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UMBC High Performance Computing Facility
Please note that this page is under construction. We are documenting the 240-node cluster maya that will be available after Summer 2014. Currently, the 84-node cluster tara still operates independently, until it becomes part of maya at the end of Summer 2014. Please see the 2013 Resources Pages under the Resources tab for tara information.
In silico screening of library of CNS bioavailable compounds to identify potential Aβ toxicity inhibitors
Theresa Good, Ben Keshet, Department of Chemical and Biochemical Engineering

β-Amyloid (Aβ) protein aggregates are the main constituents of the senile plaque found in brains of Alzheimer's disease patients. The mechanism by Aβ induces a wide range of biological phenomena in neuronal cells is mostly unknown. In our lab we have recently found a specific region of Aβ protein that plays a role in Aβ binding to cell membrane, and is the binding site of several known toxicity inhibitors. Elucidation of new molecules that bind at locations of biological significance on Aβ may provide new candidates for therapeutics for Alzheimer's disease. To that end, we are now interested in virtually screening a library of small molecules for their ability to bind to Aβ aggregates at the location we have found to be important for membrane binding. The library of ~350,000 molecules was taken from the ZINC database, and is composed of molecules that are likely capable of crossing the blood-brain-barrier. The NMR structure of the Aβ fibril will be used as the receptor for binding. The energy of binding of the molecules in the library to Aβ will be estimated using DOCK (UCSF). The molecules will be then ranked according to their DOCK binding energies. The top 100 molecules from computational docking will be tested experimentally in-vitro using SH-SY5Y cells for potency as Aβ toxicity inhibitors. To the best of our knowledge this would be the first virtual screening of toxicity inhibitors of Aβ.