Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling

Clinically used RAF inhibitors are ineffective in RAS mutant tumors because they enhance homo- and heterodimerization of RAF kinases, leading to paradoxical activation of ERK signaling. Overcoming enhanced RAF dimerization and the resulting resistance is a challenge for drug design. Combining multiple inhibitors could be more effective, but it is unclear how the best combinations can be chosen. We built a next-generation mechanistic dynamic model to analyze combinations of structurally different RAF inhibitors, which can efficiently suppress MEK/ERK signaling. This rule-based model of the RAS/ERK pathway integrates thermodynamics and kinetics of drug-protein interactions, structural elements, posttranslational modifications, and cell mutational status as model rules to predict RAF inhibitor combinations for inhibiting ERK activity in oncogenic RAS and/or BRAFV600E backgrounds. Predicted synergistic inhibition of ERK signaling was corroborated by experiments in mutant NRAS, HRAS, and BRAFV600E cells, and inhibition of oncogenic RAS signaling was associated with reduced cell proliferation and colony formation. [Display omitted] •RAF dimers are effectively targeted by two structurally different RAF inhibitors•Next-generation model integrates kinetic, thermodynamic, and cellular data•Best RAF inhibitor combinations are selected for diverse genetic backgrounds•Predicted RAF inhibitor combinations overcome oncogenic RAS signaling to ERK To overcome oncogenic RAS signaling, suitable combinations of conformation-selective RAF inhibitors are predicted by a structure-based model that integrates thermodynamic, kinetic, structural, and cell mutation data. Predictions are validated in vitro using signaling, proliferation, and colony-formation assays. Generally, our data suggest that if a kinase dimerizes for full activation, two inhibitors targeting this kinase in different conformations will likely synergize for target inhibition.