(S)-Morpholine-3-carboxylic acid hydrochloride is primarily used in the synthesis of pharmaceutical compounds. It serves as a key intermediate in the production of various drugs, particularly those targeting neurological and cardiovascular disorders. Its chiral structure makes it valuable in the development of enantiomerically pure substances, which are crucial for enhancing drug efficacy and reducing side effects. Additionally, it is employed in research laboratories for the study of enzyme inhibition and receptor binding, aiding in the discovery of new therapeutic agents. The compound’s stability and reactivity also make it suitable for use in peptide synthesis and other organic chemistry applications.