Identification of novel ligands for the RNA pseudoknot that regulate −1 ribosomal frameshifting

In many viruses, −1 ribosomal frameshifting (−1RF) regulates synthesis of proteins and is crucial for virus production. An RNA pseudoknot is one of the essential components of the viral −1RF system. Thermodynamic or kinetic control of pseudoknot folding may be important in regulating the efficiency of −1RF. Thus, small molecules that interact with viral RNA pseudoknots may disrupt the −1RF system and show antiviral activity. In this study, we conducted virtual screening of a chemical database targeting the X-ray crystal structure of RNA pseudoknot complexed with biotin to identify ligands that may regulate an −1RF system containing biotin-aptamer as an RNA pseudoknot component. After docking screening of about 80,000 compounds, 58 high-ranked hits were selected and their activities were examined by in vitro and cell-based −1 frameshifting assays. Six compounds increased the efficiency of −1 frameshifting, and these are novel small molecule compounds that regulate the −1RF.