Abstract
LSD1 is an epigenetic modulator associated with transcriptional regulation of genes involved in a broad spectrum of key cellular processes, and its activity is often altered under pathological conditions. LSD1 inhibitors are considered to be candidates for therapy of cancer, viral diseases and neurodegeneration. Many LSD1 inhibitors with various scaffolds have been disclosed, and a few potent molecules are in different stages of clinical development. In this review, we summarize recent biological findings on the roles of LSD1 and the current understanding of the clinical significance of LSD1, and focus on the medicinal chemistry strategies used in the design and development of LSD1 inhibitors as drug-like epigenetic modulators since 2012, including a brief consideration of structure–activity relationships.
Papers of special note have been highlighted as: •• of considerable interest
References
- 1 . Chromatin proteins and modifications as drug targets. Nature 502(7472), 480–488 (2013).
- 2 Metabolic regulation of histone post-translational modifications. ACS Chem. Biol. 10(1), 95–108 (2015).
- 3 . Lysine demethylases inhibitors. J. Med. Chem. 54(24), 8236–8250 (2011). •• Introduction to the enzymology of the lysine demethylases, emerging small molecule inhibitors, discuss the potential and challenges of therapeutically targeting them.
- 4 Targeting histone lysine demethylases – progress, challenges, and the future. Biochim. Biophys. Acta 1839(12), 1416–1432 (2014).
- 5 A systematic review of histone lysine-specific demethylase 1 and its inhibitors. Med. Res. Rev.
doi: 10.1002/med.21350 (2015) (Epub ahead of print). - 6 . Targeting histone lysine methylation in cancer. Pharmacol. Ther. 150, 1–22 (2015).
- 7 . Histone lysine demethylases as targets for anticancer therapy. Nat. Rev. Drug Discov. 12(12), 917–930 (2013). •• Demonstrates the roles of members of the histone lysine demethylases in the development of cancers and highlights the therapeutic possibilities and challenges associated with targeting.
- 8 Reversible inhibitors of LSD1 as therapeutic agents in acute myeloid leukemia: clinical significance and progress to date. Med. Res. Rev. 35(3), 586–618 (2015).
- 9 . Histone lysine methylation and demethylation pathways in cancer. Biochim. Biophys. Acta 1815(1), 75–89 (2011).
- 10 Overexpression of LSD1 contributes to human carcinogenesis through chromatin regulation in various cancers. Int. J. Cancer. 128(3), 574–586 (2011).
- 11 . The histone LSD1 demethylase in stemness and cancer transcription programs. Biochim. Biophys. Acta 1829(10), 981–986 (2013).
- 12 Expression of Lysine-specific demethylase 1 in human epithelial ovarian cancer. J. Ovarian. Res. 8(1), 28 (2015).
- 13 Over-expression of lysine-specific demethylase 1 predicts tumor progression and poor prognosis in human esophageal cancer. Int. J. Clin. Exp. Pathol. 7(12), 8929–8934 (2014).
- 14 Lysine-specific demethylase 1 (LSD1) in hematopoietic and lymphoid neoplasms. Blood 124(1), 151–152 (2014).
- 15 Over-expression of LSD1 promotes proliferation, migration and invasion in non-small cell lung cancer. PLoS ONE 7(4), e35065 (2012).
- 16 Histone demethylase LSD1 inhibitors prevent cell growth by regulating gene expression in esophageal squamous cell carcinoma cells. Ann. Surg. Oncol. (2015) (Epub ahead of print).
- 17 The emerging role of histone lysine demethylases in prostate cancer. Mol. Cancer. 11, 52 (2012).
- 18 Lysine demethylase LSD1 coordinates glycolytic and mitochondrial metabolism in hepatocellular carcinoma cells. Cancer Res. 75(7), 1445–1456 (2015).
- 19 FAD-dependent lysine-specific demethylase-1 regulates cellular energy expenditure. Nat. Commun. 3, 758 (2012).
- 20 Epigenetic regulation of Atrophin1 by lysine-specific demethylase 1 is required for cortical progenitor maintenance. Nat. Commun. 5, 5815 (2012).
- 21 Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature 482, 221–225 (2012).
- 22 LSD1 promotes oxidative metabolism of white adipose tissue. Nat. Commun. 5, 4093 (2014).
- 23 Regulation of lipogenic gene expression by lysine-specific histone demethylase-1 (LSD1). J. Biol. Chem. 289, 29937–29947 (2014).
- 24 . Suppression of gluconeogenic gene expression by LSD1-mediated histone demethylation. PLoS ONE 8, e66294 (2013).
- 25 Lysine-specific demethylase 1 has dual functions as a major regulator of androgen receptor transcriptional activity. Cell Rep. 9(5), 1618–1627 (2014).
- 26 Cryptotanshinone down-regulates androgen receptor signaling by modulating lysine-specific demethylase 1 function. Int. J. Cancer 131(6), 1423–1434 (2012).
- 27 . Integration of ERα-PELP1-HER2 signaling by LSD1 (KDM1A/AOF2) offers combinatorial therapeutic opportunities to circumventing hormone resistance in breast cancer. Breast Cancer Res. 14, 112 (2012).
- 28 Targeting the PELP1-KDM1 axis as a potential therapeutic strategy for breast cancer. Breast Cancer Res. 14(4), R108 (2012).
- 29 Lysine-specific histone demethylase 1 inhibitors control breast cancer proliferation in ERα-dependent and -independent manners. ACS Chem. Biol. 7(7), 1221–1231 (2012).
- 30 A specific LSD1/KDM1A isoform regulates neuronal differentiation through H3K9 demethylation. Mol. Cell. 57(6), 957–970 (2015).
- 31 . Molecular toggle switch of histone demethylase LSD1. Mol. Cell. 57(6), 949–950 (2015).
- 32 Destabilizing LSD1 by Jade-2 promotes neurogenesis: an antibraking system in neural development. Mol. Cell. 55(3), 482–494 (2014).
- 33 Lysine-specific demethylase 1 inhibitors protect cochlear spiral ganglion neurons against cisplatin-induced damage. Neuroreport 26(9), 539–547 (2015).
- 34 A novel selective LSD1/KDM1A inhibitor epigenetically blocks herpes simplex virus lytic replication and reactivation from latency. mBio 4(1), e00558–e005512 (2013).
- 35 A dihydro-pyrido-indole potently inhibits HSV-1 infection by interfering the viral immediate early transcriptional events. Antiviral Res. 105, 126–134 (2014).
- 36 Expanding the druggable space of the LSD1/CoREST epigenetic target: new potential binding regions for drug-like molecules, peptides, protein partners, and chromatin. PLoS Comput. Biol. 9(7), e1003158 (2013).
- 37 Histone demethylase LSD1 is a folate-binding protein. Biochemistry 50(21), 4750–4756 (2011).
- 38 Crystal structure of the histone lysine specific demethylase LSD1 complexed with tetrahydrofolate. Protein Sci. 23(7), 993–998 (2014).
- 39 . An overview of phenylcyclopropylamine derivatives: biochemical and biological significance and recent developments. Med. Res. Rev. 33(4), 873–910 (2013).
- 40 Synthesis, biological activity and mechanistic insights of 1-substituted cyclopropylamine derivatives: a novel class of irreversible inhibitors of histone demethylase KDM1A. Eur. J. Med. Chem. 86, 352–363 (2014).
- 41 Further insights into the SAR of α-substituted cyclopropylamine derivatives as inhibitors of histone demethylase KDM1A. Eur. J. Med. Chem. 92, 377–386 (2015).
- 42 Pure enantiomers of benzoylamino-tranylcypromine: LSD1 inhibition, gene modulation in human leukemia cells and effects on clonogenic potential of murine promyelocytic blasts. Eur. J. Med. Chem. 94, 163–174 (2015).
- 43 Pure diastereomers of a tranylcypromine-based LSD1 inhibitor: enzyme selectivity and in-cell studies. ACS Med. Chem. Lett. 6(2), 173–177 (2014).
- 44 Inhibition of LSD1 as a therapeutic strategy for the treatment of acute myeloid leukemia. Blood 122(21), 3964 (2013).
- 45 . Novel anti-tumor activity of targeted LSD1 inhibition. Presented at: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research. San Diego, CA, USA, 5–9 April (2014).
- 46 Brain-penetrant LSD1 inhibitors can block memory consolidation. ACS Chem. Neurosci. 3(2), 120–128 (2012).
- 47 RN-1, a potent and selective LSD1 inhibitor, increases γ-globin expression, f-retics, and f-cells in a sickle cell disease mouse model. Exp. Hematol. 43(7), 546–553 (2015).
- 48 Conformational restriction: an effective tactic in ‘follow-on’-based drug discovery. Future Med. Chem. 6(8), 885–901 (2014).
- 49 Pyrrole- and indole- containing tranylcypromine derivatives as novel lysine-specific demethylase 1 inhibitors active on cancer cells. Med. Chem. Commun. 6, 665–670 (2014).
- 50 Recent advances in the structure-based rational design of TNKSIs. Mol. Biosyst. 10(11), 2783–2799 (2014).
- 51 'Old dogs with new tricks': exploiting alternative mechanisms of action and new drug design strategies for clinically validated HIV targets. Mol. Biosyst. 10(8), 1998–2022 (2014).
- 52 Identification of cell-active lysine specific demethylase 1-selective inhibitors. J. Am. Chem. Soc. 131(48), 17536–17537 (2009). •• Reports on the identification of the first small-molecule LSD1-selective inhibitors.
- 53 NCL1, a highly selective lysine-specific demethylase 1 inhibitor, suppresses prostate cancer without adverse effect. Oncotarget 6(5), 2865–2878 (2015).
- 54 The KDM1A histone demethylase is a promising new target for the epigenetic therapy of medulloblastoma. Acta Neuropathol. Commun. 1(1), 19 (2013).
- 55 : WO2010043721 (2010).
- 56 Design, synthesis, and biological activity of N-alkylated analogue of NCL1, a selective inhibitor of lysine-specific demethylase 1. Med. Chem. Commun. 6, 407–412 (2015).
- 57 . Synthesis and evaluation of novel cyclic peptide inhibitors of lysine-specific demethylase 1. ACS Med. Chem. Lett. 5(1), 29–33 (2013).
- 58 Protein recognition by short peptide reversible inhibitors of the chromatin-modifying LSD1/CoREST lysine demethylase. ACS Chem. Biol. 8(8), 1677–82 (2013).
- 59 Histone H3 peptide based LSD1-selective inhibitors. Bioorg. Med. Chem. Lett. 25(9), 1925–1928 (2015).
- 60 Lysine-specific demethylase 1-selective inactivators: protein-targeted drug delivery mechanism. Angew. Chem. Int. Ed. Engl. 52(33), 8620–8624 (2013).
- 61 Synthesis, LSD1 inhibitory activity, and LSD1 binding model of optically pure lysine-PCPA conjugates. Comput. Struct. Biotechnol. J. 9, e201402002 (2014).
- 62 . Rationally designed multitarget anti-HIV agents. Curr. Med. Chem. 20(13), 1743–58 (2013).
- 63 . Designed multiple ligands: an emerging anti-HIV drug discovery paradigm. Curr. Pharm. Des. 15(16), 1893–917 (2009).
- 64 Synergistic re-activation of epigenetically silenced genes by combinatorial inhibition of DNMTs and LSD1 in cancer cells. PLoS ONE 8(9), e75136 (2013).
- 65 Novel oligoamine analogues inhibit lysine-specific demethylase 1 and induce reexpression of epigenetically silenced genes. Clin. Cancer Res. 15, 7217–7228 (2009).
- 66 Crosstalk between lysine-specific demethylase 1 (LSD1) and histone deacetylases mediates antineoplastic efficacy of HDAC inhibitors in human breast cancer cells. Carcinogenesis 34(6), 1196–1207 (2013).
- 67 Preclinical activity of combined HDAC and KDM1A inhibition in glioblastoma. Neuro Oncol. 17(11), 1463–1473 (2015).
- 68 Cooperative demethylation by JMJD2C and LSD1 promotes androgen receptor-dependent gene expression. Nat. Cell Biol. 9(3), 347–353 (2007).
- 69 8-Hydroxyquinoline: a privileged structure with broad-ranging pharmacological potentials. Med. Chem. Commun. 6, 61–74 (2015).
- 70 Pan-histone demethylase inhibitors simultaneously targeting Jumonji C and lysine-specific demethylases display high anticancer activities. J. Med. Chem. 57, 42–55 (2014).
- 71 Nonpeptidic propargylamines as inhibitors of lysine specific demethylase 1 (LSD1) with cellular activity. J. Med. Chem. 56(18), 7334–7342 (2013).
- 72 Novel histone demethylase LSD1 inhibitors selectively target cancer cells with pluripotent stem cell properties. Cancer Res. 71(23), 7238–7249 (2011).
- 73 CBB1003, a lysine-specific demethylase 1 inhibitor, suppresses colorectal cancer cells growth through down-regulation of leucine-rich repeat-containing G-protein-coupled receptor 5 expression. J. Cancer Res. Clin. Oncol. 141(1), 11–21 (2015).
- 74 A selective phenelzine analogue inhibitor of histone demethylase LSD1. ACS Chem. Biol. 9(6), 1284–1293 (2014).
- 75 High-throughput virtual screening identifies novel N’;-(1-phenylethylidene)-benzohydrazides as potent, specific, and reversible LSD1 inhibitors. J. Med. Chem. 56(23), 9496–9508 (2013). •• The first reversible and specific LSD1 inhibitor was identified by high-throughput virtual screening.
- 76 Reversible inhibition of lysine specific demethylase 1 is a novel anti-tumor strategy for poorly differentiated endometrial carcinoma. BMC Cancer 14, 752 (2014).
- 77 Highly effective combination of LSD1 (KDM1A) antagonist and pan-histone deacetylase inhibitor against human AML cells. Leukemia 28(11), 2155–2164 (2014).
- 78 Synthesis and biological evaluation of novel (E)-N’-(2, 3-dihydro-1H-inden-1-ylidene) benzohydrazides as potent LSD1 inhibitors. Bioorg. Med. Chem. Lett.
doi: 10.1016/j.bmcl.2015.06.054 (2015). - 79 Low molecular weight amidoximes that act as potent inhibitors of lysine-specific demethylase 1. J. Med. Chem. 55(17), 7378–7391 (2012).
- 80 Triazole-dithiocarbamate based selective lysine specific demethylase 1 (LSD1) inactivators inhibit gastric cancer cell growth, invasion, and migration. J. Med. Chem. 56(21), 8543–8560 (2013).
- 81 Synthesis and biological evaluation of coumarin-1, 2, 3-triazole-dithiocarbamate hybrids as potent LSD1 inhibitors. Med. Chem. Commun. 5, 650–654 (2014).
- 82 Design, synthesis, and structure-activity relationship of novel LSD1 inhibitors based on pyrimidine-thiourea hybrids as potent, orally active antitumor agents. J. Med. Chem. 58(4), 1705–1716 (2015).
- 83 Synthesis and evaluation of 3-amino/guanidine substituted phenyl oxazoles as a novel class of LSD1 inhibitors with anti-proliferative properties. Org. Biomol. Chem. 11(19), 3103–3107 (2013).
- 84 3,5-Diamino-1,2,4-triazoles as a novel scaffold for potent, reversible LSD1 (KDM1A) inhibitors. Med. Chem. Commun. 5(12), 1863–1870 (2014).
- 85 . Small molecule epigenetic modulators for the treatment of cardiovascular disorders. Presented at: Abstracts of Papers, 249th ACS National Meeting and Exposition. CO, USA, 22–26 March (2015).
- 86 . Natural products as sources of new drugs over the 30 years from 1981 to 2010. J. Nat. Prod. 75(3), 311–335 (2012).
- 87 . Natural products as sources of new drugs over the last 25 years. J. Nat. Prod. 70(3), 461–477 (2007).
- 88 . Natural products as sources of new drugs over the period 1981–2002. J. Nat. Prod. 66(7), 1022–1037 (2003).
- 89 . Natural polyphenols inhibit lysine-specific demethylase-1 in vitro. J. Biochem. Pharmacol. Res. 1(1), 56–63 (2013).
- 90 Inhibition of lysine-specific demethylase 1 by polyamine analogues results in reexpression of aberrantly silenced genes. Proc. Natl Acad. Sci. USA 104, 8023–8028 (2007).
- 91 Polyamine analogs modulate gene expression by inhibiting lysine-specific demethylase 1 (LSD1) and altering chromatin structure in human breast cancer cells. Amino Acids 42, 887–898 (2012).
- 92 . The re-expression of the epigenetically silenced e-cadherin gene by a polyamine analogue lysine-specific demethylase-1 (LSD1) inhibitor in human acute myeloid leukemia cell lines. Amino Acids 46, 585–594 (2014).
- 93 . Medicinal chemistry of target family-directed masterkeys. Drug Discov. Today. 8(15), 681–691 (2003).
- 94 'Old friends in new guise': exploiting privileged structures for scaffold re-evolution/refining. Comb. Chem. High Throughput Screen. 17(6), 536–553 (2014).
- 95 . Covalent inhibitors in drug discovery: from accidental discoveries to avoided liabilities and designed therapies. Drug Discov. Today 20(9), 1061–1073 (2015).
- 96 Extranucleosomal DNA enhances the activity of the LSD1/CoREST histone demethylase complex. Nucleic Acids Res. 43(10), 4868–4880 (2015).
- 97 Strategies for the discovery of target-specific or isoform-selective modulators. J. Med. Chem.
doi:10.10-763321/acs.jmedchem.5b00229 (2015). •• Discusses currently available rational design strategies for obtaining class- and isoform-selective inhibitors. - 98 Refining the chemical toolbox to be fit for educational and practical purpose for drug discovery in the 21st Century. Drug Discov. Today
doi: 10.1016/j.drudis.2015.04.010 (2015). - 99 Repurposing of HDAC inhibitors towards anti-HCV drug discovery: how to teach old dog new tricks? Future Med. Chem. 7(11), 1367–1371 (2015).