SynDISCO: A Mechanistic Modeling-Based Framework for Predictive Prioritization of Synergistic Drug Combinations Directed at Cell Signaling Networks

The widespread development of resistance to cancer monotherapies has prompted the need to identify combinatorial treatment approaches that circumvent drug resistance and achieve more durable clinical benefit. However, given the vast space of possible combinations of existing drugs, the inaccessibility of drug screens to candidate targets with no available drugs, and the significant heterogeneity of cancers, exhaustive experimental testing of combination treatments remains highly impractical. There is thus an urgent need to develop computational approaches that complement experimental efforts and aid the identification and prioritization of effective drug combinations. Here, we provide a practical guide to SynDISCO, a computational framework that leverages mechanistic ODE modeling to predict and prioritize synergistic combination treatments directed at signaling networks. We demonstrate the key steps of SynDISCO and its application to the EGFR-MET signaling network in triple negative breast cancer as an illustrative example. SynDISCO is, however, a network- and cancer-independent framework, and given a suitable ODE model of the network of interest, it could be leveraged to discover cancer-specific combination treatments.