Virtual screening and in-vitro validation of novel inhibitors of influenza virus PA endonuclease

Vaccination and antiviral agents are the primary measures against human influenza viruses. However, both interventions have shortcomings, and hence, there is an urgent need to develop new and more efficacious anti-influenza virus drugs. The influenza virus RNA-dependent RNA polymerase complex (RdRp), a heterotrimeric protein complex that is responsible for viral RNA transcription, represents an unexplored target for antiviral drug development. One particularly attractive approach is interference with the endonucleolytic "cap-snatching" reaction by the PA subunit of the RdRp, more precisely by inhibiting the metal-dependent catalytic activity which resides in the N-terminal part of PA (PA-Nter). In the last two decades, several small molecule PA inhibitors (PAIs) have been discovered. Among them, compounds belonging to the class of substituted 2,4-dioxobutanoic acids were identified as particularly potent and selective PAIs in both enzyme and cell-based assays. A few other classes of potential PAIs have been identified. All these diverse compounds bear distinct pharmacophoric fragments with chelating motifs able to bind the bivalent metal ions in the catalytic core of PANter. More recently, the availability of crystallographic structures of PANter has enabled rational design of PAIs with improved binding properties. Here, we present a new coupled pharmacophore/docking virtual screening approach that allowed us to identify novel PAIs having interesting inhibitory activity in a PA-Nter enzymatic assay, as well as antiviral activity in a cell-based influenza virus yield assay.