Structure-based design of novel naproxen derivatives targeting monomeric nucleoprotein of Influenza A virus

Abstract

The nucleoprotein (NP) binds the viral RNA genome as oligomers assembled with the polymerase in a ribonucleoprotein complex required for transcription and replication of influenza A virus. Novel antiviral candidates targeting the nucleoprotein either induced higher order oligomers or reduced NP oligomerization by targeting the oligomerization loop and blocking its insertion into adjacent nucleoprotein subunit. In this study, we used a different structure-based approach to stabilize monomers of the nucleoprotein by drugs binding in its RNA-binding groove. We recently identified naproxen as a drug competing with RNA binding to NP with antiinflammatory and antiviral effects against influenza A virus. Here, we designed novel derivatives of naproxen by fragment extension for improved binding to NP. Molecular dynamics simulations suggested that among these derivatives, naproxen A and C0 were most promising. Their chemical synthesis is described. Both derivatives markedly stabilized NP monomer against thermal denaturation. Naproxen C0 bound tighter to NP than naproxen at a binding site predicted by MD simulations and shown by competition experiments using wt NP or single-point mutants as determined by surface plasmon resonance. MD simulations suggested that impeded oligomerization and stabilization of monomeric NP is likely to be achieved by drugs binding in the RNA grove and inducing close to their binding site conformational changes of key residues hosting the oligomerization loop as observed for the naproxen derivatives. Naproxen C0 is a potential antiviral candidate blocking influenza nucleoprotein function.

Keywords:

• viral RNA
• nucleoprotein
• oligomerization
• molecular modelling
• drug design

Additional information

Funding

Funding. This work was supported by the French agency for research (ANR) for funding (Flunucleovir, ANR-2010-Blanc-1307-01 to A.S.). This work was granted access to the HPC resources of IDRIS made by GENCI (Grand Equipment National de Calcul Intensif) under the grants 2010-99636, 2011-076378 and 2012-076378 attributed to A.S and B.T. We are grateful to the structural biology facility (UMS 3033/US001) of the Institut Européen de Chimie et Biologie (Pessac, France) for access to the Biacore 3000 instrument. We thank Nathalie Lejal for technical assistance.