BPS2026 – Study of small-molecule binders to a conserved influenza A virus RNA structural motif by NMR

Influenza A virus (IAV) is a significant and growing global health threat. RNA structural elements within its genome perform functions required for viral replication and provide promising targets for drug-like small molecules because of their strong conservation across segments and viral strains. One such element, the packaging stem-loop 2 (PSL2), is conserved across all known IAV isolates and has been shown to mediate in vitro packaging and disease in in-vivo models. We selected PSL2 as the target for structure determination and screening against our small-molecule libraries. Using nuclear magnetic resonance (NMR) spectroscopy in combination with small-angle X-ray scattering (SAXS), we investigated the three-dimensional structure of an RNA fragment (pSL39nt) encompassing the critical PSL2 region of the IAV genome. Structure modeling with experimental restraints identifies a structurally plastic 11-nucleotide internal loop abutted by two stable helices. Partially structured internal loops represent attractive binding targets for small molecules, which can potentially stabilize the RNA conformation upon binding. Consistent with this, we found certain small molecules to bind pSL39nt with nanomolar affinity. We are establishing the thermodynamic characteristics of this interaction using biophysical approaches, such as fluorescence and will seek to establish the three-dimensional structure of the complex. These findings highlight the feasibility of targeting highly conserved RNA elements in the IAV genome with small molecules, providing a framework for the development of novel antiviral strategies that may overcome the limitations of current protein-focused approaches.