Molecular glue neferine induces BAP31 homodimerisation to disrupt endoplasmic reticulum–mitochondria crosstalk for anti‐neuroinflammation in ischaemic stroke

Background and Purpose B‐cell receptor‐associated protein 31 (BAP31), an endoplasmic reticulum (ER)‐resident transmembrane protein, has emerged as a critical regulator of immune cell activation, yet its role in neuroinflammation remains unexplored. Here, we uncovered the natural compound neferine (Nef) as a pharmacological modulator of BAP31 that suppressed microglial activation. Experimental Approach Using thermal protein profiling (TPP), we identified BAP31 as the primary target of Nef. Biochemical and structural analyses were employed to characterise Nef‐BAP31 interactions. We evaluated ER stress and mitochondrial energy metabolism homeostasis using techniques such as STER super‐resolution technology, flow cytometry, western blot, etc . In vivo validation utilised two models: lipopolysaccharide (LPS)‐induced endotoxaemia and middle cerebral artery occlusion (MCAO) for ischaemic stroke, combining behavioural tests, cytokine profiling and histopathological assessments. Key Results Nef functioned as a ‘molecular glue’ by binding to BAP31's coiled‐coil CC2 domain to induce stable dimerisation. We revealed that dimerised BAP31 triggered ER membrane remodelling, which disrupted ER–mitochondria contact sites and preserved mitochondrial energy metabolism homeostasis, thereby blocking inflammatory cytokine release. In vivo, Nef attenuated neuroinflammation in endotoxaemia mice and further conferred neuroprotection against ischaemic stroke in a MCAO model by inhibiting microglia‐driven neuronal injury. Conclusions and Implications In summary, our work reveals that BAP31 is a master regulator of ER‐mitochondria communication during microglial activation and introduces a paradigm‐shifting ‘molecular glue’ strategy for targeting ER‐resident proteins. Additionally, these findings redefine the pharmacological landscape for modulating organelle interactions in microglia involved in neuroinflammatory diseases.