Bioorganic studies on recognition of soluble amyloid oligomers using small molecules

Senile plaques composed of aggregates of amyloid peptides are the hallmark of Alzheimer's disease (Chapter 1). Recent studies indicated that soluble oligomers of the amyloid peptides are in fact the main neurotoxic species that impair neuronal function. The nature of these soluble oligomers still remains to be clarified, and spectroscopic detection of these soluble amyloid species using small molecular probes is currently an underdeveloped area of research.;Dye-binding assays based on Congo red and thioflavin T dyes are the most widely used methods of assessing the aggregation of amyloid peptides. However, both dyes suffer from a number of disadvantages that often preclude the correct structural assessment of amyloid aggregates. In particular, when applied for the evaluation of the anti-aggregation ability of small molecules, these dyes often produce false-positive/negative results.;Several recent accounts demonstrated that amphotericin B (AmB) could efficiently suppress amyloid aggregation. However, the inhibitory effect of AmB was established with one of the aforementioned dye-binding assays. Using circular dichroism spectroscopy as a dye-free tool, we were able to distinguish between the binding and inhibition of aggregation events (Chapter 2). It appeared that AmB could distinctly interact with both unordered and ordered beta-structure-rich soluble amyloid oligomers, yet it had no measurable impact neither on the secondary structure nor on the time-dependent aggregation profile of the amyloid peptide. Thus, AmB could potentially be used as a CD-probe for studying conformational changes of soluble amyloid oligomers.;In order to take advantage of the sensitivity of fluorescence-based techniques, we sought to develop novel small molecule probes that would not be subject to the limitations of the currently used dyes. Toward this end, we explored the ability of so-called BODIPY dyes to act as small molecule fluorescent probes for soluble amyloid oligomers. A straightforward functionalization of the BODIPY dyes via the incorporation of a triazole moiety produced fluorescent dyes that were capable of recognizing distinct conformations of soluble oligomeric species of amyloid peptides (Chapter 3). Subsequently, using the methodology developed in our laboratory, we prepared a series of iodo-triazole-containing BODIPY dyes that even further enhanced the sensitivity of these dyes towards various conformations of soluble amyloid oligomers (Chapter 4). Overall, our results demonstrate that these triazole-containing dyes could prove to be useful probes for monitoring conformational transitions of amyloid peptides in vitro.