Fig. 4: Risdiplam and branaplam specificities are incompletely explained by the bulge-repair mechanism.
From: Specificity, synergy, and mechanisms of splice-modifying drugs
A, B Bulge-repair mechanism proposed for the specificity of risdiplam. NMR structures (PDB:6HMI [https://doi.org/10.2210/pdb6HMI/pdb] and PDB:6HMO [https://doi.org/10.2210/pdb6HMO/pdb], from ref. 20) show a U1 RNA/5’ss RNA complex in the (A) presence and (B) absence of SMN-C5, a risdiplam analog. A schematic of each structure is also shown. Red, U1 snRNA; brown, exonic 5’ss RNA; gray, intronic 5’ss RNA; green, SMN-C5; salmon, bulged A−1 stabilized by SMN-C5. Blue highlight, intronic positions observed to affect the activities of risdiplam and branaplam in panels (F) and (G). C–E Structures of (C) SMN-C5, (D) risdiplam, and (E) three tautomeric forms of branaplam (cis-keto, enol, and trans-keto). Yellow highlight, potential hydrogen-bonding partners for the amino group of A−1. Green highlight, rotational degree of freedom. F, G qPCR validation of intronic specificities for (F) risdiplam and (G) branaplam, assayed on the indicated single-nucleotide variants of AGGA/GUAAGU in the context of an SMN1 minigene. \(E\) denotes drug effect, which was measured by qPCR as described in SI Sec. 1.8. Note that \(E=1\) corresponds to no drug effect. Dots, n = 2 biological replicates; error bars, standard error across n = 4 technical replicates; dashed line, no effect; dashed/dotted line, wild-type effect value (geometric mean of biological replicates). Daggers indicate 5’ss variants for which the dominant inclusion isoform uses a cryptic 5’ss at position +52 of SMN1 intron 7.
