The search for medicinal agents in NYC dirt

The dirt of New York City parks may seem an unlikely way to benefit modern medicine, but scientists in an Upper East Side university lab in Manhattan say they found genes from the dirt’s bacteria that could lead to use in antibiotics and anti-cancer treatments.

NEW YORK CITY, NEW YORK, UNITED STATES (DECEMBER 08, 2016) (REUTERS) – Researchers at The Rockefeller University in New York City have found that bacteria extracted from the dirt from parks in Manhattan, Brooklyn and Staten Island contain genes “that might encode drug-like molecules” like antibiotics, immunosuppressants and cancer-curing agents.

“We did a large scale screen of samples from New York looking for these genes and we were able to find many genes that we don’t know what they do, but a subset of genes that we can predict would make molecules that are currently in the clinic,” said Dr. Sean Brady, head of the laboratory of genetically encoded small molecules at The Rockefeller University. “Almost any drug that’s coming from a bacteria that was found someplace else in the world, we could identify a sequence that suggests a bug like that exists in a sample of a New York City park.”

“Many of the molecules that we’ve used in the clinic have historically been isolated from organisms that have had their origin all over the world and we’re able to find genetic evidence that you’d be able to find the similar or the same gene clusters and therefore similar or the same molecules in New York City’s park soil,” said Zach Charlop-Powers, postdoctoral fellow at the laboratory of genetically encoded small molecules at The Rockefeller University.

The team published their findings in the Proceedings of the National Academy of Sciences of the United States of America in November. They looked at 275 soil samples taken from Central Park in Manhattan, Prospect Park in Brooklyn and parks in Staten Island in the hope that locally found dirt may throw up chemical novelties and lead to new drugs.

“Not just antibiotics, but a large number of our pharmaceutical agents, the things we use in the clinic to cure cancer, immunosuppression, anti-bacterial agents come originally from studying bacteria,” said Brady. “And so the idea here is to guide you to not only those old molecules, but guide you to bacteria that might produce new molecules that have new activities.”

“Almost any molecule you can think of that might have come from bacteria, so if you don’t know those types of molecules, things like vancomycin, the antibiotic of last resort, we can find molecules or genes that we think would encode molecules like that. Rapamycin, immunosuppressant, we can find genes that encode molecules that look like that, or even new versions of those molecules,” continued Brady.

More than half of all medicines used today were inspired by or derived from bacteria, animals or plants. Humans share the Earth with an awful lot of bacteria – around 5 million trillion trillion of them, according to an estimate in 1998 by scientists at the University of Georgia. Brady says scientists no longer have to go to far-flung places like the Amazon rainforest, a great cauldron of biodiversity, to produce potential medicine.

“The traditional approach for finding molecules that would be therapies from bacteria is that you culture bacteria, and because you can only culture a small fraction of bacteria from the environment, it means you’ve made a very shallow search all over the world,” said Brady. “Now that we can sequence into all of these bacteria that we can’t culture, or we don’t know what’s going on in their genomes, means we can make much deeper searches and it suggests there’s far more diversity even in our backyard than we thought in the past, which means maybe we don’t have to go to these rare environments or environments that are endangered to go find some of these molecules, so you could just find them in a simple place like parks in New York City.”

Brady will analyze the dirt further at Lodo Therapeutics, a drug discovery company he co-founded that’s partially funded by the Bill and Melinda Gates Foundation. Charlop-Powers joined Lodo Therapeutics as its scientist.