Princeton Engineering researchers have isolated a compound that kills bacteria that can cause incurable infections.


Artist’s rendering of Enterobacter

The compound, called cloacaenodin (chloa-say-nodin), is a short, slip-knotted chain of amino acids known as a lasso peptide, encoded by gut-dwelling bacteria as a defense mechanism.

This peptide works by attacking rival bacteria, and it’s a very potent killer, according to A. James Link, professor of chemical and biological engineering. If harnessed by science, it could be redirected to fight infections that are not treatable by today’s medicines.

When released, the peptide hooks into a target cell’s RNA-producing enzymes and shuts down basic cell functions. It targets an especially fearsome group of pathogens belonging to the genus Enterobacter, which the Center for Disease Control and Prevention (CDC) has identified as a primary driver in an accelerating global crisis - bacterial infections that increasingly do not respond to conventional antibiotics.

“Not only does [this peptide] kill off-the-shelf, historical Enterobacter strains, it also kills Enterobacter strains that actually have come from patients in the hospital and that are drug resistant,” said Link, who published a paper on the findings in ACS Infectious Diseases.

Link’s research group has discovered several peptides in this same class — structured with a ring knotted to a tail that threads back down through the ring, like a lasso in a rodeo trick — that show promising antibacterial properties.

He said cloacaenodin is unique because it can kill clinically relevant drug-resistant strains, making it a promising subject for antibiotic development. The finding also suggests his peptide-mining and synthetic biology techniques could reveal more antimicrobial compounds with strong drug-development potential, an essential step in quelling the growing superbug crisis.

“If it’s made by one Enterobacter species, it’s likely going to kill other species of Enterobacter. So it’s this sort of guilt by association approach,” Link said.

This gives researchers a way to prioritize peptide-mining hits, since peptides that are encoded in strains related to pathogens are more likely to have interesting bioactivity, he said.

“It’s one thing to kill bacteria,” said Drew Carson, a fourth-year PhD student in chemical and biological engineering and the paper’s first author. “It’s another thing to kill bacteria that can actually make people really sick.”

Guilt by association 

While cloacaenodin shows strong antibacterial properties, it’s only the first of many steps to a new treatment. Determining a compound’s safety is difficult and expensive, and moving from initial testing through the regulatory process takes a minimum of 10 years.

CARB-X research chief Erin Jorgensen said that, historically, some peptides have proven toxic to the kidneys, curbing their use in drugs. But peptides with bacterial-selective activity that don’t harm animal cells will likely lack this toxicity, according to Link.

But this new compound shows promising antibacterial properties and the researchers have only just begun to consider what comes next. They plan to start by testing it in animal infection models to confirm that it can clear the infection and that it is safe for animal cells. More broadly, however, this compound’s discovery suggests that Link and his team have developed a peptide-mining toolkit that will turn up many other interesting compounds in the future, and there is no telling where that will lead.

“The way that we find these peptides is by looking at the genome sequence of an organism,” Link said. “If you give us any DNA sequence, we can very rapidly and very accurately figure out if there’s a lasso peptide encoded within it. We also know about certain sequences within lasso peptides that means there’s a good chance that they’re antimicrobial. And that’s how we homed in on this one.”

Link said there are thousands of Enterobacter genome sequences that have been entered into scientific databases, and the lasso peptide his team discovered is found in only a handful. One of those organisms came from a hospital patient who had a lung infection. And because of his guilt-by-association approach to finding the peptide, they knew it would likely kill many related organisms that don’t have the exact same genes.

“We tested it against a dozen or so strains and saw activity,” Link said, referring to antibacterial activity. “But it potentially has activity against several hundred and maybe even thousands of these sequenced isolates of Enterobacter.”

The paper, “Cloacaenodin, an antimicrobial lasso peptide with activity against Enterobacter,” was published in ACS Infectious Diseases.