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Identification of small molecule inhibitors targeting the SMARCA2 bromodomain from a high-throughput screening assay


SMARCA2 is a critical catalytic subunit of the switch/sucrose non-fermenting (SWI/SNF) chromatin remodeling complexes. Dysregulation of SMARCA2 is associated with several diseases, including some cancers. SMARCA2 is multi-domain protein containing a bromodomain (BRD) that specifically recognizes acetylated lysine residues in histone tails, thus playing an important role in chromatin remodeling. Many potent and specific inhibitors targeting other BRDs have recently been discovered and have been widely used for cancer treatments and biological research. However, hit discovery targeting SMARCA2-BRD is particularly lacking. To date, there is a paucity of reported high-throughput screening (HTS) assays targeting the SMARCA2-BRD interface. In this study, we developed an AlphaScreen HTS system for the discovery of SMARCA2-BRD inhibitors and optimized the physicochemical conditions including pH, salt concentrations and detergent levels. Through an established AlphaScreen-based high-throughput screening assay against an in-house compound library, DCSM06 was identified as a novel SMARCA2-BRD inhibitor with an IC50 value of 39.9±3.0 μmol/L. Surface plasmon resonance demonstrated the binding between SMARCA2-BRD and DCSM06 (K d=38.6 μmol/L). A similarity-based analog search led to identification of DCSM06-05 with an IC50 value of 9.0±1.4 μmol/L. Molecular docking was performed to predict the binding mode of DCSM06-05 and to decipher the structural basis of the infiuence of chemical modifications on inhibitor potency. DCSM06-05 may be used as a starting point for further medicinal chemistry optimization and could function as a chemical tool for SMARCA2-related functional studies.

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  1. 1

    Hirschhorn JN, Brown SA, Clark CD, Winston F. Evidence that Snf2/Swi2 and Snf5 activate transcription in yeast by altering chromatin structure. Gene Dev 1992; 6: 2288–98.

  2. 2

    Wilson BG, Helming KC, Wang X, Kim Y, Vazquez F, Jagani Z, et al. Residual complexes containing SMARCA2 (BRM) underlie the oncogenic drive of SMARCA4 (BRG1) mutation. Mol Cell Biol 2014; 34: 1136–44.

  3. 3

    Zhou J, Zhang M, Fang H, El-Mounayri O, Rodenberg JM, Imbalzano AN, et al. The SWI/SNF chromatin remodeling complex regulates myocardin-induced smooth muscle-specific gene expression. Arterioscler Thromb Vasc Biol 2009; 29: 921–8.

  4. 4

    Wang GG, Allis CD, Chi P. Chromatin remodeling and cancer, Part II: ATP-dependent chromatin remodeling. Trends Mol Med 2007; 13: 373–80.

  5. 5

    Zhang Z, Wang F, Du C, Guo H, Ma L, Liu X, et al. BRM/SMARCA2 promotes the proliferation and chemoresistance of pancreatic cancer cells by targeting JAK2/STAT3 signaling. Cancer Lett 2017; 402: 213–24.

  6. 6

    Philpott M, Yang J, Tumber T, Fedorov O, Uttarkar S, Filippakopoulos P, et al. Bromodomain-peptide displacement assays for interactome mapping and inhibitor discovery. Mol Biosyst 2011; 7: 2899–908.

  7. 7

    Chandrasekaran R, Thompson M. Polybromo-1-bromodomains bind histone H3 at specific acetyl-lysine positions. Biochem Biophys Res Commun 2007; 355: 661–6.

  8. 8

    Sun Z, Zhang H, Chen Z, Xie Y, Jiang H, Chen L, et al. Discovery of novel BRD4 inhibitors by high-throughput screening, crystallography, and cell-based assays. Bioorg Med Chem Lett 2017; 27: 2003–9.

  9. 9

    Muchardt C, Reyes JC, Bourachot B, Leguoy E, Yaniv M. The HBRM and BRG-1 proteins, components of the human SNF/SWI complex, are phosphorylated and excluded from the condensed chromosomes during mitosis. EMBO J 1996; 15: 3394–402.

  10. 10

    Sanchez R, Zhou MM. The role of human bromodomains in chromatin biology and gene transcription. Curr Opin Drug Discov Devel 2009; 12: 659–65.

  11. 11

    Marmorstein R, Berger SL. Structure and function of bromodomains in chromatin-regulating complexes. Gene 2001; 272: 1–9.

  12. 12

    Biegel JA, Busse TM, Weissman BE. SWI/SNF chromatin remodeling complexes and cancer. Am J Med Genet C Semin Med Genet 2014; 166C: 350–66.

  13. 13

    Gui Y, Guo G, Huang Y, Hu X, Tang A, Gao S, et al. Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat Genet 2011; 43: 875–8.

  14. 14

    Hohmann AF, Vakoc CR. A rationale to target the SWI/SNF complex for cancer therapy. Trends Genet 2014; 30: 356–63.

  15. 15

    Delmore JE, Issa GC, Lemieux ME, Rahl PB, Shi J, Jacobs HM, et al. BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell 2011; 146: 904–17.

  16. 16

    Perez-Salvia M, Esteller M. Bromodomain inhibitors and cancer therapy: From structures to applications. Epigenetics 2017; 12: 323–39.

  17. 17

    Smith SG, Zhou MM. The bromodomain: a new target in emerging epigenetic medicine. ACS Chem Biol 2016; 11: 598–608.

  18. 18

    Jung M, Gelato KA, Fernandez-Montalvan A, Siegel S, Haendler B. Targeting BET bromodomains for cancer treatment. Epigenomics 2015; 7: 487–501.

  19. 19

    Sanchez R, Meslamani J, Zhou MM. The bromodomain: from epigenome reader to druggable target. Biochim Biophys Acta 2014; 1839: 676–85.

  20. 20

    Gerstenberger BS, Trzupek JD, Tallant C, Fedorov O, Filippakopoulos P, Brennan PE, et al. Identification of a chemical probe for family VIII bromodomains through optimization of a fragment hit. J Med Chem 2016; 59: 4800–11.

  21. 21

    Zhang WY, Lu WC, Jiang H, Lv ZB, Xie YQ, Lian FL, et al. Discovery of alkyl bis (oxy) dibenzimidamide derivatives as novel protein arginine methyltransferase 1 (PRMT1) inhibitors. Chem Biol Drug Des 2017; 1–11.

  22. 22

    Baell JB, Holloway GA. New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. J Med Chem 2010; 53: 2719–40.

  23. 23

    Wen Y, Xu L, Chen FL, Gao J, Li JY, Hu LH, et al. Discovery of a novel inhibitor of NAD(P)(+)-dependent malic enzyme (ME2) by high-throughput screening. Acta Pharmacol Sin 2014; 35: 674–84.

  24. 24

    Zhang TT, Huang ZT, Dai Y, Chen XP, Zhu P, Du GH. High-throughput fluorescence polarization method for identifying ligands of LOX-1. Acta Pharmacol Sin 2006; 27: 447–52.

  25. 25

    Zhu MR, Du DH, Hu JC, Li LC, Liu JQ, Ding H, et al. Development of a high-throughput fluorescence polarization assay for the discovery of EZH2-EED interaction inhibitors. Acta Pharmacol Sin 2018; 39: 302–10.

  26. 26

    Zhang JH, Chung TDY, Oldenburg KR. A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J Biomol Screen 1999; 4: 67–73.

  27. 27

    Shockley KR. Quantitative high-throughput screening data analysis: challenges and recent advances. Drug Discov Today 2015; 20: 296–300.

  28. 28

    Sui Y, Wu Z. Alternative statistical parameter for high-throughput screening assay quality assessment. J Biomol Screen 2007; 12: 229–34.

  29. 29

    Vangamudi B, Paul TA, Shah PK, Kost-Alimova M, Nottebaum L, Shi X, et al. The SMARCA2/4 ATPase domain surpasses the bromodomain as a drug target in SWI/SNF-Mutant cancers: insights from cDNA rescue and PFI-3 inhibitor studies. Cancer Res 2015; 75: 3865–78.

  30. 30

    Myszka DG. Kinetic analysis of macromolecular interactions using surface plasmon resonance biosensors. Curr Opin Biotech 1997; 8: 50–7.

  31. 31

    Harner MJ, Chauder BA, Phan J, Fesik SW. Fragment-based screening of the bromodomain of ATAD2. J Med Chem 2014; 57: 9687–92.

  32. 32

    Picaud S, Fedorov O, Thanasopoulou A, Leonards K, Jones K, Meier J, et al. Generation of a selective small molecule inhibitor of the CBP/p300 bromodomain for leukemia therapy. Cancer Res 2015; 75: 5106–19.

  33. 33

    Laskowski RA, Swindells MB. LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J Chem Inf Model 2011; 51: 2778–86.

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The authors disclose receipt of the following financial support for the research and/or authorship of this article: the Ministry of Science and Technology of China (2017YFB0202600 to Shi-jie CHEN and 2015CB910304 to Yuan-yuan ZHANG); the National Natural Science Foundation of China (21472208 and 81625022 to Cheng LUO and 81430084 to Kai-xian CHEN). We are extremely grateful to the National Centre for Protein Science Shanghai (Shanghai Science Research Center, Protein Expression and Purification system) for their instrumental support and technical assistance.

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Correspondence to Kai-xian Chen or Hui-fang Chai or Cheng Luo.

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  • AlphaScreen
  • high-throughput screening
  • bromodomain
  • small molecule inhibitor

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