Specificity, synergy, and mechanisms of splice-modifying drugs

Ishigami, Y.; Wong, M. S.; Marti-Gomez, C.; Ayaz, A.; Kooshkbaghi, M.; Hanson, S.; McCandlish, D. M.; Krainer, A. R.; Kinney, J. B.

doi:10.1101/2022.12.30.522303

bioRxiv · 10.1101/2022.12.30.522303

Specificity, synergy, and mechanisms of splice-modifying drugs

Ishigami, Y.·Wong, M. S.·Marti-Gomez, C.·Ayaz, A.·Kooshkbaghi, M.·Hanson, S.·McCandlish, D. M.·Krainer, A. R.·Kinney, J. B.

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Abstract

Drugs that target pre-mRNA splicing hold great therapeutic potential, but the quantitative understanding of how these drugs work is limited. Here we introduce mechanistically interpretable quantitative models for the sequence-specific and concentration-dependent behavior of splice-modifying drugs. Using massively parallel splicing assays, RNA-seq experiments, and precision dose-response curves, we obtain quantitative models for two small-molecule drugs, risdiplam and branaplam, developed for treating spinal muscular atrophy. The results quantitatively characterize the specificities of risdiplam and branaplam for 5 splice site sequences, suggest that branaplam recognizes 5 splice sites via two distinct interaction modes, and disprove the prevailing two-site hypothesis for risdiplam activity at SMN2 exon 7. The results also show that anomalous single-drug cooperativity, as well as multi-drug synergy, are widespread among small-molecule drugs and antisense-oligonucleotide drugs that promote exon inclusion. Our quantitative models thus clarify the mechanisms of existing treatments and provide a basis for the rational development of new therapies.

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Ishigami, Y., Wong, M. S., Marti-Gomez, C., Ayaz, A., Kooshkbaghi, M., Hanson, S., McCandlish, D. M., Krainer, A. R., Kinney, J. B.. 2022-12-31. Specificity, synergy, and mechanisms of splice-modifying drugs. https://doi.org/10.1101/2022.12.30.522303

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