(S)-methyl 2-amino-2-(2,4-difluorophenyl)acetate hydrochloride is primarily used as an intermediate in the synthesis of pharmaceuticals. It plays a crucial role in the production of antifungal agents, particularly those targeting fungal infections in humans. The compound's structure, featuring a difluorophenyl group, enhances its binding affinity to specific biological targets, making it valuable in drug development. Additionally, it is utilized in research settings to study enzyme interactions and develop novel therapeutic compounds with improved efficacy and reduced side effects. Its application extends to the preparation of chiral molecules, which are essential in creating drugs with higher specificity and potency.