L-Threonine Benzyl Ester Hydrochloride is primarily used in peptide synthesis as a protected form of L-threonine. The benzyl ester group serves as a protective group for the carboxyl function, preventing unwanted reactions during the synthesis process. This compound is particularly valuable in the production of complex peptides and proteins, where selective protection and deprotection of amino acids are crucial. It is also employed in the development of pharmaceuticals, especially in the creation of peptide-based drugs, where precise control over the peptide chain is necessary. Additionally, it finds use in biochemical research for studying enzyme mechanisms and protein interactions, providing insights into biological processes.