zhangjiang Hi-Tech Park, Shanghai, 201203, PR China
| | - Jia Li
- Chinese National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guoshoujing Road, Zhangjiang Hi-Tech Park, Shanghai, 201203, PR China.
| | - Fa-Jun Nan
- Chinese National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guoshoujing Road, Zhangjiang Hi-Tech Park, Shanghai, 201203, PR China.
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Reddy DN, Ballante F, Chuang T, Pirolli A, Marrocco B, Marshall GR. Design and Synthesis of Simplified Largazole Analogues as Isoform-Selective Human Lysine Deacetylase Inhibitors. J Med Chem 2016; 59:1613-33. [PMID: 26681404 DOI: 10.1021/acs.jmedchem.5b01632] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Selective inhibition of KDAC isoforms while maintaining potency remains a challenge. Using the largazole macrocyclic depsipeptide structure as a starting point for developing new KDACIs with increased selectivity, a combination of four different simplified largazole analogue (SLA) scaffolds with diverse zinc-binding groups (for a total of 60 compounds) were designed, synthesized, and evaluated against class I KDACs 1, 3, and 8, and class II KDAC6. Experimental evidence as well as molecular docking poses converged to establish the cyclic tetrapeptides (CTPs) as the primary determinant of both potency and selectivity by influencing the correct alignment of the zinc-binding group in the KDAC active site, providing a further basis for developing new KDACIs of higher isoform selectivity and potency.
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Affiliation(s)
- Damodara N Reddy
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , 700 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , 700 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Timothy Chuang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , 700 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Adele Pirolli
- Rome Center for Molecular Design, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma , P. le A. Moro 5, 00185 Roma, Italy
| | - Biagina Marrocco
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma , P. le A. Moro 5, 00185 Roma, Italy
| | - Garland R Marshall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , 700 South Euclid Avenue, St. Louis, Missouri 63110, United States
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Zhao S, Dai J, Hu M, Liu C, Meng R, Liu X, Wang C, Luo T. Photo-induced coupling reactions of tetrazoles with carboxylic acids in aqueous solution: application in protein labelling. Chem Commun (Camb) 2016; 52:4702-5. [DOI: 10.1039/c5cc10445a] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The coupling reactions of diaryltetrazoles with carboxylic acids under UV irradiation were investigated. Application of these transformations in chemical biology was demonstrated in photo-labelling the proteinogenic carboxylic acids in purified proteins, cell lysates and living cells.
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Affiliation(s)
- Shan Zhao
- Peking-Tsinghua Center for Life Sciences
- Academy for Advanced Interdisciplinary Studies
- Peking University
- Beijing 100871
- China
| | - Jianye Dai
- Peking-Tsinghua Center for Life Sciences
- Academy for Advanced Interdisciplinary Studies
- Peking University
- Beijing 100871
- China
| | - Mo Hu
- Beijing National Laboratory for Molecular Science (BNLMS)
- College of Chemistry and Molecular Engineering
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
| | - Chang Liu
- Beijing National Laboratory for Molecular Science (BNLMS)
- College of Chemistry and Molecular Engineering
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
| | - Rong Meng
- Beijing National Laboratory for Molecular Science (BNLMS)
- College of Chemistry and Molecular Engineering
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
| | - Xiaoyun Liu
- Beijing National Laboratory for Molecular Science (BNLMS)
- College of Chemistry and Molecular Engineering
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
| | - Chu Wang
- Peking-Tsinghua Center for Life Sciences
- Academy for Advanced Interdisciplinary Studies
- Peking University
- Beijing 100871
- China
| | - Tuoping Luo
- Peking-Tsinghua Center for Life Sciences
- Academy for Advanced Interdisciplinary Studies
- Peking University
- Beijing 100871
- China
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38
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Madsen AS, Olsen CA. A potent trifluoromethyl ketone histone deacetylase inhibitor exhibits class-dependent mechanism of action. MEDCHEMCOMM 2016. [DOI: 10.1039/c5md00451a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Kinetic evaluation of HDAC inhibitors containing different zinc-binding chemotypes demonstrates that trifluoromethyl ketone-containing compounds can inhibit individual HDAC isozymes via differential mechanisms.
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Affiliation(s)
- Andreas S. Madsen
- Center for Biopharmaceuticals and Department of Drug Design & Pharmacology
- University of Copenhagen
- Copenhagen
- Denmark
| | - Christian A. Olsen
- Center for Biopharmaceuticals and Department of Drug Design & Pharmacology
- University of Copenhagen
- Copenhagen
- Denmark
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39
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Mukherjee J, Sil S, Chattopadhyay SK. Diversity-oriented synthesis of analogues of the novel macrocyclic peptide FR-225497 through late stage functionalization. Beilstein J Org Chem 2015; 11:2487-92. [PMID: 26734096 PMCID: PMC4685926 DOI: 10.3762/bjoc.11.270] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 11/23/2015] [Indexed: 12/14/2022] Open
Abstract
A concise synthetic approach to a class of biologically interesting cyclic tetrapeptides is reported which involves a late-stage functionalization of a macrocyclic scaffold through cross metathesis in an attempt to create diversity. The utility of this protocol is demonstrated through the preparation of three structural analogues of the important naturally occurring histone deacetylase inhibitor FR-225497.
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Affiliation(s)
- Jyotiprasad Mukherjee
- Department of Chemistry, University of Kalyani, Kalyani - 741235, West Bengal, India
| | - Suman Sil
- Department of Chemistry, University of Kalyani, Kalyani - 741235, West Bengal, India
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40
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Investigation on the ZBG-functionality of phenyl-4-yl-acrylohydroxamic acid derivatives as histone deacetylase inhibitors. Bioorg Med Chem Lett 2015; 25:4457-60. [DOI: 10.1016/j.bmcl.2015.09.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 12/30/2022]
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41
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Cai J, Wei H, Hong KH, Wu X, Zong X, Cao M, Wang P, Li L, Sun C, Chen B, Zhou G, Chen J, Ji M. Discovery, bioactivity and docking simulation of Vorinostat analogues containing 1,2,4-oxadiazole moiety as potent histone deacetylase inhibitors and antitumor agents. Bioorg Med Chem 2015; 23:3457-71. [DOI: 10.1016/j.bmc.2015.04.028] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 12/30/2022]
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42
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Anthore L, Zard SZ. A Convergent Radical Based Route to Trifluoromethyl Ketones and to α,β-Unsaturated Trifluoromethyl Ketones. Org Lett 2015; 17:3058-61. [DOI: 10.1021/acs.orglett.5b01344] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lucile Anthore
- Laboratoire de Synthèse
Organique, CNRS UMR 7652 Ecole Polytechnique, 91128 Palaiseau,
Cedex, France
| | - Samir Z. Zard
- Laboratoire de Synthèse
Organique, CNRS UMR 7652 Ecole Polytechnique, 91128 Palaiseau,
Cedex, France
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43
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44
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Mottamal M, Zheng S, Huang TL, Wang G. Histone deacetylase inhibitors in clinical studies as templates for new anticancer agents. Molecules 2015; 20:3898-941. [PMID: 25738536 PMCID: PMC4372801 DOI: 10.3390/molecules20033898] [Citation(s) in RCA: 477] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 02/13/2015] [Accepted: 02/15/2015] [Indexed: 02/04/2023] Open
Abstract
Histone dacetylases (HDACs) are a group of enzymes that remove acetyl groups from histones and regulate expression of tumor suppressor genes. They are implicated in many human diseases, especially cancer, making them a promising therapeutic target for treatment of the latter by developing a wide variety of inhibitors. HDAC inhibitors interfere with HDAC activity and regulate biological events, such as cell cycle, differentiation and apoptosis in cancer cells. As a result, HDAC inhibitor-based therapies have gained much attention for cancer treatment. To date, the FDA has approved three HDAC inhibitors for cutaneous/peripheral T-cell lymphoma and many more HDAC inhibitors are in different stages of clinical development for the treatment of hematological malignancies as well as solid tumors. In the intensifying efforts to discover new, hopefully more therapeutically efficacious HDAC inhibitors, molecular modeling-based rational drug design has played an important role in identifying potential inhibitors that vary in molecular structures and properties. In this review, we summarize four major structural classes of HDAC inhibitors that are in clinical trials and different computer modeling tools available for their structural modifications as a guide to discover additional HDAC inhibitors with greater therapeutic utility.
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Affiliation(s)
- Madhusoodanan Mottamal
- RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA.
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA 70125, USA.
| | - Shilong Zheng
- RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA.
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA 70125, USA.
| | - Tien L Huang
- RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA.
- College of Pharmacy, Xavier University of Louisiana, New Orleans, LA 70125, USA.
| | - Guangdi Wang
- RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA.
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA 70125, USA.
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45
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Gleeson D, Gleeson MP. Application of QM/MM and QM methods to investigate histone deacetylase 8. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00471j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computational chemistry plays an important supporting role in the early stages of drug discovery research.
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Affiliation(s)
- Duangkamol Gleeson
- Department of Chemistry
- Faculty of Science
- King Mongkut’s Institute of Technology Ladkrabang
- Bangkok 10520
- Thailand
| | - M. Paul Gleeson
- Department of Chemistry
- Faculty of Science
- Kasetsart University
- Bangkok 10900
- Thailand
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46
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Wieting JM, Fisher TJ, Schafer AG, Visco MD, Gallucci JC, Mattson AE. Preparation and Catalytic Activity of BINOL-Derived Silanediols. European J Org Chem 2014. [DOI: 10.1002/ejoc.201403441] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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47
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Martin DP, Blachly PG, McCammon JA, Cohen SM. Exploring the influence of the protein environment on metal-binding pharmacophores. J Med Chem 2014; 57:7126-35. [PMID: 25116076 PMCID: PMC4148168 DOI: 10.1021/jm500984b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The binding of a series of metal-binding pharmacophores (MBPs) related to the ligand 1-hydroxypyridine-2-(1H)-thione (1,2-HOPTO) in the active site of human carbonic anhydrase II (hCAII) has been investigated. The presence and/or position of a single methyl substituent drastically alters inhibitor potency and can result in coordination modes not observed in small-molecule model complexes. It is shown that this unexpected binding mode is the result of a steric clash between the methyl group and a highly ordered water network in the active site that is further stabilized by the formation of a hydrogen bond and favorable hydrophobic contacts. The affinity of MBPs is dependent on a large number of factors including donor atom identity, orientation, electrostatics, and van der Waals interactions. These results suggest that metal coordination by metalloenzyme inhibitors is a malleable interaction and that it is thus more appropriate to consider the metal-binding motif of these inhibitors as a pharmacophore rather than a "chelator". The rational design of inhibitors targeting metalloenzymes will benefit greatly from a deeper understanding of the interplay between the variety of forces governing the binding of MBPs to active site metal ions.
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Affiliation(s)
- David P Martin
- Departments of Chemistry and Biochemistry, ‡Pharmacology, and §Howard Hughes Medical Institute, University of California, San Diego , 9500 Gilman Drive, MC 0358, La Jolla, California 92093, United States
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Dhanak D, Jackson P. Development and classes of epigenetic drugs for cancer. Biochem Biophys Res Commun 2014; 455:58-69. [PMID: 25016182 DOI: 10.1016/j.bbrc.2014.07.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/23/2014] [Accepted: 07/01/2014] [Indexed: 12/16/2022]
Abstract
Emerging evidence supports an important, etiologic role for epigenetic modifications in cancer. Various post translational modifications of histone proteins together with DNA methylation constitute an 'epigenetic code' regulating the transcriptional status of the cell and aberrant writing and/or interpretation of the code can contribute to a dysregulated, hyperproliferative state. In some cases, epigenetic deregulation has also been reported to result in tumor initiation. The discovery of somatic mutations in some chromatin binding proteins associated with subtypes of lymphomas and the ability to regulate expression of proto oncogenes such as Myc has spurred the development of specific small molecule modulators of histone binding proteins. Several of these compounds have entered clinical development for the treatment of heme malignancies. This review summarizes progress in the discovery and advancement of epigenetic therapeutics for cancer and provides a perspective for future development.
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Affiliation(s)
- Dashyant Dhanak
- Discovery Sciences, Janssen Pharmaceuticals, 1400 McKean Road, Spring House, PA 19477, USA.
| | - Paul Jackson
- Discovery Sciences, Janssen Pharmaceuticals, 1400 McKean Road, Spring House, PA 19477, USA
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