Computing for a Cure - page 2
One We'd Like to End
The key to blocking the development of HIV lies in something called the HIV protease. A protease is an enzyme that breaks down a protein into smaller molecules. In this case, it breaks down protein molecules to create the virus that leads to AIDS. Scientists have known about this sequence of events for years and created drugs called protease inhibitors that had mixed success blocking the actions of the HIV protease.
To create more effective protease inhibitors, it is necessary to know the molecular structure of the protease. According to Simmerling, the problem with developing such drugs is that most of the time the protease molecules are in one of several "closed" states, where they are not susceptible to attack from the drugs. The research team, therefore, had to determine the structure of the molecules when they were in an "open" state.
"You have to watch in detail how the molecules move and every now and then you see it opening up, then it would close down again," he says. "That process of opening and closing is what is thought to be a lot of the drug resistance in AIDS patients."
He compares it to watching someone's daily activities. You may see that the person spends about half of her day inside the house and the other half outside. What you need to do is zero in on that point where she transitions from an outside state to an inside state--the few seconds out of the 24 hours where she unlocks the door and enters the house. In the case of the HIV protease, the open state is measured in nanoseconds and is not likely to be found by physical observation. It can, however, be done through simulation.
"These simulations show the behavior of the molecule and where all the atoms are moving as a function of time," says Simmerling.