Mass Spectrometric Footprinting and DFT Calculations Explain the Effect of Curcumin on the Aggregation of Amyloid β 42 (Aβ42)

Abstract Curcumin, a polyphenolic natural product, binds to Aβ42, a protein involved in Alzheimer’s Disease, to inhibit self-aggregation in vitro. Molecular understanding of the binding is important in designing new molecules to inhibit Aβ42 aggregation. We performed OH radical footprinting of Aβ42 in the presence and absence of curcumin by using fast photochemical oxidation of proteins (FPOP), followed by mass spectral analysis, to monitor changes in Aβ42 protein dynamics in the presence of curcumin. The results reveal that curcumin binding reduces oxidative footprinting at the N-terminus and middle region, indicating binding at these sites. Kinetic modeling of the percentage modification shows a significant change in the aggregation of Aβ42 in the presence of curcumin, whereby one aggregate population nearly disappears. The [Aβ42:curcumin] binding complexes were also explored using density functional theory (DFT), optimizating the starting structures at the B3LYP/6–31G(d) level for both the N-terminal/middle and C-terminal/middle regions. The structure of the lowest-energy complex has curcumin binding at the N-terminal plus middle regions, and this was validated by reoptimization using 6–311G(d,p) and applying Grimme’s dispersion function (GD3). This structure was further confirmed by reoptimization in aqueous media using the Conductor-like Polarizable Continuum Model (CPCM). The new structure not only accounts for the observed changes in •OH footprinting of the N-terminal, middle, and C-terminal regions but also forecasts how this approach can provide insight into protein aggregation. A molecular-level understanding of the binding site of curcumin with Aβ42 should be helpful in the design of new aggregation modulators.