Commercially available eye-drops scarcely penetrate the eye because of the cornea, which is located at the surface of the eye and function of barrier to keep out foreign matter. To enhance the penetration ratio of eye-drop, we have proposed nanometer-sized eye-drops called "nano eye-drops." A series of prodrug compounds derived from brinzolamide, a glaucoma therapeutic agent, connected with a trimethyl lock (TML) group were synthesized and the nano eye-drops of the resulting prodrugs were successfully fabricated by the reprecipitation method. We found that the drug release of nano eye-drops critically depended on the chemical structure of the prodrugs comprising the nano eye-drops. As a result, the timing of the ocular hypotensive effect was controlled by altering the chemical structure of brinzolamide prodrug. These results provide insight into drug design for effective controlled release.