Insights into the development of chemical probes for RNA

Morgan, Brittany S; Forte, Jordan E; Hargrove, Amanda E

High-throughput and focused computational screens were used to identify four small molecules [ Figure 4A ]. Two small molecules were identified by docking against experimentally determined structures of HIV-1 TAR (54) and RRE RNA (48) . In another example, small molecules were modeled into an X-ray diffraction structure of the xpt-pbuE guanine riboswitch aptamer after the native ligand was removed (46) . Criteria such as geometrical constraints, hydrogen bonding patterns, and molecule planarity were used to assess the 'fit' of the ligand, leading to the selection of two small molecules, one of which had antimicrobial activity against 9 of the 15 Gram-positive bacteria species tested and was selective for species with the guaA gene under riboswitch control. The fourth example utilized a computationally-predicted 3D structure of the severe acute respiratory syndrome coronavirus (SARS-CoV) pseudoknot (55) . A library of 80 000 small molecules was docked against the predicted structure, and the 58 highest scoring molecules were tested in an in vitro activity-based assay. The screen resulted in a biologically active ligand with an IC 50 value of 0.45 M in cell-based models. Additional advances in computational structural prediction and RNA:ligand docking will undoubtedly lead to improved computational primary screens and thus more efficient experimental screens (56, 57) .