Computational design of protein-protein interactions to engineer novel inhibitors of the p53 pathway and the polycomb repressive complex

Abstract

Here I present 2 examples of the application of the Rosetta macromolecular modeling software suite to the successful development of novel protein-based inhibitors with the aim of creating useful tools for the greater cancer research community. Rosetta was used to engineer the first examples of high affinity, highly specific inhibitors of Mdmx that are useful in mammalian cells. These inhibitors bind either Mdmx or Mdm2 with sub-nanomolar affinities and specificities for one or the other estimated at 1000 to 10,000-fold. In mammalian cancer cell lines, these inhibitors retain their affinities and specificities, halt the cell cycle, and trigger apoptosis. The x-ray crystal structures of 3 of these Mdmx inhibitors were determined and validate the design models and methodology. Rosetta was also employed to engineer high affinity inhibitors of the EED-Ezh2 interaction. These inhibitors bind a large, charged surface of EED with sub-nanomolar affinities.