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Background: Intracerebral hemorrhage (ICH) is a deadly stroke with high mortality or disability. Although recentresearch has demonstrated the efficacy of Panax notoginseng in ICH therapy, it is unclear which proteins may betargeted to achieve these advantages.

Methods: First, we generated polyclonal antibodies against notoginsenosides by immunizing rats with a ginsenosideRh1-mcKLH conjugate. Second, the potential target proteins of notoginsenosides in brain tissue of ICHmice were identified using LC-MS-based hapten immunoaffinity fishing (HIAF). Third, the disease target databasesand these proteins intersected. Fourth, biolayer interferometry (BLI), molecular docking, and site-directedmutagenesis were performed to validate allograft inflammatory factor 1 (AIF1) as a protein target of notoginsenosides.

Last, bioinformatics analysis was performed to examine AIF1’s biological characteristics.

Results: A potential protein target of notoginsenosides, AIF1, was found by intersecting the identified proteintargets with the disease target databases via LC-MS-based HIAF. BLI analysis revealed that Compound K (CK) andAIF1 had the highest direct interaction, with an average shift value of 0.1091 nm. Subsequently, site-directedmutagenesis, molecular docking, and BLI kinetic analysis demonstrated that CK specifically bound to AIF1with an affinity value of 4.33 ± 0.17E-6 M, with a significant reliance on residues L122 and E125. Bioinformaticsanalysis showed that AIF1 and its directly interacting proteins were associated with microglial activation.

Conclusion: Our study proposed a new technology for screening natural small molecule protein targets, andsuccessfully identified AIF1 as a protein target of notoginsenosides, providing a chemical and biological basis forfurther research into targeting AIF1 to treat ICH.

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