Rational design of antiviral drug combinations based on equipotency using HCV subgenomic replicon as an in vitro model

Combination therapy of directly acting antivirals (DAA's) for the treatment of chronic HCV infections has proven to be a highly effective strategy to cure chronic infections with this virus. Here we studied, using HCV as an example, how to best design in vitro studies that explore the combined antiviral efficiency of combinations of three or more DAA's. To that end we used a HCV NS3 protease inhibitor, a NS5A targeting compound and two non-nucleoside NS5B polymerase inhibitors (each one targeting a different drug binding site). We demonstrate, employing HCV subgenomic replicon containing Huh 9–13 hepatoma cells, that quadruple therapy with these 4 different DAA's each at 1x their EC75, results in a highly efficient inhibition of viral replication. This is further reflected in the rapid clearance of the HCV replicon from the host cell. By contrast, neither equipotent combinations that consist of either molecules alone at 4x EC75 nor triple combinations at 1.33x the EC75 resulted in clearance. In contrast to the quadruple combo, drug-resistant variants emerged under mono-treatment and in most triple combo's. These data thus demonstrate that quadruple combinations at total suboptimal concentrations [i.e. concentrations at which neither mono- nor triple therapy is sufficiently potent] result rapidly in a pronounced antiviral efficacy. Altogether, this work provides an example as to how to design studies to explore the antiviral efficacy of combinations of more than two compounds. •Quadruple combinations of DAA HCV inhibitors rapidly cure hepatoma cells from their replicon.•Equipotent concentrations of single compounds or triple combinations are less efficient than quadruple combinations.•A methodology for the design of experiments to explore the antiviral efficacy of combinations of >2 compounds.