CX-5461 is primarily used in research settings to study the mechanisms of transcription and RNA polymerase I activity. It acts as a selective inhibitor of RNA polymerase I, making it a valuable tool for understanding ribosomal RNA synthesis and its regulation in cells. This compound is particularly useful in cancer research, where it helps investigate the role of ribosomal biogenesis in tumor growth and survival. Additionally, CX-5461 is employed in studies exploring potential therapeutic strategies targeting RNA polymerase I in diseases characterized by dysregulated ribosome production. Its application extends to neurobiology, where researchers use it to examine the relationship between ribosomal function and neurological disorders.