How would you interpret conflicting cell-based and biochemical assay results?

Why

A potent purified-enzyme inhibitor may show little cellular activity because it is poorly permeable, actively effluxed, rapidly metabolized or unable to engage a target in its native complex. The opposite pattern can arise from active metabolites, indirect signaling effects or toxicity rather than direct inhibition. Compare assay timing, ATP or substrate concentrations, protein forms, solvent and readout quality.

Measure free intracellular exposure and direct target engagement when practical, then test pathway-specific biomarkers and rescue experiments. Repeat the effect in an orthogonal cell assay and check viability. For example, if a compound inhibits purified HDAC but does not change cellular engagement, the divergence may reflect intracellular availability rather than absence of biochemical binding.

Maintain alternative explanations until experiments distinguish them.