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Precise small-molecule recognition of a toxic CUG RNA repeat expansion

Abstract

Excluding the ribosome and riboswitches, developing small molecules that selectively target RNA is a longstanding problem in chemical biology. A typical cellular RNA is difficult to target because it has little tertiary, but abundant secondary structure. We designed allele-selective compounds that target such an RNA, the toxic noncoding repeat expansion (r(CUG)exp) that causes myotonic dystrophy type 1 (DM1). We developed several strategies to generate allele-selective small molecules, including non-covalent binding, covalent binding, cleavage and on-site probe synthesis. Covalent binding and cleavage enabled target profiling in cells derived from individuals with DM1, showing precise recognition of r(CUG)exp. In the on-site probe synthesis approach, small molecules bound adjacent sites in r(CUG)exp and reacted to afford picomolar inhibitors via a proximity-based click reaction only in DM1-affected cells. We expanded this approach to image r(CUG)exp in its natural context.

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Figure 1: A rationally designed small molecule improves DM1-associated defects in patient-derived cells.
Figure 2: Covalent (Chem-CLIP) approach to inhibit r(CUG)exp dysfunction and assess cellular selectivity.
Figure 3: Cleavage-based (Ribo-SNAP) approach to inhibit r(CUG)exp dysfunction and assess cellular selectivity.
Figure 4: r(CUG)exp-dependent synthesis of multivalent RNA-binding compounds in vitro and in cells.
Figure 5: FRET-based approach to image RNA targets in cells.

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Acknowledgements

We thank T. Kodadek, G. Joyce, W. Ja, J. Childs-Disney, K. Sobczak and J. Cleveland for advice and critical review of the manuscript, and M.D.D. acknowledges J. and H. (nee McDougall) Disney. We also thank the platform for immortalization of human cells from the Institut de Myologie. This work was funded by the US National Institutes of Health (grants DP1NS096898 to M.D.D. and DP1NS096787 to R.Y.) and the Muscular Dystrophy Association (grant 380467 to M.D.D.). S.G.R. was partially supported by a postdoctoral fellowship from the Myotonic Dystrophy Foundation.

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Authors

Contributions

M.D.D. directed the study, conceived of the ideas and designed experiments. S.G.R. designed experiments, synthesized all of the compounds and conducted all of the biochemical and cellular studies. Y.N. contributed to the synthesis of compounds. L.A.C. performed the FRET imaging. R.Y. contributed to the FRET studies. M.D.C. contributed to compound stability studies. D.F. provided critical reagents.

Corresponding author

Correspondence to Matthew D Disney.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Figures 1–14 and Supplementary Tables 1 and 2. (PDF 3349 kb)

Supplementary Note

Synthetic Procedures. (PDF 3737 kb)

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Rzuczek, S., Colgan, L., Nakai, Y. et al. Precise small-molecule recognition of a toxic CUG RNA repeat expansion. Nat Chem Biol 13, 188–193 (2017). https://doi.org/10.1038/nchembio.2251

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