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

Abstract

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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Acknowledgements

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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Keywords

  • AlphaScreen
  • high-throughput screening
  • SMARCA2
  • bromodomain
  • small molecule inhibitor

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