L-Isoleucine methyl ester hydrochloride is primarily used in the synthesis of peptides and proteins, serving as a building block in the production of complex biomolecules. It is also utilized in pharmaceutical research for the development of drugs, particularly those targeting metabolic disorders and muscle-related conditions. Additionally, this compound plays a role in the study of enzyme mechanisms and protein interactions, aiding in biochemical and biophysical research. Its esterified form enhances solubility, making it suitable for various experimental applications in laboratory settings.