Novel neuraminidase inhibitors: identification, biological evaluation and investigations of the binding mode

Background: The pathogenicity of influenza A and B viruses depends on the function of influenza neuraminidase (NA). Emerging resistant influenza A viruses of subtype H1N1 increasingly challenge the effectiveness of established NA inhibitors. Recent computational studies have indicated several weak points of NA that can be exploited for rational inhibitor design to conquer this imminent threat, such as the opening of the binding pocket due to the flexibility of the 150-, 245- and 430-loops. Methods: We employed shape-focused virtual screening based on a recently discovered lead compound, katsumadain A, to identify novel promising compounds with significant inhibitory efficacy on NA and resistance-breaking capacity on oseltamivir-resistant strains. A potential binding mode of these compounds was derived employing ligand-based techniques and protein-ligand docking using representative protein conformations selected from molecular dynamics simulations. Results: Five novel compounds were identified by virtual screening. Their IC50 values, determined in chemiluminescence-based NA inhibition assays, are in the range of 0.18-17 mu M. In particular, artocarpin exhibits high affinity toward three H1N1 oseltamivir-sensitive influenza A viruses. It also inhibits the NA of an oseltamivir-resistant H1N1 isolate.