Amyloid-β (Aβ) aggregates are recognized as initiators of Alzheimer"s disease, and their interaction with the nervous system contributes to the progression of neurodegeneration. Therefore, there is an urgent need for researchers to discover the biomolecules that interact with Aβ peptides to determine the molecular basis.

To enable profiling of Aβ-interacting proteins, we developed the novel Peptide-ligand-induced Abundance Change of proTeinS (PACTS)-assisted TPP strategy for the identification of peptide-interacting proteins based on the peptide-ligand-induced change in protein abundance. The interactome of amyloid beta (Aβ) 1-42 in THP-1 cells was described and resulted in the identification of 103 interacting proteins. Validation experiments indicated that Aβ1-42 interacted directly with fatty acid synthase (FAS) and inhibited its enzymatic activity, providing insights into fatty acid metabolic disorders in Alzheimer's disease. Furthermore, we applied the PACTS-assisted TPP approach to analyze clinical samples to identify Aβ1-42-interacting proteins. We detected 115 proteins that interact with Aβ1-42 in human frontal lobe tissue. Further orthogonal validation revealed that Aβ1-42 interacted with the AD-associated protein mitogen-activated protein kinase 3 (MAPK3), and knockdown of the Aβ1-42 amyloid precursor protein (APP) inhibited the MAPK signaling pathway, suggesting potential functional roles for Aβ1-42 in interacting with MAPK3.

To enable profiling of Aβ-interacting neuropeptides, we established a native mass spectrometry (MS)-centric workflow for screening Aβ-interacting neuropeptides, and six out of twelve neuropeptides formed noncovalent complexes with Aβ species in the MS gas phase. Thioflavin-T fluorescence assays and gel separation indicated that leptin and cerebellin decreased Aβ aggregation, whereas kisspeptin increased this process. In addition, leptin and cerebellin attenuated Aβ-induced cytotoxicity, which was independent from the influence of metal ions. Leptin can chelate copper from copper-bound Aβ species, reducing cytotoxicity caused by the aggregation of Aβ and metal ion complexes. Overall, our study demonstrated that neuropeptides frequently interact with Aβ and revealed that leptin and cerebillin are potential inhibitors of Aβ aggregation, providing great insight into understanding the molecular mechanism of Aβ interacting with nervous system and facilitating drug development.