Screening Methods to Identify RNA-Targeting Small Molecules

RNA molecules are promising drug targets due to their genomic prevalence, disease involvement, and druggable complex structures. Successful examples include RNA-targeting small molecule drugs for spinal muscular atrophy (SMA), with on-going efforts in other RNA-related diseases.

Here, Dr. Zhifeng Yu presents our toolbox for discovering RNA-targeting small molecules, with a focus on unique DNA-encoded libraries (DEL). Using DEL, we have identified several compounds against diverse RNA targets, including the human SMN2 (survival of motor neuron 2) mRNA. Rigorous validation using established assays such as SPR, ASMS, FID, and cellular splicing assays confirms the functionality of the DEL-selected compound in regulating SMN2 splicing. Additionally, SHAPE-MaP analysis provides insights into the compound’s potential mechanism of action.

Our findings demonstrate the feasibility of screening RNA-targeting small molecules using DEL. Furthermore, we highlight alternative screening methods to identify RNA-targeting compounds, along with valuable downstream biophysical and biochemical validation techniques.