Wortmannin is widely used in biochemical research as a potent and specific inhibitor of phosphoinositide 3-kinases (PI3Ks). It is particularly valuable in studying the PI3K signaling pathway, which plays a critical role in cellular processes such as growth, proliferation, survival, energy metabolism, and cell division. Researchers use it to investigate the effects of PI3K inhibition on various diseases, including cancer (where the pathway is often dysregulated), diabetes, and immune disorders. Additionally, Wortmannin is employed in studies related to autophagy, as it can block the formation of autophagosomes, providing insights into cellular degradation mechanisms. Its ability to inhibit other kinases, such as mTOR and DNA-PK, also makes it a useful tool for exploring their roles in cellular functions.

In pharmacology, Wortmannin serves as a tool to test the efficacy of new PI3K inhibitors, assessing their potential in treating PI3K pathway-related disorders. However, due to its high toxicity, its use is limited to laboratory research and it is not applied directly in human medicine.