Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
Beam Therapeutics, Cambridge, MA, 02142, USA.
Nat Commun. 2024 Feb 29;15(1):1880. doi: 10.1038/s41467-024-46090-5.
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 contradict 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.
靶向前体 mRNA 剪接的药物具有很大的治疗潜力，但人们对这些药物如何发挥作用的定量理解有限。在这里，我们引入了用于解释剪接修饰药物序列特异性和浓度依赖性行为的基于机制的可解释定量模型。我们使用大规模平行剪接测定、RNA-seq 实验和精确剂量反应曲线，获得了两种用于治疗脊髓性肌萎缩症的小分子药物，risdiplam 和 branaplam 的定量模型。研究结果定量描述了 risdiplam 和 branaplam 对 5'剪接位点序列的特异性，表明 branaplam 通过两种不同的相互作用模式识别 5'剪接位点，并且与 risdiplam 在 SMN2 外显子 7 上的活性的流行的双位点假说相矛盾。研究结果还表明，异常的单药协同作用以及促进外显子包含的小分子药物和反义寡核苷酸药物的多药协同作用非常普遍。因此，我们的定量模型阐明了现有治疗方法的机制，并为新疗法的合理开发提供了基础。
