A nanobiosensor prototype capable of detecting interactions between molecules is being proposed and characterized. The analyzed system was composed by 4-hydroxyphenylpyruvate dioxygenase (HPPD) enzyme and its inhibitor, mesotrione herbicide. A method based on Atomic force microscope mesotrione-functionalized-cantilever was employed to detect the interaction of herbicide molecules with HPPD enzyme. This detection was related to a surface stress on the functionalized cantilever generated by enzyme-herbicide binding. Tests showed that the prototype was specific to detect mesotrione-HPPD interaction.