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Structure-guided development of YEATS domain inhibitors by targeting π-π-π stacking

Nature Chemical Biology volume 14, pages 1140–1149 (2018)Cite this article

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Abstract

Chemical probes of epigenetic ‘readers’ of histone post-translational modifications (PTMs) have become powerful tools for mechanistic and functional studies of their target proteins in normal physiology and disease pathogenesis. Here we report the development of the first class of chemical probes of YEATS domains, newly identified ‘readers’ of histone lysine acetylation (Kac) and crotonylation (Kcr). Guided by the structural analysis of a YEATS–Kcr complex, we developed a series of peptide-based inhibitors of YEATS domains by targeting a unique π-π-π stacking interaction at the proteins’ Kcr recognition site. Further structure optimization resulted in the selective inhibitors preferentially binding to individual YEATS-containing proteins including AF9 and ENL with submicromolar affinities. We demonstrate that one of the ENL YEATS-selective inhibitors, XL-13m, engages with endogenous ENL, perturbs the recruitment of ENL onto chromatin, and synergizes the BET and DOT1L inhibition-induced downregulation of oncogenes in MLL-rearranged acute leukemia.

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Fig. 1: Targeting the π-π-π stacking for YEATS inhibition.
Fig. 2: Characterization and optimization of inhibitory effects.
Fig. 3: Molecular basis underlying the AF9 YEATS and XL-07i interaction.
Fig. 4: Development of ENL YEATS-selective inhibitors.
Fig. 5: Selective engagement of XL-13m with endogenous ENL.
Fig. 6: XL-13m perturbs ENL–chromatin interaction and synergizes with BET and DOT1L inhibition.

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Data availability

Crystal structure data of AF9 YEATS domain bound to inhibitor XL-07i has been deposited in the Protein Data Bank (PDB) under accession code 5YYF. Other data support the findings of this study are included in the article and/or the associated supplementary files, or available from the corresponding authors upon reasonable request.

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Acknowledgements

We acknowledge support from the Hong Kong Research Grants Council Collaborative Research Fund (CRF C7029-15G to X.D.L.), the Areas of Excellence Scheme (AoE/P-705/16 to X.D.L.), the General Research Fund (GRF 17126618, 17125917 and 17303114 to X.D.L.), and the Early Career Scheme (ECS; HKU 709813P to X.D.L.). We acknowledge the National Natural Science Foundation of China (21572191 and 91753130 to X.D.L and 31725014 to H.L.), National Key R&D Program of China (2016YFA0500700 to H.L.), National Institutes of Health (1R01CA204639-01 to C.D.A.), the Leukemia and Lymphoma Society (LLS-SCOR 7006-13 to C.D.A), and funds from The Rockefeller University (to C.D.A.). Y.L. is a Tsinghua Advanced Fellow. L.W. is a fellow of the Jane Coffin Childs Memorial Fund. We acknowledge support from Beijing Metropolis for the Beijing Novo Program (Z181100006218068 to Y.L.) and China Association for Science and Technology for the Young Elite Scientists Sponsorship Program (to Y.L.). We thank the staff members at beamline BL17U1 the Shanghai Synchrotron Radiation Facility and S. Fan at Tsinghua Center for Structural Biology for their assistance in data collection and the China National Center for Protein Sciences Beijing for providing facility support. We thank H. Sun at Department of Chemistry, City University of Hong Kong for providing plasmid of the second BrD of BRD4. We thank A.Y.-H. Leung at Department of Medicine, the University of Hong Kong for providing the MV4;11 cell line.

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  1. These authors contributed equally: Xin Li, Xiao-Meng Li.

Authors and Affiliations

  1. Department of Chemistry, The University of Hong Kong, Hong Kong, China

    Xin Li, Xiao-Meng Li, Yixiang Jiang, Zheng Liu, Yiwen Cui, Ka Yi Fung, Stan H. E. van der Beelen, Gaofei Tian & Xiang David Li

  2. Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, USA

    Liling Wan & C. David Allis

  3. Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

    Xiaobing Shi

  4. MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China

    Haitao Li & Yuanyuan Li

  5. Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China

    Haitao Li & Yuanyuan Li

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Contributions

X.D.L. conceived the research project. X.L., X.-M.L., H.L., Y.L., and X.D.L. designed the experiments and analyzed the data. X.L., Y.J., Z.L., K.Y.F., and S.H.E.v.d.B. carried out the small-molecule and peptide synthesis. X.L., Y.C., Z.L., G.T., and Y.L. expressed and purified the proteins. X.L. performed the in vitro competition assay and ITC experiments. Y.L. and H.L. resolved the crystal structure and performed in silico modeling studies. X.-M.L. carried out the CETSA, ChIP-qPCR, and RT-qPCR experiments. L.W., C.D.A, and X.S. provided discussions and unpublished preliminary data. H.L. and X.D.L. supervised the work in their respective fields. X.L., Y.L. and X.D.L. wrote the manuscript with inputs from X.-M.L. and H.L.

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Correspondence to Yuanyuan Li or Xiang David Li.

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Competing interests

X.L. and X.D.L. have filed a patent application (US Provisional Application No. 62/590,690) related to the peptide-based inhibitors reported in this manuscript.

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Li, X., Li, XM., Jiang, Y. et al. Structure-guided development of YEATS domain inhibitors by targeting π-π-π stacking. Nat Chem Biol 14, 1140–1149 (2018). https://doi.org/10.1038/s41589-018-0144-y

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