Frogs have thrived for hundreds of millions of years, spreading across virtually every corner of the earth, from tropical jungles to subarctic forests. Throughout their evolution, they have developed remarkable defenses — including previously unreported antibiotics — against the hordes of bacteria that thrive in their moist environments. Variants of these compounds may one day protect humans from drug-resistant pathogens.
In a new paper in Trends in Biotechnology (Cell Press), Cesar de la Fuente , Presidential Associate Professor in Bioengineering and in Chemical and Biomolecular Engineering in the University of Pennsylvania School of Engineering and Applied Science (Penn Engineering), in Psychiatry and Microbiology in the Perelman School of Medicine (PSOM), and in Chemistry in the School of Arts & Sciences , describes the creation of synthetic peptides, a class of antibiotics, derived from the secretions of a frog commonly found in South Asia.
Nature's Antibiotic Toolkit
The paper builds on previous work from de la Fuente's lab, which has discovered novel antibiotics in a range of unlikely places: the DNA of extinct organisms , including the wooly mammoth; the DNA of Neanderthals ; and the human gut microbiome .
"Each study is motivated by imagining environments where evolution would spur the creation of antibiotics", says de la Fuente. "Amphibians live in very microbe-rich environments. They very rarely get infected despite being surrounded by microbes, so they must produce antimicrobial compounds."
In 2012, researchers in China discovered that Odorrana andersonii, a species of frog first described in the late 19th century by a Belgian naturalist and named for its distinctive odor, secretes a peptide with antimicrobial activity, dubbed Andersonnin-D1.
However, that peptide tends to form clumps, increasing the likelihood of toxic side effects and diminishing its efficacy at fighting bacteria, making it unsuitable for clinical use.
Improving Nature's Molecules
In the new paper, de la Fuente and his co-authors demonstrate how "structure-guided design," a process involving minute changes to the peptide's chemical structure, yields multiple antibiotic candidates without the drawbacks of the unmodified peptide.
"With structure-guided design, we change the sequence of the molecule," says Marcelo Torres , a research associate in the de la Fuente lab and co-author of the paper, "and then we see how those mutations affect the function that we are trying to improve."
Turning Peptides into Potential Therapies
After going through two rounds of structure-guided design, the researchers then tested the resulting synthetic peptides against a range of bacteria. In preclinical models, the team found that the new compounds were as effective as last-resort antibiotics like polymyxin B in targeting harmful bacteria, without affecting human cells or beneficial gut bacteria.
The researchers developed and tested their peptides not only in single cultures but also in more complex bacterial communities, which allowed them to measure the effects in a more realistic microbial setting. "Those experiments are very difficult to set up because you need to grow different bacteria at once," says de la Fuente. "We had to come up with the specific ratio of each bacterium to have a sustained community."
If additional preclinical testing goes well, the researchers will submit the peptides for what are known as Investigational New Drug (IND) enabling studies, the last step prior to applying for approval from the U.S. Food and Drug Administration, at which point the drugs could be clinically tested.
De la Fuente underscores nature's profound potential in medical innovation. "We are excited that frogs — and nature in general — can inspire new molecules that could be developed into antibiotics," he says. "Thanks to the power of engineering, we can take those natural molecules and turn them into something more useful for humanity."
This study was conducted at the University of Pennsylvania School of Engineering and Applied Science. Cesar de la Fuente-Nunez holds a Presidential Professorship at the University of Pennsylvania and acknowledges funding from the Procter & Gamble Company, United Therapeutics, a BBRF Young Investigator Grant, the Nemirovsky Prize, Penn Health-Tech Accelerator Award, Defense Threat Reduction Agency grants HDTRA11810041 and HDTRA1-23-1-0001, and the Dean's Innovation Fund from the Perelman School of Medicine at the University of Pennsylvania. Research reported in this publication was supported by the Langer Prize (AIChE Foundation), the NIH R35GM138201, and DTRA HDTRA1-21-1-0014.
Additional co-authors include co-first authors Lucía Ageitos, Andreia Boaro and Angela Cesaro, and Esther Broset.
