HDAC-IN-3 is primarily used in biomedical research as a potent and selective inhibitor of histone deacetylases (HDACs), particularly targeting Class I HDAC enzymes. It is employed to study epigenetic regulation of gene expression, where HDAC inhibition leads to increased histone acetylation, promoting an open chromatin structure and activation of specific genes. This compound has shown utility in cancer research due to its ability to induce cell cycle arrest, differentiation, and apoptosis in various tumor cell lines. It is also used to investigate the role of HDAC activity in inflammation, neurodegenerative diseases, and metabolic disorders. Due to its cell permeability and stability, HDAC-IN-3 is suitable for both in vitro assays and cellular models, making it a valuable tool in drug discovery and mechanistic studies of epigenetic pathways.