Fig. 1: Library-versus-library screening defines new RNA-binding small molecules and druggable targets.

a, 2DCS analysis of more than 61 million theoretical interactions, identifying new interactions between small molecules and RNA motifs. b, The newly identified small-molecule RNA binders (n = 344) included 156 different scaffolds that fall into 79 major classes based on scaffold similarities. Among the top 10 most abundant classes (collectively covering 59.6% of all hits), six are new classes (green). c, Motif distribution from a 3 × 3 randomized RNA library used for 2DCS screening. As expected, 3 × 3 and 2 × 2 internal loops comprise the majority (85.4% total) of the library. Motifs that bound to C1–C6 showed a significant enrichment for 3 × 3 internal loops (P < 0.001) and one-nucleotide bulges (P < 0.001). A total of 1,044 motifs bound to C1–C20 with Z_obs > 8. Preference for 3 × 3 internal loops and one-nucleotide bulges was collectively observed for these compounds. Of these 1,044 motifs, only 23 (2.2%) are present in highly expressed human transcripts (n = 2,712 total motifs), and 375 are new motifs with no previously known small-molecule binder. Inforna contains over 100,000 RNA–small molecule interactions and 6,453 unique RNA motifs of various types. d, Although around 6% of all miRNAs can be bound by C1–C6, only about 30% of targetable sites within them are functional (Drosha or Dicer processing site) and are therefore predicted to induce a biological effect. The other approximately 70% are unproductive interactions that are predicted to be biologically silent. We identified that 48% of miRNAs that have ligandable non-functional sites are potential substrates for RNase L, which could be targeted by RIBOTACs. Thus, biologically inert binders can be converted into bioactive RIBOTACs that provoke targeted degradation. Statistical significance referred to in c was calculated using two-tailed Student’s t-tests.