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Gordon Supercomputer Helps Guide New Drug Designs

Researchers at SDSC are using the flash-based Gordon supercomputer in the fight against Alzheimer’s disease. By studying peptides using Gordon, the scientists have found new ways to elucidate the creation of the toxic oligomers associated with this devastating illness.

Single amyloid-beta monomers can pair up to form a variety of dimers that can aggregate into larger peptide rings that reside on cell membranes such as those pictured. This process has been implicated in the development of Alzheimer’s disease.

Single amyloid-beta monomers can pair up to form a variety of dimers that can aggregate into larger peptide rings that reside on cell membranes such as those pictured. This process has been implicated in the development of Alzheimer’s disease.

Igor Tsigelny, a research scientist with SDSC, the UCSD Moores Cancer Center, and the Department of Neurosciences, focused on the small peptide called amyloid-beta, which pairs up with itself to form dimers and oligomers. The scientists surveyed all the possible ways to look at the dynamics of conformational changes of these peptides and the possibility that they might organize into the oligomers theorized to be responsible for the degenerative brain disease. In the February 14 issue of the Journal of Alzheimer’s Disease, the researchers suggest their results may generate new targets for drug development.

Our research has identified amino acids for point mutations that either enhanced or suppressed the formation and toxicity of oligomer rings,” said Tsigelny, the study’s lead author. “Aggregation of misfolded neuronal proteins and peptides may play a primary role in neurodegenerative disorders, including Alzheimer’s disease.”

Tsigelny also noted that recent improvements in computational processing speed have allowed him and other researchers to use a variety of tools, including computer simulations, to take new approaches to examining amyloid-beta, which has proven too unstable for traditional approaches such as x-ray crystallography.

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