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Identifying the optimal drug treatment is like hitting a moving target. To stop disease, small-molecule drugs bind tightly to an important protein, blocking its effects in the body. Even approved drugs don't usually work in all patients. And over time, infectious agents or cancer cells can mutate, rendering a once-effective drug useless.
A core physical problem underlies all these issues: optimizing the interaction between the drug molecule and its protein target. The variations in drug candidate molecules, the mutation range in proteins and the overall complexity of these physical interactions make this work difficult.
Shantenu - Jha - Department - Energy - DOE
Shantenu Jha of the Department of Energy's (DOE's) Brookhaven National Laboratory and Rutgers University leads a team trying to streamline computational methods so that supercomputers can take on some of this immense workload. They've found a new strategy to tackle one part: differentiating how drug candidates interact and bind with a targeted protein.
For their work, Jha and his colleagues won last year's IEEE International Scalable Computing Challenge (SCALE) award, which recognizes scalable computing solutions to real-world science and engineering problems.
Drug - Company - Library - Millions - Candidate
To design a new drug, a pharmaceutical company might start with a library of millions of candidate molecules that they narrow to the thousands that show some initial binding to a target protein. Refining these options to a useful drug that can be tested in humans can involve extensive experiments to add or subtract atom groups at key locations on the molecule and test how each of these changes alters how the small molecule and protein interact.
Simulations can help with this process. Larger, faster supercomputers and increasingly sophisticated algorithms can incorporate realistic physics and calculate the binding energies between various small molecules and proteins. Such methods can consume significant computational resources, however, to attain the needed accuracy. Industry-useful simulations also must provide quick answers. Because of the tug-of-war between...
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