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Shokri G, Doudi S, Fathi-Roudsari M, Kouhkan F, Sanati MH. Targeting histone demethylases KDM5A and KDM5B in AML cancer cells: A comparative view. Leuk Res 2018; 68:105-111. [DOI: 10.1016/j.leukres.2018.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 01/23/2018] [Accepted: 02/05/2018] [Indexed: 02/07/2023]
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Mould DP, Alli C, Bremberg U, Cartic S, Jordan AM, Geitmann M, Maiques-Diaz A, McGonagle AE, Somervaille TCP, Spencer GJ, Turlais F, Ogilvie D. Development of (4-Cyanophenyl)glycine Derivatives as Reversible Inhibitors of Lysine Specific Demethylase 1. J Med Chem 2017; 60:7984-7999. [PMID: 28892629 DOI: 10.1021/acs.jmedchem.7b00462] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Inhibition of lysine specific demethylase 1 (LSD1) has been shown to induce the differentiation of leukemia stem cells in acute myeloid leukemia (AML). Irreversible inhibitors developed from the nonspecific inhibitor tranylcypromine have entered clinical trials; however, the development of effective reversible inhibitors has proved more challenging. Herein, we describe our efforts to identify reversible inhibitors of LSD1 from a high throughput screen and subsequent in silico modeling approaches. From a single hit (12) validated by biochemical and biophysical assays, we describe our efforts to develop acyclic scaffold-hops from GSK-690 (1). A further scaffold modification to a (4-cyanophenyl)glycinamide (e.g., 29a) led to the development of compound 32, with a Kd value of 32 nM and an EC50 value of 0.67 μM in a surrogate cellular biomarker assay. Moreover, this derivative does not display the same level of hERG liability as observed with 1 and represents a promising lead for further development.
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Affiliation(s)
- Daniel P Mould
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester , Wilmslow Road, Manchester, M20 4BX, U.K
| | - Cristina Alli
- CRT Discovery Laboratories , Babraham Campus, Babraham, Cambridgeshire CB22 3AT, U.K
| | - Ulf Bremberg
- Beactica AB , Uppsala Business Park, Virdings allé 2, 75450, Uppsala, Sweden
| | - Sharon Cartic
- CRT Discovery Laboratories , Babraham Campus, Babraham, Cambridgeshire CB22 3AT, U.K
| | - Allan M Jordan
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester , Wilmslow Road, Manchester, M20 4BX, U.K
| | - Matthis Geitmann
- Beactica AB , Uppsala Business Park, Virdings allé 2, 75450, Uppsala, Sweden
| | - Alba Maiques-Diaz
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, University of Manchester , Wilmslow Road, Manchester, M20 4BX, U.K
| | - Alison E McGonagle
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester , Wilmslow Road, Manchester, M20 4BX, U.K
| | - Tim C P Somervaille
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, University of Manchester , Wilmslow Road, Manchester, M20 4BX, U.K
| | - Gary J Spencer
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, University of Manchester , Wilmslow Road, Manchester, M20 4BX, U.K
| | - Fabrice Turlais
- CRT Discovery Laboratories , Babraham Campus, Babraham, Cambridgeshire CB22 3AT, U.K
| | - Donald Ogilvie
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester , Wilmslow Road, Manchester, M20 4BX, U.K
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Probing the interaction of the p53 C-terminal domain to the histone demethylase LSD1. Arch Biochem Biophys 2017; 632:202-208. [PMID: 28784588 DOI: 10.1016/j.abb.2017.07.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/10/2017] [Accepted: 07/13/2017] [Indexed: 12/18/2022]
Abstract
The p53 transcription factor plays a central role in the regulation of the expression of several genes, and itself is post-translationally regulated through its different domains. Of particular relevance for p53 function is its intrinsically disordered C-terminal domain (CTD), representing a hotspot for post-translational modifications and a docking site for transcriptional regulators. For example, the histone H3 lysine demethylase 1 (LSD1) interacts with p53 via the p53-CTD for mutual regulation. To biochemically and functionally characterize this complex, we evaluated the in vitro interactions of LSD1 with several p53-CTD peptides differing in length and modifications. Binding was demonstrated through thermal shift, enzymatic and fluorescence polarization assays, but no enzymatic activity could be detected on methylated p53-CTD peptides in vitro. These experiments were performed using the wild-type enzyme and LSD1 variants that are mutated on three active-site residues. We found that LSD1 demethylase activity is inhibited by p53-CTD. We also noted that the association between the two proteins is mediated by mostly non-specific electrostatic interactions involving conserved active-site residues of LSD1 and a highly charged segment of the p53-CTD. We conclude that p53-CTD inhibits LSD1 activity and that the direct association between the two proteins can contribute to their functional cross-talk.
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Abstract
LSD1 has become an important biologically validated epigenetic target for cancer therapy since its identification in 2004. LSD1 mediates many cellular signaling pathways and is involved in the initiation and development of cancers. Aberrant overexpression of LSD1 has been observed in different types of cancers, and inactivation by small molecules suppresses cancer cell differentiation, proliferation, invasion and migration. To date, a large number of LSD1 inhibitors have been reported, RG6016, GSK-2879552, INCB059872, IMG-7289 and CC-90011 are currently undergoing clinical assessment for the treatment of acute myeloid leukemia, small-cell lung cancer, etc. In this review, we briefly highlight recent advances of LSD1 inhibitors mainly covering the literatures from 2015 to 2017 and tentatively propose our perspectives on the design of new LSD1 inhibitors for cancer therapy.
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Niwa H, Umehara T. Structural insight into inhibitors of flavin adenine dinucleotide-dependent lysine demethylases. Epigenetics 2017; 12:340-352. [PMID: 28277979 PMCID: PMC5453194 DOI: 10.1080/15592294.2017.1290032] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Until 2004, many researchers believed that protein methylation in eukaryotic cells was an irreversible reaction. However, the discovery of lysine-specific demethylase 1 in 2004 drastically changed this view and the concept of chromatin regulation. Since then, the enzymes responsible for lysine demethylation and their cellular substrates, biological significance, and selective regulation have become major research topics in epigenetics and chromatin biology. Many cell-permeable inhibitors for lysine demethylases have been developed, including both target-specific and nonspecific inhibitors. Structural understanding of how these inhibitors bind to lysine demethylases is crucial both for validation of the inhibitors as chemical probes and for the rational design of more potent, target-specific inhibitors. This review focuses on published small-molecule inhibitors targeted at the two flavin adenine dinucleotide-dependent lysine demethylases, lysine-specific demethylases 1 and 2, and how the inhibitors interact with the tertiary structures of the enzymes.
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Affiliation(s)
- Hideaki Niwa
- a Epigenetics Drug Discovery Unit , RIKEN Center for Life Science Technologies , Suehiro-cho, Tsurumi, Yokohama , Kanagawa , Japan
| | - Takashi Umehara
- a Epigenetics Drug Discovery Unit , RIKEN Center for Life Science Technologies , Suehiro-cho, Tsurumi, Yokohama , Kanagawa , Japan.,b PRESTO, Japan Science and Technology Agency (JST) , Honcho, Kawaguchi , Saitama , Japan
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