RNA-targeting small molecule drug discovery has greatly benefitted from the available cellular models for disease. The use of cell culture in early development has become a requirement for assessing the basic efficacy of a drug candidate. Thus, more research groups have implemented these techniques in their programs. In a leading example, Al-Hashimi and coworkers identified six small molecules with high affinity for TAR of HIV-1 through a computational approach. They docked a library of small molecules onto RNA dynamic structures generated by NMR and Molecular Dynamics (MD) simulations. The hit molecules inhibited the Tat—TAR interaction in vitro. They arrived at lead molecule, netilmicin, that had the best selectivity for HIV-1 TAR and inhibited HIV-1 replication in cells with a low IC50. The Disney group has studied aminoglycoside derivatives in 2009 for their ability to inhibit interactions between repeat RNA and proteins. Using their prediction database INFORNA, they discovered that a compound could bind to 1 x 1 UU internal loops on an N-methyl peptide backbone. They confirmed that like other compounds that target DM1 r(CUG), they could inhibit the complex between r(CUG)-MBNL1, disrupt nuclear foci, and increase nucleocytoplasmic transport of the gene in patient-derived DM1 fibroblasts. In that study the Disney group also described several approaches to validate the RNA targets of small molecules. In the first approach termed chemical cross-linking and isolation by pull down (Chem-CLIP) and chemical cross-linking and isolation by pull down to map binding sites (Chem-CLIP-Map).
