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Computer-Driven Development of an in Silico Tool for Finding Selective Histone Deacetylase 1 Inhibitors. Molecules 2020; 25:molecules25081952. [PMID: 32331470 PMCID: PMC7221830 DOI: 10.3390/molecules25081952] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 04/18/2020] [Accepted: 04/20/2020] [Indexed: 12/19/2022] Open
Abstract
Histone deacetylases (HDACs) are a class of epigenetic modulators overexpressed in numerous types of cancers. Consequently, HDAC inhibitors (HDACIs) have emerged as promising antineoplastic agents. Unfortunately, the most developed HDACIs suffer from poor selectivity towards a specific isoform, limiting their clinical applicability. Among the isoforms, HDAC1 represents a crucial target for designing selective HDACIs, being aberrantly expressed in several malignancies. Accordingly, the development of a predictive in silico tool employing a large set of HDACIs (aminophenylbenzamide derivatives) is herein presented for the first time. Software Phase was used to derive a 3D-QSAR model, employing as alignment rule a common-features pharmacophore built on 20 highly active/selective HDAC1 inhibitors. The 3D-QSAR model was generated using 370 benzamide-based HDACIs, which yielded an excellent correlation coefficient value (R2 = 0.958) and a satisfactory predictive power (Q2 = 0.822; Q2F3 = 0.894). The model was validated (r2ext_ts = 0.794) using an external test set (113 compounds not used for generating the model), and by employing a decoys set and the receiver-operating characteristic (ROC) curve analysis, evaluating the Güner-Henry score (GH) and the enrichment factor (EF). The results confirmed a satisfactory predictive power of the 3D-QSAR model. This latter represents a useful filtering tool for screening large chemical databases, finding novel derivatives with improved HDAC1 inhibitory activity.
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Reis SA, Ghosh B, Hendricks JA, Szantai-Kis DM, Törk L, Ross KN, Lamb J, Read-Button W, Zheng B, Wang H, Salthouse C, Haggarty SJ, Mazitschek R. Light-controlled modulation of gene expression by chemical optoepigenetic probes. Nat Chem Biol 2016; 12:317-23. [PMID: 26974814 PMCID: PMC4836974 DOI: 10.1038/nchembio.2042] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 01/07/2016] [Indexed: 12/20/2022]
Abstract
Epigenetic gene regulation is a dynamic process orchestrated by chromatin-modifying enzymes. Many of these master regulators exert their function through covalent modification of DNA and histone proteins. Aberrant epigenetic processes have been implicated in the pathophysiology of multiple human diseases. Small-molecule inhibitors have been essential to advancing our understanding of the underlying molecular mechanisms of epigenetic processes. However, the resolution offered by small molecules is often insufficient to manipulate epigenetic processes with high spatiotemporal control. Here we present a generalizable approach, referred to as 'chemo-optical modulation of epigenetically regulated transcription' (COMET), enabling high-resolution, optical control of epigenetic mechanisms based on photochromic inhibitors of human histone deacetylases using visible light. COMET probes may be translated into new therapeutic strategies for diseases where conditional and selective epigenome modulation is required.
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Affiliation(s)
- Surya A Reis
- Chemical Neurobiology Laboratory, Massachusetts General Hospital, Boston, Massachusetts, USA.,Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA
| | - Balaram Ghosh
- Chemical Neurobiology Laboratory, Massachusetts General Hospital, Boston, Massachusetts, USA.,Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA.,Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - J Adam Hendricks
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - D Miklos Szantai-Kis
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lisa Törk
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kenneth N Ross
- Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Justin Lamb
- Genometry Inc., Cambridge, Massachusetts, USA
| | | | | | - Hongtao Wang
- Department of Electrical &Computer Engineering, University of Massachusetts, Amherst, Massachusetts, USA.,Center for Personalized Health Monitoring, University of Massachusetts, Amherst, Massachusetts, USA
| | - Christopher Salthouse
- Department of Electrical &Computer Engineering, University of Massachusetts, Amherst, Massachusetts, USA.,Center for Personalized Health Monitoring, University of Massachusetts, Amherst, Massachusetts, USA
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Massachusetts General Hospital, Boston, Massachusetts, USA.,Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of Harvard &Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of Harvard &Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Fun HK, Quah CK, Abdel-Aziz HA, Ghabbour HA. 3-Oxo-3-(piperidin-1-yl)propanenitrile. Acta Crystallogr Sect E Struct Rep Online 2012; 68:o2726. [PMID: 22969610 PMCID: PMC3435739 DOI: 10.1107/s1600536812035015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 08/08/2012] [Indexed: 11/10/2022]
Abstract
In the title compound, C8H12N2O, the piperidine ring exhibits a chair conformation and its least-squares plane (all atoms) makes a dihedral angle of 32.88 (12)° with the propanenitrile unit (r.m.s. deviation = 0.001 Å). In the crystal, molecules are linked by C—H⋯O hydrogen bonds, forming chains along [001].
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Graham MA, Raw SA, Andrews DM, Good CJ, Matusiak ZS, Maybury M, Stokes ESE, Turner AT. Flexible and Scalable Route to HDAc Inhibitors Containing an Unusual Trisubstituted Pyridine Core. Org Process Res Dev 2012. [DOI: 10.1021/op300021m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mark A. Graham
- Oncology Innovative Medicines, AstraZeneca, Mereside, Alderley Park, Macclesfield
SK10 4TG, U.K
| | - Steven A. Raw
- Medicines
Evaluation Chemistry,
Pharmaceutical Development, AstraZeneca, Charter Way, Macclesfield SK10 2NA, U.K
| | - David M. Andrews
- Oncology Innovative Medicines, AstraZeneca, Mereside, Alderley Park, Macclesfield
SK10 4TG, U.K
| | - Catherine J. Good
- Chemical Science, Pharmaceutical
Development, AstraZeneca, Charter Way,
Macclesfield SK10 2NA, U.K
| | - Zbigniew S. Matusiak
- Oncology Innovative Medicines, AstraZeneca, Mereside, Alderley Park, Macclesfield
SK10 4TG, U.K
| | - Mark Maybury
- Chemical Science, Pharmaceutical
Development, AstraZeneca, Charter Way,
Macclesfield SK10 2NA, U.K
| | - Elaine S. E. Stokes
- Oncology Innovative Medicines, AstraZeneca, Mereside, Alderley Park, Macclesfield
SK10 4TG, U.K
| | - Andrew T. Turner
- Chemical Science, Pharmaceutical
Development, AstraZeneca, Charter Way,
Macclesfield SK10 2NA, U.K
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Abstract
IMPORTANCE OF THE FIELD Following FDA approval of vorinostat in 2006, several novel HDAC inhibitors (HDACis) have entered clinical trials, and there are numerous published patent applications claiming novel HDACis which were optimized as potential drug candidates, designed for regional or systemic release, and created as dual or multifunctional inhibitors. Given the breadth and depth of recent reporting of novel HDACis, there has emerged a need to review the field from a chemist's perspective in one compact article. AREAS COVERED IN THIS REVIEW This review provides a summary of published patent applications claiming novel HDACis from 2007 until mid-2009, covering mainly classes I, II and IV anticancer HDACis including those that have recently advanced to the clinic. WHAT THE READER WILL GAIN Readers will rapidly gain an overview of the majority of HDACi scaffolds with representative structure-activity relationships; they will learn how these new compounds were created, how their drug like properties were improved and which companies are the main players in the field. TAKE HOME MESSAGE Although competition in this field is intense, the future application of HDACis to treat human disease either as single agents or in combination with existing drugs holds real promise.
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Affiliation(s)
- Haishan Wang
- Chemistry Discovery, S*BIO Pte Ltd, The Capricorn, Singapore Science Park II, Singapore, Singapore.
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