We present a computational approach for studying the effect of potential drug combinations on the protein networks associated with tumor cells. The majority of therapeutics are designed to target single proteins, yet most diseased states are characterized by a combination of many interacting genes and proteins. Using the topology of protein-protein interaction networks, our methods can explicitly model the possible synergistic effect of targeting multiple proteins using drug combinations in different cancer types. The methodology can be conceptually split into two distinct stages. Firstly, we integrate protein interaction and gene expression data to develop network representations of different tissue types and cancer types. Secondly, we model network perturbations to search for target combinations which cause significant damage to a relevant cancer network but only minimal damage to an equivalent normal network. We have developed sets of predicted target and drug combinations for multiple cancer types, which are validated using known cancer and drug associations, and are currently in experimental testing for prostate cancer. Our methods also revealed significant bias in curated interaction data sources towards targets with associations compared with high-throughput data sources from model organisms. The approach developed can potentially be applied to many other diseased cell types.
Keywords: Networks; cancer; drug combinations; network perturbation; protein-protein interactions.