SMN2 splice modulators enhance U1–pre-mRNA association and rescue SMA mice

A Corrigendum to this article was published on 18 March 2016

A Corrigendum to this article was published on 18 August 2015

This article has been updated

Abstract

Spinal muscular atrophy (SMA), which results from the loss of expression of the survival of motor neuron-1 (SMN1) gene, represents the most common genetic cause of pediatric mortality. A duplicate copy (SMN2) is inefficiently spliced, producing a truncated and unstable protein. We describe herein a potent, orally active, small-molecule enhancer of SMN2 splicing that elevates full-length SMN protein and extends survival in a severe SMA mouse model. We demonstrate that the molecular mechanism of action is via stabilization of the transient double-strand RNA structure formed by the SMN2 pre-mRNA and U1 small nuclear ribonucleic protein (snRNP) complex. The binding affinity of U1 snRNP to the 5′ splice site is increased in a sequence-selective manner, discrete from constitutive recognition. This new mechanism demonstrates the feasibility of small molecule–mediated, sequence-selective splice modulation and the potential for leveraging this strategy in other splicing diseases.

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Figure 1: Screening paradigm and molecules.
Figure 2: Small molecules modulate SMN levels in vivo.
Figure 3: Gene- and transcript-level changes in response to NVS-SM1.
Figure 4: NVS-SM2 sequence selectively alters exon splicing.
Figure 5: NVS-SM2 binds to and stabilizes the U1 snRNP:5′ss RNA complex.
Figure 6: Computational model and schematic of mechanism of action.

Change history

  • 15 July 2015

    The authors forgot to include a description of the measurement of SMN protein levels in tissue samples in the Online Methods. This description has been included in the HTML and PDF versions of the article.

  • 11 February 2016

    In the version of this article originally published online, the schematic for the construct in Figure 4a was incorrect. A corrected figure has been provided in the HTML and PDF versions of the article.

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Acknowledgements

The authors wish to acknowledge members of the Novartis Institutes for BioMedical Research (NIBR) Leadership Spinal Muscular Atrophy Advisory Board (J. Hastewell, J. Bell, K. Briner, P. Bouchard, E. Beckman and G. Kwei), NIBR Project Management (D. Silva and C. Gauthier) and NIBR Translational Medicine (R. Roubenoff) for their advice and contributions to the drug discovery efforts; J.R. Kerrigan, D. Glass, P. Manos, F. Harbinski, C. Mickanin, R.E.J. Beckwith, R. Sun, W. Broom, S.J. Luchanksy, L. Murphy, M. Schirle, J. Duca, R. Chopra and K. Clark for their contributions to experimental efforts and insights on the manuscript; S.J. Burden (NYU School of Medicine) for his gift of SMNΔ7 mouse myoblasts; K. Mineev and A.S. Arseniev for their assistance with NMR peak assignments; A. Abrams for his artwork in the schematic diagram; the SMA Foundation (K. Chen, D. Kobayashi, S. Paushkin and L. Eng) for their advice and contributions to the drug discovery efforts; Psychogenics (S. Ramboz and K. Cirillo); and PharmOptima (D. Decker, R. Poorman and P. Zaworski) for their contributions to in vivo studies.

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Contributions

C.S., T.M.S. and R.S. performed the high-throughput screen. A.K.C., L.S., L.G.H. and N.A.D. performed the chemical synthesis. C.S., M.V.H., Y.S., C. Blaustein, F.B., A.L. and R.S. performed cell-based structure-activity experiments. M.V.H., Y.S., R.S., M.J., L.D., C. Bullock, M.M., W.F.D. and R.S. performed in vivo experiments. J.P., C.G.K., M.B., N.A.R., X.S., M.H., S.S., L.M., G.R. and R.S. performed the RNAseq experiments. J.P. and C.S. performed the chimera experiments. S.E.S., M.S. and J.R.T. performed the biochemistry and biophysics experiments. X.Z. and M.J.J.B. performed the NMR experiments. D.N.C. performed the computational modeling. L.G.H. and N.A.D. supervised the medicinal chemistry experiments. M.J., B.S.T., W.F.D. and R.S. provided intellectual input to the in vivo mouse biology experiments. B.S.T., J.A.P., D.C., M.C.F. and R.S. provided intellectual input to the overall drug discovery studies. G.A.M., J.A.P., V.E.M. and J.A.T. provided intellectual input to the mechanism of action studies. N.A.D. and R.S. directed the drug discovery experiments. J.P. and S.E.S. directed the mechanism-of-action experiments. J.P., S.E.S., J.A.T., N.A.D. and R.S. prepared the manuscript.

Corresponding authors

Correspondence to Susanne E Swalley or Rajeev Sivasankaran.

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Palacino, J., Swalley, S., Song, C. et al. SMN2 splice modulators enhance U1–pre-mRNA association and rescue SMA mice. Nat Chem Biol 11, 511–517 (2015). https://doi.org/10.1038/nchembio.1837

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