SuperbugsPlugging an antibiotic pump

Each year in the U.S., at least 23,000 people die from infections caused by antibiotic resistant bacteria, according to the Centers for Disease Control and Prevention.

Using computer modeling, researchers from Sandia National Laboratories and the University of Illinois at Urbana-Champaign are helping to develop the means to prevent some of those deaths.

One way bacteria develop resistance to many different antibiotics is by producing pumps that spit out unfamiliar small molecules, such as antibiotics, before they can do any damage. The researchers teased out the details of how one antibiotic pump works.

The eventual goal is to develop new drugs to plug the pump so it cannot spit out antibiotics, perhaps restoring their effectiveness, said Susan Rempe, Sandia computational biophysicist. She added, “Now that we have the structure of the pump and know how it works, scientists can design a molecule that sticks tightly to the transporter. I think that’s doable in the near-term, maybe five years.”

This research was recently published in the Proceedings of the National Academy of Sciences.

Refining data to determine pump’s detailed structure
The specific pump researchers studied, called EmrE, comes from E. coli, common bacteria that occasionally cause food poisoning. The pump recognizes and removes moderately oily, positively charged small molecules, said Josh Vermaas, a former Illinois graduate student whose work with Rempe was supported through Sandia’s Campus Executive Program. Many common antibiotics including streptomycin, doxycycline and chloramphenicol are oily and positively charged.

Their first step was to determine a detailed structure of the pump. The starting structure of the pump was very rough, missing much of the essential chemical details, and misshapen, Vermaas said. Rempe added it can be particularly challenging to get good structural data of drug transporters like EmrE because they are flexible. Imagine having to take a picture of a wriggling toddler with a sluggish camera: the resulting photo is more of a blur than an exact likeness.

They combined experimental data from a variety of common biophysical methods such as X-ray crystallography, cryo-electron microscopy and electron paramagnetic resonance spectroscopy as well as decades of knowledge of the most likely internal arrangements of amino acids, the building blocks of proteins, to produce a high-resolution structure of the pump.