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Aluminium (Al) can trigger protein misfolding, beta amyloid (Aβ) aggregation and induced Alzheimer’s disease (AD)-like in rat model. Lepedium sativum (LS) water extract proved promising curative effects and its ability to restore the protein integrity was reported in our previous reports. In this study, we utilized Synchrotron Fourier Transform Infrared Microspectroscopy (SFTIRM) and multivariate analysis to investigate and monitor more thoroughly the process of protein misfolding in response to Al and LS treatment in rat hippocampal brain tissue. The results revealed a marked increase in the protein β-structure in AD group after 42d over the random coil structure. Meanwhile, after 65d ~ 91% of the amide I is random coil and the rest is anti-parallel β-sheets, alpha helix structure is absent in both tested times. Incredibly, this random coil structure is totally absent in the curative group; instead it is dominated by a drastic increase in the protein β-structure suggesting the clearance of Aβ takes place through β-structure transit phase. The role of β –structure & random coil as a transit phase in transformation of Aβ and/or clearance in response to AL and LS treatment is supported by different calculated %area ratios measurements. SFTIRM gave unique and deeper cluster of data.