The rapid development of fluorescent probes for monitoring target enzymes is still agreat challenge owingtothe lacko fe fficient ways to optimizeaspecific fluorophore. Herein, ap ractical two-dimensional strategy was designed for the development of an isoform-specific probe for CYP3A4, ak ey cytochrome P450 isoform responsible for the oxidation of most clinical drugs.Infirst dimension of the design strategy, ap otential two-photon fluorescent substrate (NN)f or CYP3A4 was effectively selected using ensemble-based virtual screening.Inthe second dimension, various substituent groups were introduced into NN to optimize the isoform-selectivity and reactivity.F inally,w ith ideal selectivity and sensitivity, NEN was successfully applied to the real-time detection of CYP3A4 in living cells and zebrafish. These findings suggested that our strategy is practical for developing an isoform-specific probe for atarget enzyme.Cytochrome P450 monooxygenase (CYP) is as uperfamily of oxidative enzymes that metabolizes thousands of endogenous and exogenous substances through alkyl carbon and aromatic ring hydroxylation, O-a nd N-dealkylation, and epoxidation. [1] CYP3A4 is regarded as the most important CYP isoform in humans owing to its high abundance in liver and broad substrate spectrum, which contributes to the metabolism of more than 50 %o fclinical drugs. [2,3] Unfortunately,C YP3A4 activity can be modulated by many clinical drugs,t hereby frequently causing unfavorable drug-drug interactions (DDI), further leading to altered clinical outcomes or even life-threatening adverse reactions. [4] Additionally,asignificant inter-individual variability of CYP3A4 activity is frequently reported, arising from an umber of sources including genetic polymorphism and the response to environmental influences. [5] These factors have greatly limited the understanding of the precise role of CYP3A4 in drug metabolism and DDI, as aresult, negatively impacted clinical medication safety and effectiveness.To accurately characterize CYP3A4 activity,s ensitive technologies capable of the real-time monitoring of CYP3A4 activity are urgently needed. Tr aditional detection methods mainly rely upon mass spectrometry or high-performance liquid chromatography, [6,7] which are not compatible with living cell or in vivo applications.T wo-photon (TP) fluorescence microscopy,byvirtue of its higher sensitivity,real-time high spatial resolution imaging,a nd amenability to deeptissue bioimaging,h as shed new light on the monitoring of target enzyme activity in complex systems. [8, 9] However,n o TP fluorescent probe has been developed for the real-time and selective imaging of endogenous CYP3A4 activity in living systems.Previous attempts to develop af luorescent probe for CYP3A4 were based on adealkylation mechanism to release ad etectable moiety.T he O-alkyl derivatives of coumarin, resorufin, and fluorescein were designed and synthesized but met with limited success in isoform selectivity. [10] Theleading cause for the poor specificity of these probes is th...