There are two approaches to inhibiting viral replication, either by directly targeting viral proteins or by targeting the host proteins essential for the viral life cycle.

In the FLUPHARM project we propose to directly target the viral polymerase protein complex by exploiting recent advances in the detailed understanding of the mechanism of the influenza virus RNA-dependent RNA polymerase. This enzyme, a trimeric complex composed of subunits PA, PB1, and PB2 is central to the life cycle of the virus since it is responsible for the replication and transcription of viral RNA.

In previous work within the EU funded FLUPOL project, EMBL and UJF have identified and determined the atomic structure of two key domains of the polymerase: The mRNA cap-binding domain in the PB2 subunit, and the endonuclease-active site in the PA subunit. These two sites are both critical for the unique cap-snatching mode of transcription used by influenza virus to generate viral mRNAs.

llustration of the cap-snatching mechanism of transcription by the viral polymerase and the two molecular targets (cap–binding domain and endonuclease active site) for novel inhibitors.

Left: Crystal structure of the PB2 cap-binding domain with its natural ligand, m7GTP bound.
Right: Crystal structure of the PA endonuclease domain with the active site residues annotated and the two essential divalent cations shown as green spheres

Based on the atomic structures, follow-up screenings and structure based design efforts have identified novel compounds that specifically inhibit the cap-binding site, including some which have significant antiviral activity in cells. These exciting findings underpin the FLUPHARM project for the development of novel drugs inhibiting the transcription activity of the polymerase.

Selective inhibitors against the cap-binding and endonuclease active sites of the viral polymerase should significantly attenuate influenza virus infection by stopping the viral reproductive cycle. In addition, since both active sites contain residues conserved in all influenza A strains, such inhibitors are ideal drug candidates to combat both seasonal and pandemic influenza.