How GPU-Driven Drug Discovery is Finding New Targets to Cure Cancer

by Liz Austin

The race is on to understand how cell mutation causes cancer, which kills hundreds of thousands worldwide each year and is the second leading cause of death in the U.S.

Setting the pace is Rommie Amaro, Ph.D, associate professor at the University of California, San Diego, whose research on how to interrupt the mutation process is aided by high-performance computers.

Amaro is focused on the anti-cancer drug discovery pipeline using advanced molecular dynamics simulations powered by GPUs. The work recently earned her a $200,000 grant as part of the NVIDIA Foundation’s Compute the Cure initiative.

“Enormous gains in computing power are enabling a new framework for drug discovery,” Amaro said in a presentation she gave at our GPU Technology Conference this week.

Recent work involves using computer simulations to capture various shapes of a tumor suppressor, the protein called p53. It’s known as “the guardian of the genome” because it’s a key regulator of cell growth and development in normal cells.

In its healthy form, p53 helps with cell repair or triggers cell death if the damage is too great. When p53 doesn’t function properly, or mutates, it allows cancer cells that it would normally attack to escape.

“P53 protects the cell, usually,” Amaro said. “But in more than 50 percent of human cancers, if this cell is damaged, tumors grow.”

Computer simulations capture not just how proteins are built, but how they function inside the body. The simulations run on GPU-powered computers revealed a new “binding site” that may help cancer researchers create new drugs to help “reactivate” p53 when it mutates and doesn’t do its job.

The computational approach led to the discovery of p53 reactivation compounds in six months, compared to all the research efforts of the previous 20 years combined,” she said. “This is a great example of the power of the model.”

By building shareable computer-aided drug discovery workflows, her team can create recipes that other researchers can follow to find new drug targets or reproduce the work done by their peers.  The goal: to accelerate the discovery of new and safer medicines to fight cancer.

“Cancer is a big complex disease and it’ll take as many people as possible to come up with cures,” Amaro said.