Small molecules play an essential role throughout plants life cycle. Our inability to directly introduce small molecules into specific tissues, cells or organelles severely limits our ability to study their unique roles. To address this gap, we are developing a method to control the activity of small molecules with spatial resolution in Arabidopsis thaliana plants. Our project is based on the prodrug approach, used to achieve specific activation of bioactive drug molecules at designated locations. Using molecular biology and genetic techniques, we intend to introduce the enzyme penicillin G amidase (PGA) from E. coli expressed into specific tissues, cells and organelles of the model plant Arabidopsis thaliana. In parallel, we are synthesizing small molecules of interest as substrates for the enzyme. Thus, PGA would cleave the modified molecules, releasing the original, bioactive molecules of interest, specifically in the predesigned locations. We expect that this approach will enable us, and others, to investigate the functions and movement of many important endogenous small molecules, as well as synthetic molecules, in plant research. To test our hypothesis and evaluate the system, we generated appropriate Arabidopsis lines that express PGA under cell types and organelles specific promoters with good coverage of root cell types. We show that the enzyme is functional in planta and that it is capable of releasing bioactive molecules.