Abstract
The discovery of inhibitors of methyl- and acetyl-binding domains has provided evidence for the 'druggability' of epigenetic effector molecules. The small-molecule probe UNC1215 prevents methyl-dependent protein-protein interactions by engaging the aromatic cage of MBT domains and, with lower affinity, Tudor domains. Using a library of tagged UNC1215 analogs, we screened a protein-domain microarray of human methyllysine effector molecules to rapidly detect compounds with new binding profiles with either increased or decreased specificity. Using this approach, we identified a compound (EML405) that acquired a novel interaction with the Tudor-domain-containing protein Spindlin1 (SPIN1). Structural studies facilitated the rational synthesis of SPIN1 inhibitors with increased selectivity (EML631–633), which engage SPIN1 in cells, block its ability to 'read' H3K4me3 marks and inhibit its transcriptional-coactivator activity. Protein microarrays can thus be used as a platform to 'target-hop' and identify small molecules that bind and compete with domain-motif interactions.
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Acknowledgements
M.T.B. was supported by an NIH grant (DK062248) and a CPRIT grant (RP130432) for the protein array analysis. The deep sequencing was supported by a CPRIT grant (RP120348) to J.S. The Center for Cancer Epigenetics at MDACC also supported this study. G.S. was supported by grants from the Italian Ministero dell'Istruzione, dell'Universita e della Ricerca (MIUR), Progetti di Ricerca di Interesse Nazionale (PRIN 2012ZHN9YH), the Universita di Salerno (Italy) and the European Cooperation in Science and Technology (COST Action CM1406). H.L. was supported by grants from the Major State Basic Research Development Program in China (2015CB910503 and 2016YFA0500700) and the Tsinghua University Initiative Scientific Research Program. N.B. was supported by the Odyssey Fellowship Program at the University of Texas MD Anderson Cancer Center. We thank the staff members at beamlines BL17U and BL18U of the Shanghai Synchrotron Radiation Facility for assistance in data collection.
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M.T.B. and G.S. conceived the project. N.B. and D.C. carried out the cell-based and competition experiments. C.S., C.J. and M.I.K. constructed, maintained and probed the protein-domain microarrays. M.V., S.C. and G.S. designed and synthesized the compounds used in this study. X.S., X.B. and H.L. performed the structural studies and ITC experiments. J.S. performed the deep sequencing. K.C. and J.L. performed the bioinformatics analysis of the RNA-seq data sets. M.T.B., G.S. and H.L. wrote the manuscript and supervised the work in their respective fields.
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Bae, N., Viviano, M., Su, X. et al. Developing Spindlin1 small-molecule inhibitors by using protein microarrays. Nat Chem Biol 13, 750–756 (2017). https://doi.org/10.1038/nchembio.2377
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DOI: https://doi.org/10.1038/nchembio.2377
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