Overcoming kinase inhibitor resistance and oncogenic RAS signaling

Major problem encountered using small molecule cancer therapeutics in clinic is that even in susceptible cancers, these drugs rarely give durable responses, almost inevitably being hampered by signaling reactivation and development of resistance. Studying the causes of this resistance has revealed severe limitations in our understanding of the network properties and molecular mechanisms that control drug responses. We show that contrary to a common opinion, feedback loops by themselves cannot restore or overshoot steady state signaling

. De novo synthesized negative feedback regulators can lead to a transient overshoot but still cannot fully restore output signaling. These findings can rationalize recent scientific and clinical disappointments that were based on the hypothesis that negative feedback loops can fully explain drug resistance. We demonstrate that there are two major means of complete, steady state revival of signaling, enabled by (1) the network topology or (2) molecular mechanisms rendering the primary drug target active again. Network topology analysis shows that at least two, activating and inhibitory, connection routes from a primary drug target to the output, must exist for complete reactivation or overshoot of steady-state output activity that existed before the inhibition

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Irrespective of the network topology, drug-induced overexpression of the primary drug target or druginduced increase in its dimerization or oligomerization can restore the pathway output activity. The

formation of kinase homo- or heterodimers is a major course of resistance. In this constellation one protomer is drug-bound and allosterically activates the other, drug-free protomer thereby conferring resistance. The emergence of different drug affinities between protomers in a dimer has been enigmatic, but can be explained by thermodynamics

. A striking example is so-called paradoxical activation of the extracellular regulated kinase (ERK) pathway by RAF inhibitors, which is caused by RAF homo- or heterodimerization. This dimerization is promoted by RAF inhibitors and amplified by mutant RAS and negative feedback regulations, but if an inhibitor does not facilitate dimerization, negative feedback can only result in a transient overshoot of the pathway activity. Exciting and counterintuitive discoveries of ways to overcome resistance were made using next generation modelling, which combines aspects of protein structure, posttranslational modifications, thermodynamics, network architecture, mutation data and dynamic reaction mechanisms

. As a specific example, we show that a treatment with Type I½ and Type II RAF inhibitors can counterbalance ERK pathway reactivation and concomitant drug resistance.