2-Boc-2,6-diaza-spiro[3.3]heptane hydrochloride is primarily used in organic synthesis and medicinal chemistry as a building block for the development of pharmaceutical compounds. Its spirocyclic structure makes it valuable for creating constrained and rigid molecular frameworks, which are often desirable in drug design to enhance selectivity and stability.

In drug discovery, it serves as an intermediate for synthesizing compounds targeting neurological disorders, such as anxiety, depression, and schizophrenia, due to its ability to modulate receptors in the central nervous system. Additionally, it is employed in the preparation of peptidomimetics, which mimic the structure and function of peptides, aiding in the development of enzyme inhibitors or receptor modulators.

The Boc (tert-butoxycarbonyl) protecting group in the molecule allows for selective deprotection during multi-step synthetic processes, enabling the precise construction of complex molecules. This compound is particularly useful in the synthesis of heterocyclic compounds, which are prevalent in many biologically active molecules. Its application extends to the development of novel therapeutic agents with improved pharmacokinetic properties.