Targeted protein degradation in autoimmune diseases: from mechanisms to therapeutic breakthroughs

Autoimmune diseases pose significant challenges due to the high risks associated with abnormal immune responses to self-antigens and the limitations of broad-spectrum immunosuppressants. Current therapeutic approaches primarily rely on immunosuppressive drugs, yet their non-specificity and side effects urge researchers to explore novel targets and the advancement of precision medicine. Recent advances in targeted protein degradation (TPD) technologies, including PROTAC, MGD and LYTAC, offer therapeutic potential by precisely eliminating pathogenic proteins. By leveraging cellular degradation machinery such as ubiquitin-proteasome an endolysosomal systems to overcome the undruggable targets, these TPD technologies offer promising therapeutic strategies for precise immune regulation. Preclinical studies demonstrate PROTAC-mediated degradation of IRAK4 reduce inflammatory cytokines. RIPK2 degraders are expected to become a new approach for treating inflammatory diseases. While BTK degraders L18I surpass inhibitors in blocking autoantibodies. There are still challenges to overcome, such as delivery barriers, off-target effects and limited E3 ligase diversity. Emerging solutions such as AI-driven design and modular platforms may improve the specificity and efficacy. This review summarizes the underlying mechanisms, therapeutic breakthroughs, and translational hurdles of TPD technologies, and explores how integrating AI can optimize the technologies. TPD strategies have the potential to revolutionize the treatment of autoimmune diseases by providing more targeted and personalized therapies.