Network Architecture Predisposes an Enzyme to Either Pharmacologic or Genetic Targeting

Chemical inhibition and genetic knockdown of enzymes are not equivalent in cells, but network-level mechanisms that cause discrepancies between knockdown and inhibitor perturbations are not understood. Here we report that enzymes regulated by negative feedback are robust to knockdown but susceptible to inhibition. Using the Raf–MEK–ERK kinase cascade as a model system, we find that ERK activation is resistant to genetic knockdown of MEK but susceptible to a comparable degree of chemical MEK inhibition. We demonstrate that negative feedback from ERK to Raf causes this knockdown-versus-inhibitor discrepancy in vivo. Exhaustive mathematical modeling of three-tiered enzyme cascades suggests that this result is general: negative autoregulation or feedback favors inhibitor potency, whereas positive autoregulation or feedback favors knockdown potency. Our findings provide a rationale for selecting pharmacologic versus genetic perturbations in vivo and point out the dangers of using knockdown approaches in search of drug targets. [Display omitted] •The network around an enzyme affects its susceptibility to knockdown or inhibition•Negative feedback enhances pharmacologic inhibitor potency compared with knockdown•Positive feedback enhances knockdown potency compared with pharmacologic inhibition By modeling enzyme-catalyzed cascades, Jensen et al. report that specific regulatory configurations are disproportionately susceptible to pharmacologic inhibition or genetic knockdown. Experiments with the Ras-MEK-ERK cascade show that ERK –| Raf feedback creates a >100-fold discrepancy between MEK knockdown and inhibition.