Night of the Living Bacteria: How GPUs Aid Fight Against Zombie-Like Bugs

by Jamie Beckett

When health officials use words like “nightmare” and “apocalypse” to describe a problem, it’s probably time to pay attention.

We’re in a war with antibiotic-resistant bacteria, and we’re losing. Antibiotics that saved millions of lives in the last century are increasingly powerless against a growing number of superbugs that have evolved to survive our pharmacological onslaught.

There’s a dearth of new antibiotics to treat what the U.S. Centers for Disease Control calls “nightmare bacteria.” This has led some — including the U.K.’s chief medical advisor — to warn of a post-antibiotic “apocalypse” in which ordinary infections, surgery, tuberculosis and even a papercut could be a death sentence.

A new paper in Science magazine offers some hope. Using GPU-accelerated supercomputer simulations and lab experiments, researchers discovered why staph bacteria — the leading cause of healthcare-related infections — can be so tough to beat. Their work could point the way to new treatments for now-invincible bacterial foes.

methicillin-resistant Staph bacteria
Methicillin-resistant staff bacteria (in magenta). Image courtesy of the National Institutes of Health.

Stronger Than Superglue

The researchers, from the Beckman Institute at the University of Illinois and the University of Munich, studied a type of staph infection known as methicillin-resistant Staphylococcus aureus (MRSA), which fails to respond to the antibiotic commonly used to treat it. Left unchecked, it can lead to sepsis and even death.

The researchers discovered the mechanism that makes MRSA cling so tightly to its human host: a series of hydrogen bonds arranged in a corkscrew shape that works like superglue to clamp bacteria protein molecules to human ones. Next, they attempted to pry apart the two types of molecules to determine the strength of these bonds under stress.

“The bacteria are so well-glued to humans that you can’t detach them,” said Rafael Bernardi, a research scientist at the Beckman Institute. “It’s easy to break one hydrogen bond. What makes this so strong is that you have to break all the bonds at once.”

The Tie That Binds

Staph infections are common in hospitals and nursing homes where patients are already sick or weak. Medical implants like a hip replacement or pacemaker also pose a risk because bacteria commonly stick to their surfaces.

The researchers used two methods to figure out why MRSA infections are so hard to conquer. Working with a high-resolution atomic-force microscope, the University of Munich team tried to physically separate bacteria molecules from the human ones. The Beckman Institute team attempted the same feat by running 2,400 molecular dynamics simulations on the GPU-powered Blue Waters supercomputer at the University of Illinois.

The results were identical: both pointed to the super-strong hydrogen bonds as the culprit for MRSA’s invulnerability.

“We usually get good agreement between the two methods, but this was just amazing,” Bernardi said. “The simulation let us see every atom at every second, so it gave us many more details than the microscope.”

An illustration of the hydrogen bonds (in purple) that attach the bacterial protein (blue and green) to the human protein (orange). These bonds are the mechanism that makes some Staph infections and other antibiotic-resistant bugs so hard to treat. Image courtesy of Rafael Bernardi, Beckman Institute.
An illustration of the hydrogen bonds (in purple) that attach the bacterial protein (blue and green) to the human protein (orange). These bonds are the mechanism that makes some Staph infections and other antibiotic-resistant bugs so hard to treat. Image courtesy of Rafael Bernardi, Beckman Institute.

New Treatments Possible

Bernardi ran his experiment solely on Blue Waters’ GPU nodes, using CUDA-accelerated molecular dynamics and visualization software. Without the GPUs, he said, he could not have done so many simulations and achieved such an accurate result.

“I really hope people can use what we learned to develop new strategies to treat staph infections,” he said. For example, drug companies could develop a treatment that blocks or weakens bond formation.

* The top image is an illustration showing the beginning of a bacterial infection. At the bottom,  human proteins coat the surface of a medical implant. The colorful rods are bacteria initiating the infection. The transparent structure below the center bacteria is the protein that anchors bacteria to the implant surface. Image courtesy of the NIH Center for Macromolecular Modeling and Bioinformatics.

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