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Small Molecule Screening for Parkinson’s Disease

Protein-DNA interactions are essential for fundamental cellular processes such as transcription, DNA damage repair, and apoptosis.  As such, small molecule disruptors of these interactions could be powerful tools for investigation of these biological processes, and such compounds would have great potential as therapeutics.  Unfortunately, there are few methods available for the rapid identification of compounds that disrupt protein-DNA interactions.  Here we show that photonic crystal (PC) technology can be utilized to detect protein-DNA interactions, and can be used in a high-throughput screening mode to identify compounds that prevent protein-DNA binding. The PC technology is used to detect binding between protein-DNA interactions that are DNA sequence-dependent (the bacterial toxin-antitoxin system MazEF), and those that are DNA sequence-independent (the human Apoptosis Inducing Factor (AIF)).  The PC technology was further utilized in a screen for inhibitors of the AIF-DNA interaction, and through this screen aurin tricarboxylic acid (ATA) was identified as the first in vitro inhibitor of AIF.  The generality and simplicity of the photonic crystal method should enable this technology to find broad utility for identification of compounds that inhibit protein-DNA binding.
Funded by the National Institute of Health (NIH), this work is the first time that high throughput screening has been performed using a label free detection system on 200,000 small molecules.  The research is in collaboration with Dr. Paul Hergenrother and James Heeres in the department biochemistry and chemistry.

Diagram of protein-DNA binding experiments performed with PC biosensors.  Streptavidin coated biosensors are used to bind biotinylated DNA oligomers.  After overnight incubation, Starting BlockTM(Pierce Biotechnologies) is added to prevent nonspecific binding, and finally AIF is added.

Inhibition data for all compounds screened, where ATA is the only compound out of the ~1000 screened to show significantly higher inhibition (~80%).

References:

1. "General Method for Discovering Inhibitors of Protein-DNA Interactions using Photonic Crystal Biosensors,” L.L. Chan, M.F. Pineda, J. Heeres, P. Hergenrother, and B T. Cunningham, ACS Chemical Biology, Vol. 3, No. 7, p. 437-448, 2008 (Featured on cover of journal).
2.  “A General Method for Discovering Inhibitors of Protein-DNA Interactions Using SRU BIND Optical Biosensor Microplates,” Leo L. Chan, Maria F. Pineda, James T. Heeres, Paul J. Hergenrother, and Brian T. Cunningham, Society of Biomolecular Screening, St. Louis, Missouri,  April 2008