Methyl protogracillin is primarily used in research settings for its potential bioactive properties. It has shown interest in pharmaceutical studies due to its structural similarity to compounds with anti-inflammatory and antimicrobial activities. It serves as a useful intermediate in the synthesis of more complex natural product derivatives, particularly in the development of novel therapeutic agents. Its application extends to biochemical assays where it is evaluated for enzyme inhibition, especially in pathways related to oxidative stress and cellular metabolism. Additionally, it is employed in structure-activity relationship (SAR) studies to optimize lead compounds in drug discovery programs.