Fossil antibiotics

Stat covers a medicine-making strategy right out of Jurassic Park, with a UPenn researcher named Cesar de la Fuente, who is looking for protein-chains called peptides in the fossilized remains of Neanderthals, giant sloths, mammoths, and other prehistoric creatures in order to discover chemicals that can be used to make medicines:

His team uses robots to resurrect the most promising snippets and then tests whether they can clear infections in mice at rates comparable to the standard antibiotic polymyxin B. Last year, he named the approach “molecular de-extinction” — a much safer, more feasible and perhaps less lucrative version of Jurassic Park.

“What if we brought back molecules instead of just an entire organism?” he said.

De la Fuente’s research, detailed in a July publication and preprint earlier this month, relies on genomes painstakingly cobbled together by paleogeneticists over decades: Fragments of A, T, G, and Cs fished out of ancient bones, tundra-buried carcasses, and 19th century taxidermy and strung together into a coherent text.

Those scientists were interested in understanding evolution, work that won Svante Pääbo a Nobel Prize last year. With the sequences freely available online, de la Fuente saw a potential medical trove.

De la Fuente says modern mammals are next, along with most known viruses and most known bacteria.

His early work improved on nature’s wimpier molecules. He’d take a peptide in guava seeds or wasp venom already known to have activity against bacteria and design an algorithm to generate thousands of variants before selecting the ones likely to be the most potent — evolution on a chip.

But he and his team also built algorithms that acted as a magnifying glass, searching for new sequences that might have previously undiscovered bacteria-killing properties. In 2021, they looked at the entire human proteome — every portion of DNA known to code for a protein — and found over 2,000 such peptides.

Many were surprising. Biology textbooks say that genes code for proteins. Really, though, genes code for peptides. Some peptides, such as insulin, function on their own. Most act like machine parts, folding with other peptides into proteins that do the real work.

De la Fuente’s paper showed that many of those machine parts had antimicrobial properties, even if the machine itself was dedicated to, say, keeping neurons alive or the heart pumping.