Substrate Recognition in HCV NS3/4A Protease

The generality of the substrate envelope hypothesis have been evaluated by investigating other viral systems such as HCV NS3/4A serine protease. Crystal structures of protease-substrate complexes reveal that viral substrates bind to the protease active site in a conserved manner defining the NS3/4A substrate envelope. (Romano et. al., 2010)

Product complexes 4A/4B, 4B/5A and 5A/5B were superimposed onto the full-length NS3/4A structure (1CU1) to reveal the conserved mode of binding.

Drug resistance in HCV NS3/4A Protease

Resistance against the most promising NS3/4A protease inhibitors has emerged in clinical trials. The majority of reported drug resistance mutations cluster around the protease active site.

Mutations that confer the most severe resistance in the clinic occur at sites where the inhibitors protrude from the substrate envelope.

Crystal structures of inhibitor bound NS3/4A protease validate the substrate envelope hypothesis as a general model for predicting the susceptibility of protease inhibitors to resistance. Inhibitors designed to fit within the substrate envelope will be less susceptible to resistance, as mutations affecting inhibitor binding would simultaneously interfere with the recognition of viral substrates.