Grant funds supercomputer in fight against cancer


June 11th, 2014

Omaha, NE – The American Cancer Society estimates that more than 46,000 people will be diagnosed with pancreatic cancer in the U.S. this year. Of those, more than 39,500 of them will die, according to the ACS.


Pancreatic cancer is one of the most aggressive and deadly forms of cancer. The University of Nebraska campuses in Lincoln and Omaha as well as the Nebraska Medical Center will take part in the research funded by a $250,000 grant from the Nebraska Research Initiative to help find new drug matches.

Joe Runge, UNeMed’s director of business development, said the new computer will create complicated 3D models of molecules so their chemistry can be simulated. He said this drastically cuts down on costs and time of the labor intensive old form of research.

“Making drugs is really complicated because you have to have something that is effective biologically,” Runge said. “You need to have a drug that is actually going to interact with the target molecule, you need to have a drug that is going to get inside the cell and get to the cell’s nucleus. But at the same time you need a drug that is not going to be poisonous.”

Dr. Surinder Batra, professor and chairman of the UNMC’s Department of Molecular Biology. (Photo Courtesy UNMC)

Dr. Surinder Batra, professor and chairman of the UNMC’s Department of Molecular Biology. (Photo Courtesy UNMC)

Runge said he is directly collaborating with Dr. Surinder Batra, professor and chairman of the UNMC’s Department of Molecular Biology, and Dr. Jonathan Vennerstrom, professor at UNMC’s College of Pharmacy. Runge said this project will be made easier as Dr. Batra is an expert on simulating the interactions between drugs and cells.

Dr. Batra discovered an important molecule more than ten years ago. Its name is pancreatic differentiation factor 2, or PD2, and according to Runge, if it works it would take discoveries about diseases and translate them to new medicines. He said PD2 can help grow stem cells, but they start having issues if they present these same set of instructions to cancer cells. Runge said cancer cells that show higher levels of PD2 can perform like stem cells, for example, developing tumors that can be resistant to medication.

Finding a match for PD2 is the goal. Thus far, through research, Dr. Batra found PD2 can result in self-renewal of cancer cells, according to Runge.

“Lots of times what happens is you kill the majority of the cells in the tumor but there is this small population of cells left over that are able to grow after being treated with chemo-therapy,” Runge said. “What Dr. Batra discovered is PD2 is essentially a new marker of self-renewal in these resistant cancer cells.”

Runge said a deep understanding of chemistry is important when finding new drugs. He said the project is in good hands with Dr. Palermo’s simulation abilities and Dr. Vennerstrom, who is an expert chemist.
Nicholas Palermo is an application specialist with the Holland Computing Center at UNO. He is in charge of building this supercomputer. He said it has been both exciting and significant. He said he expected the project to be finished within the year time-frame given on the grant.

“I am sitting here with a finished model in front of me and I am ready to start the next piece,” Palermo said. “We are hoping sometime by May to have pushed this through to have a real chemical that works in his model and have it validated.”

Palermo said the computer model of PD2, will simulate with millions of other known molecules. He likened the process to making a key.

“To put it simply, when we are doing drug design, it’s like making keys for a lock,” Palermo said. “You typically have a picture of the lock, essentially I have to use a written description of the lock, build an image of it and build keys for it. You need extremely powerful hardware to fold a protein from scratch. That’s what we are attempting here.”

Runge said the best part about working on this project is they are utilizing everyone’s best talents and skills for a common goal.

“In addition to helping explore this opportunity to create new products that could help treat very deadly cancers,” Runge said. “We are also building the infrastructure on this campus wide scale that will make possible new kinds of research at the university that will be very, very compelling.”

Palermo said he doesn’t see the project being a failure because it opens a door to so many possibilities. He also mentioned the supercomputer will have updates and upgrades to its processing power as time goes on.

“If we can get it to work for PD2, we can get it work for about any protein as long as we can fold it with our hardware,” Palermo said.

Palermo said in the search for the fit for PD2, it they can’t find one, he said he can combine components of the best suits to custom-build potential candidates. So the supercomputer and its capabilities could shape new cancer research, according to Runge and Palermo.

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