Sinefungin is primarily utilized in biochemical research due to its role as a potent inhibitor of methyltransferases. It is extensively used in studies focused on understanding epigenetic mechanisms, particularly those involving DNA and protein methylation. Researchers employ sinefungin to investigate how methylation affects gene expression and cellular processes, providing insights into diseases like cancer where methylation plays a critical role. Additionally, it serves as a valuable tool in virology, helping to explore viral replication mechanisms by targeting viral methyltransferases. Its application extends to drug development, where it aids in identifying and validating new therapeutic targets related to methylation pathways.