Alzheimer's disease (AD) is thought to be caused by the abnormal clumping of a protein termed the amyloid beta-protein (Abeta). These Abeta clumps accumulate in the brain to form the "amyloid plaques" that are characteristic of AD. Plaque formation is linked to loss of nerve cells, particularly those associated with memory. Scientific research has shown that Abeta clumping is complex and that the ability of these clumps to kill nerve cells differs depending on their precise structure. Work in mouse models of AD has revealed that immunizing the animals against Abeta results in the production of antibodies that can eliminate plaques and improve cognition. This "immunotherapy" approach has been tried in humans. Unfortunately, although substantial disappearance of plaques is observed, patients did not improve. We thus still do not have any drugs that are effective in treating AD.
We hypothesize that the immunotherapy has failed because the antibodies are not binding to the types of Abeta clumps that actually damage nerves. A substantial body of evidence suggests the most toxic clumps, termed "oligomers," actually are very small, e.g., comprising two (dimers) or three individual Abeta proteins. To develop drugs to neutralize oligomers, scientists need to know their exact shapes so that they can tailor-make drugs that bind these shapes strongly and prevent them from killing neurons. Although much research has been done in this area, determining oligomer shape has eluded scientists thus far. We believe this is due to the fact that the Abeta protein changes shape very rapidly, which makes the use of common shape determination techniques, like X-ray crystallography and nuclear magnetic resonance spectroscopy, impossible.
We propose a novel means to achieve the goals of shape determination and drug design - the use of quantum mechanics (QM). QM is the most fundamental theory that describes how individual atoms and their associated electron clouds interact. This means that we can examine all the atoms in Abeta and see which interact with each other most strongly, thus leading to the formation of neurotoxic dimers and trimers. QM uses supercomputers to reveal these interactions. We will use this information to design and chemically synthesize Abeta proteins in which specific atoms have been altered to disrupt the atomic interactions leading to neurotoxin production. We will test the effects of these modified peptides on nerve cells grown in the laboratory. If we find that our changes prevent nerve cell death, we then will know precisely how to create drugs to bind to, and neutralize, those atoms in Abeta that lead to production of neurotoxins. The impact of this work to those suffering from AD could be immense because the ability to target these drugs precisely to those atoms responsible for disease dramatically increases the likelihood of clinical efficacy.
A predominant working hypothesis for Alzheimer's disease (AD) etiology is the formation of neurotoxic assemblies of the amyloid β-protein (Aβ). Many studies have shown that small molecules or antibodies can prevent Aβ assembly in vitro or diminish plaque burden in vivo. Nevertheless, no FDA-approved Aβ-directed therapies exist. This fact has led some to question the hypothesis, which we think is premature. We posit instead that what is needed is accurate atomic level targeting of therapeutic agents, something that has not yet been accomplished. To do so, we must first determine inter-atomic interaction energies in the Aβ monomer. These energies determine how the monomer folds and assembles into neurotoxic structures. This determination would provide the means to design drugs to destabilize interactions most important in producing toxic assemblies or to stabilize interactions most effective in producing non-toxic assemblies.
A significant barrier to such structure-activity determination is the fact that Aβ is an intrinsically disordered protein. This has complicated atomic-resolution structure analysis of Aβ using X-ray crystallographic or NMR methods. Many, including us, have turned to computational methods, such as molecular dynamics (MD), to enable these analyses. Computational approaches have had some success, revealing amino acid residues potentially involved in stabilizing monomer structure and in mediating oligomerization. However, MD and related computational methods depend on the laws of classical physics, which often rely not only on fits to previously published studies but also cannot account for many phenomena critical in mediating Aβ conformational dynamics, including charge transfer, long-range polarization, and bond forming and breaking. The result is that these methods are often inaccurate.
In contrast, quantum mechanics (QM) is the highest level of theory that governs atomic interactions and does provide accurate descriptions of these phenomena and quantitative information that can be used to guide experimental studies. We thus propose a novel strategy, comprising two aims, that:
- (a) use QM to establish inter-atomic interaction energies in the monomer state;
- (b) establish experimentally, using structurally modified peptides, how altering these interactions affects assembly and assembly neurotoxicity;
- (c) build upon and extend the results from the monomer to the dimer state.