We have probed small molecule compound CID 9998128 as a potential multitarget drug for the Alzheimer's disease (AD) using in silico and in vitro experiments. By all-atom simulation and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method, we have demonstrated that this compound strongly binds to both amyloid β42 (Aβ) fibrils and β-secretase, and the van der Waals interaction dominates over the electrostatic interaction in binding affinity. A detailed analysis at the atomic level revealed that indazole in CID 99998128 structure made a major contribution to instability of all studied complexes. In vitro experiments have shown that CID 9998128 inhibits the Aβ amyloid fibrillization and is capable to clear Aβ fibrils. Moreover, the compound dose-dependently decreases β-site amyloid precursor protein cleaving enzyme (BACE-1) activity with EC value in micromolar range. Thus, our study has revealed that CID 9998128 is a good candidate for AD treatment through preventing production of Aβ peptides and degrading their aggregates. For drug design, we predict that the chemical structure of potent AD multitarget inhibitors should not contain indazole.

Self-assembly of Aβ peptides into amyloid aggregates has been suggested as the major cause of Alzheimer's disease (AD). Nowadays, there is no medication for AD, but experimental data indicate that reversion of the process of amyloid aggregation reduces the symptoms of disease. In this paper, all 8000 tripeptides were studied for their ability to destroy Aβ fibrils. The docking method and the more sophisticated MM-PBSA (molecular mechanics Poisson-Boltzmann surface area) method were employed to calculate the binding affinity and mode of tripeptides to Aβ fibrils. The ability of these peptides to depolymerize Aβ fibrils was also investigated experimentally using atomic force microscopy and fluorescence spectroscopy (Thioflavin T assay). It was shown that tripeptides prefer to bind to hydrophobic regions of 6Aβ9-40 fibrils. Tripeptides WWW, WWP, WPW and PWW were found to be the most potent binders. In vitro experiments showed that tight-binding tripeptides have significant depolymerizing activities and their DC50 values determined from dose-response curves were in micromolar range. The ability of nonbinding (GAM, AAM) and weak-binding (IVL and VLA) tripeptides to destroy Aβ fibrils was negligible. In vitro data of tripeptide depolymerizing activities support the predictions obtained by molecular docking and all-atom simulation methods. Our results suggest that presence of multiple complexes of heterocycles forming by tryptophan and proline residues in tripeptides is crucial for their tight binding to Aβ fibrils as well as for extensive fibril depolymerization. We recommend PWW for further studies as it has the lowest experimental binding constant.

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