Design of β-Amyloid Aggregation Inhibitors from a Predicted Structural Motif

Paul A. Novick, Dahabada H. Lopes, Kim M. Branson, Alexandra Esteras-Chopo, Isabella A. Graef, Gal Bitan, and Vijay S. Pande Journal of Medicinal Chemistry (2012)

These results have been a long time in coming and in many ways represents a major achievement for Folding@home (FAH) in general, demonstrating that the approach we started 10 years ago can make significant steps forward in our long term goals.

Specifically, our long term goals have been to 1) develop new methods to tackle the computational challenges of simulating protein folding; 2) apply these methods to gain new insights into protein folding; 3) use these methods and new insights to simulate Aß protein misfolding, a key process in the toxicity of Alzheimer’s Disease (AD); and finally 4) to use those simulations to develop new small molecule drug candidates for AD. In the early years of FAH, we concentrated on the first two goals above. In the last 5-7 years, we have worked to accomplish the third goal. I’m now very excited to report our progress on the last goal –– using FAH for the development of new therapeutic strategies for AD.

In a paper just published in the Journal of Medicinal Chemistry, we report on tests of predictions from earlier Folding@home simulations, and how these predictions have led to a new strategy to fight Alzheimer’s Disease. While this is not a cure, it is a major step towards our final goal, some light at the end of the tunnel.

The next steps, now underway in our lab, are to take this lead compound and help push it towards a viable drug. It’s too early to report on our preliminary results there (I like to only talk publicly about work after it’s passed through peer review), I’m very excited that the directions set out in this paper do appear to be bearing fruit in terms of a viable drug (not just a drug candidate).

Drug design studies targeting one of the primary toxic agents in Alzheimer’s disease, soluble oligomers of amyloid β-protein (Aβ), have been complicated by the rapid, heterogeneous aggregation of Aβ and the resulting difficulty to structurally characterize the peptide. To address this, we have developed [Nle35, d-
Pro37]Aβ42, a substituted peptide inspired from molecular dynamics simulations which forms structures stable enough to be analyzed by NMR. We report herein that [Nle35, d-Pro37]Aβ42 stabilizes the trimer and prevents mature fibril and β-sheet formation. Further, [Nle35, d-Pro37]Aβ42 interacts with WT Aβ42 and reduces aggregation levels and fibril formation in mixtures. Using ligand-based drug design based on [Nle35, d-Pro37]Aβ42, a lead compound was identified with effects on inhibition similar to the peptide. The ability of [Nle35, d-Pro37]Aβ42 and the compound to inhibit the aggregation of Aβ42 provides a novel tool to study the structure of Aβ oligomers. More broadly, our data demonstrate how molecular dynamics simulation can guide experiment for further research into AD.