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September 23, 2007

Supercomputer research fights African parasite

Sdsccomp

This is from a video posted on SciVee.tv detailing a project at the San Diego Supercomputing Center (SDSC) working on a potential treatment for African trypanosomiasis. Dr. Rommie Amaro talks about her team's effort in drug discovery using the SDSC supercomputer to help fight infectious diseases in developing countries. (The video is embedded at the end of this post.)

African trypanosomiasis (sleeping sickness) is a bloodborne disease caused by the protozoa parasites of the Trypanosoma Genus, transmitted via the tsetse fly. This disease affects the poorest of countries with estimates of up to 50,000 deaths per year.

This disease is prone to epidemics whose severity is highlighted by this passage from the WHO Web site:

During recent epidemic periods, in several villages in the Democratic Republic of Congo, Angola and Southern Sudan, prevalence has reached 50%. Sleeping sickness was considered the first or second greatest cause of mortality, even ahead of HIV/AIDS, in those communities.

Drug discovery research involves looking at specific enzymes selected as targets because of their critical role in a disease process. Traditionally, static images of molecular models of these enzymes have been produced by x-ray crystallography or nuclear magnetic resonance (NMR).

Now, with the aid of the computational power of the SDSC, a dynamic molecular simulation can be run in a realistic environment to test inhibitors to various active sites in the enzyme. The binding of an inhibitor may alter the 3D structure of the model, and it's important to visualize this new conformation of the enzyme. This simulation could involve 30,000 to hundreds of thousands of atoms interacting in this 3D model, therefore the need of a supercomputer.

Essentially, instead of the old lock and key metaphor of enzyme action that presented a fixed view, dynamic molecular simulation is comparable to placing a large rock in a moving stream and watching how the flow of water changes, then trying other obstacles or adding more to reroute the stream most effectively.

Another feature possible is a 3D virtual reality view of the enzyme in lifesized form.  In the image below, you can see a virtual reality rendition of a protein ribbon model of an enzyme in which a researcher can examine the active sites for a better appreciation of the spacial arrangement and the changes that occur when you test an inhibitor or combinations of inhibitors. This could include testing inhibitors used for other diseases, as well as custom-design protein molecules.

Sdsc2

Here's the video with Dr. Rommie Amaro describing her work at the SDSC:

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