The mechanism behind synthetic molecules latching onto the amyloid peptide fibrils thought to be responsible for Alzheimer’s disease has been discovered by researchers from Rice University and the University of Miami.
Metallic dipyridophenazine ruthenium molecules, designed at Rice, bind strongly to pockets created when fibrils form from mis-folded proteins which cells fail to destroy. When activated under a spectroscope, the molecules luminesce, indicating presence of the fibrils.
This much was already known by the researchers, but until now the exact process was a mystery. The discovery may someday point the way toward therapies for halting or even reversing Alzheimer’s disease.
Rice’s expertise in biophysics and University of Miami’s computer simulation skills allowed researchers to pinpoint four such pockets along the fibril where the water-averse molecules can bind. Their work could help chemists design molecules to keep the fibrils from forming the plaques found in Alzheimer’s patients.
Two years ago, Rice chemist Angel Martí and Nathan Cook, lead author, combined ruthenium complexes with solutions containing the spaghetti-like amyloid fibrils. The complexes did not luminesce by themselves, but when linked to an amyloid fibril, could be triggered by light at one wavelength to glow at another, helping the researchers visualize the fibrils.
Ability to track amyloids was a great step forward, but the question of why the complexes latched onto the fibrils at all was still left open, said Cook.
“We had no way to figure it out because our experimental techniques can’t identify binding sites,” he explained. “The standard (used to analyze proteins) is to crystallize your material and use X-rays to determine where everything is positioned. The problem with amyloid beta is the fibrils are not uniform, and you can’t crystallize them. All you would get is an amorphous lump.”
But when Prabhakar, a theoretical and computational chemist specializing in amyloids, contacted Martí and suggested a collaboration.
“We both knew the other was working with amyloid betas,” Martí said. “We were able to figure out how many amyloid beta monomers (molecules that can bind with each other) had to come together to form fibrils, while he modeled the interactions. When we brought all the data together, we had a perfect match.”
“Basically, we learned from the model that we need two monomers to form a binding site,” Marti said. “The cleft where the ruthenium complex binds is completely hydrophobic, the same as the complex. Neither wants to be exposed to water, so when they find each other, they don’t have a choice but to come together. It turns out that’s exactly what needs to happen to turn on the photoluminescent response of the compound.”
Testing a variety of concentrations of monomers with ruthenium complexes helped them to determine that a little more than two monomers, on average, was sufficient to get the “light switch” effect Martí said. Prabhakar’s analysis found four specific locations along the aggregating monomers where the ruthenium complexes could bind: two at the ends where the monomers tend to bind to each other, and two in the middle.
“It was a complicated system to model and we tried hard, using a variety of computational techniques,” Prabhakar said. “In the end, we were amazed to find our results in perfect agreement with the experiments performed in the Martí lab.”
The researchers called the end locations “A and B,” and the middle clefts “C and D.” The hydrophobic A and B sites exist only at the edges of the fibrils, which limits their exposure to the complexes, Martí said.
“But there are lots of C and D sites,” he said. “That explains why the ruthenium complexes don’t inhibit the aggregation of fibrils. It seems the system prefers to bind another monomer, rather than a ruthenium complex, at the ends.
“But now that we understand the mechanism, we can design more hydrophobic complexes that could bind strongly to the ends and prevent further elongation of the fibril,” he said.