Summary
Lysine (K)-specific demethylase 4A (KDM4A) is a histone demethylase that removes methyl residues from trimethylated or dimethylated histone 3 at lysines 9 and 36. Overexpression of KDM4A is found in various cancer types. To identify KDM4A inhibitors with anti-tumor functions, screening with an in vitro KDM4A enzyme activity assay was carried out. The benzylidenehydrazine analogue LDD2269 was selected, with an IC50 of 6.56 μM of KDM4A enzyme inhibition, and the binding mode was investigated using in silico molecular docking. Demethylation inhibition by LDD2269 was confirmed with a cell-based assay using antibodies against methylated histone at lysines 9 and 36. HCT-116 colon cancer cell line proliferation was suppressed by LDD2269, which also interfered with soft-agar growth and migration of HCT-116 cells. AnnexinV staining and PARP cleavage experiments showed apoptosis induction by LDD2269. Derivatives of LDD2269 were synthesized and the structure–activity relationship was explored. LDD2269 is reported here as a strong inhibitor of KDM4A in in vitro and cell-based systems, with anti-tumor functions.
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Klose RJ, Yamane K, Bae Y, Zhang D, Erdjument-Bromage H, Tempst P, Wong J, Zhang Y (2006) The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36. Nature 442(7100):312–316. doi:10.1038/nature04853
Whetstine JR, Nottke A, Lan F, Huarte M, Smolikov S, Chen Z, Spooner E, Li E, Zhang G, Colaiacovo M, Shi Y (2006) Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125(3):467–481. doi:10.1016/j.cell.2006.03.028
Chen Z, Zang J, Whetstine J, Hong X, Davrazou F, Kutateladze TG, Simpson M, Mao Q, Pan CH, Dai S, Hagman J, Hansen K, Shi Y, Zhang G (2006) Structural insights into histone demethylation by JMJD2 family members. Cell 125(4):691–702. doi:10.1016/j.cell.2006.04.024
Huang Y, Fang J, Bedford MT, Zhang Y, Xu RM (2006) Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A. Science 312(5774):748–751. doi:10.1126/science.1125162
Loh YH, Zhang W, Chen X, George J, Ng HH (2007) Jmjd1a and Jmjd2c histone H3 Lys 9 demethylases regulate self-renewal in embryonic stem cells. Genes Dev 21(20):2545–2557. doi:10.1101/gad.1588207
Guerra-Calderas L, Gonzalez-Barrios R, Herrera LA, Cantu de Leon D, Soto-Reyes E (2015) The role of the histone demethylase KDM4A in cancer. Cancer genetics 208(5):215–224. doi:10.1016/j.cancergen.2014.11.001
Black JC, Manning AL, Van Rechem C, Kim J, Ladd B, Cho J, Pineda CM, Murphy N, Daniels DL, Montagna C, Lewis PW, Glass K, Allis CD, Dyson NJ, Getz G, Whetstine JR (2013) KDM4A lysine demethylase induces site-specific copy gain and rereplication of regions amplified in tumors. Cell 154(3):541–555. doi:10.1016/j.cell.2013.06.051
Labbe RM, Holowatyj A, Yang ZQ (2013) Histone lysine demethylase (KDM) subfamily 4: structures, functions and therapeutic potential. Am J Transl Res 6(1):1–15
Chin Y-W, Han S-Y KDM4 histone demethylase inhibitors for anti-cancer agents: a patent review. Expert Opinion on Therapeutic Patents 25(2):135–144. doi:10.1517/13543776.2014.991310
King ON, Li XS, Sakurai M, Kawamura A, Rose NR, Ng SS, Quinn AM, Rai G, Mott BT, Beswick P, Klose RJ, Oppermann U, Jadhav A, Heightman TD, Maloney DJ, Schofield CJ, Simeonov A (2010) Quantitative high-throughput screening identifies 8-hydroxyquinolines as cell-active histone demethylase inhibitors. PLoS One 5(11):e15535. doi:10.1371/journal.pone.0015535
Sekirnik R, Rose NR, Thalhammer A, Seden PT, Mecinovic J, Schofield CJ (2009) Inhibition of the histone lysine demethylase JMJD2A by ejection of structural Zn(II). Chemical communications (Cambridge, England) (42):6376–6378. doi:10.1039/b916357c
Wagner EK, Nath N, Flemming R, Feltenberger JB, Denu JM (2012) Identification and characterization of small molecule inhibitors of a plant homeodomain finger. Biochemistry 51(41):8293–8306. doi:10.1021/bi3009278
Luo X, Liu Y, Kubicek S, Myllyharju J, Tumber A, Ng S, Che KH, Podoll J, Heightman TD, Oppermann U, Schreiber SL, Wang X (2011) A selective inhibitor and probe of the cellular functions of Jumonji C domain-containing histone demethylases. J Am Chem Soc 133(24):9451–9456. doi:10.1021/ja201597b
Lee HY, Yang EG, Park H (2013) Hypoxia enhances the expression of prostate-specific antigen by modifying the quantity and catalytic activity of Jumonji C domain-containing histone demethylases. Carcinogenesis 34(12):2706–2715. doi:10.1093/carcin/bgt256
Franci G, Sarno F, Nebbioso A,Altucci L (2016) Identification and characterization of PKF118-310 as a KDM4A inhibitor. Epigenetics:0. doi:10.1080/15592294.2016.1249089
Arrowsmith CH, Bountra C, Fish PV, Lee K, Schapira M (2012) Epigenetic protein families: a new frontier for drug discovery. Nat Rev Drug Discov 11(5):384–400. doi:10.1038/nrd3674
Rose NR, Woon EC, Kingham GL, King ON, Mecinovic J, Clifton IJ, Ng SS, Talib-Hardy J, Oppermann U, McDonough MA, Schofield CJ (2010) Selective inhibitors of the JMJD2 histone demethylases: combined nondenaturing mass spectrometric screening and crystallographic approaches. J Med Chem 53(4):1810–1818. doi:10.1021/jm901680b
Wang L, Chang J, Varghese D, Dellinger M, Kumar S, Best AM, Ruiz J, Bruick R, Pena-Llopis S, Xu J, Babinski DJ, Frantz DE, Brekken RA, Quinn AM, Simeonov A, Easmon J, Martinez ED (2013) A small molecule modulates Jumonji histone demethylase activity and selectively inhibits cancer growth. Nat Commun 4:2035. doi:10.1038/ncomms3035
Cascella B, Lee SG, Singh S, Jez JM, Mirica LM (2017) The small molecule JIB-04 disrupts O2 binding in the Fe-dependent histone demethylase KDM4A/JMJD2A. Chem Commun (Camb) 53(13):2174–2177. doi:10.1039/c6cc09882g
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This research was supported by Basic Science Research Program through the National Research Foundation (NRF) funded by the Ministry of Science, ICT & Future Planning (2015R1C1A2A01053928).
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Lee, H.J., Kim, BK., Yoon, K.B. et al. Novel inhibitors of lysine (K)-specific Demethylase 4A with anticancer activity. Invest New Drugs 35, 733–741 (2017). https://doi.org/10.1007/s10637-017-0496-2
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DOI: https://doi.org/10.1007/s10637-017-0496-2