E3 ligase ligand-linker conjugates 41 are primarily utilized in the field of targeted protein degradation, a cutting-edge approach in drug discovery and therapeutic development. These conjugates are designed to recruit E3 ubiquitin ligases to specific target proteins, marking them for degradation by the proteasome. This mechanism is particularly valuable in addressing diseases caused by the overexpression or malfunction of specific proteins, such as cancer, neurodegenerative disorders, and viral infections.

In cancer therapy, for example, these conjugates can be engineered to degrade oncogenic proteins that drive tumor growth and survival, offering a potential alternative to traditional inhibitors. They are also being explored in the development of PROTACs (Proteolysis Targeting Chimeras), which are bifunctional molecules capable of selectively degrading disease-causing proteins. Additionally, their application extends to basic research, where they are used as tools to study protein function and validate drug targets by inducing the controlled degradation of specific proteins in cellular or animal models.