Drugs from Deep Down
Two hundred feet below the spot where Tennessee, Alabama and Georgia meet, a group of mud-soaked explorers picks its way through cool, wet darkness.
The cavers are outfitted with knee pads and climbing gear and wear lights on their helmets like miners. They crawl through narrow stone passageways and carefully lower themselves into 200-foot pits.
Pale stalactites hang dripping from the cavern ceiling above them, while flowstone formations make it look like rock has bubbled up from the walls and floor. There's a distinctive, earthy smell in the air, like a damp basement.
One of the men, Brian Bachmann, recognizes the scent. It's actinomycetes, a kind of bacteria people use to make antibiotics.
Colonies of the stuff—along with unknown species of bacteria, fungi and other mysterious substances—flourish as though the cave walls were Petri dishes in a lab.
Bachmann stops. He takes a piece of filter paper out of his backpack and wipes it gently along the rock before sliding it into a sterile tube, sealing it shut and putting it back in his bag.
He'll take 20 to 30 more samples like this during the expedition, collected from a variety of locations in the cave: a pool of water, a patch of soil, a stalagmite.
Bachmann, a biosynthetic chemist, is hoping that his samples will reveal sources of new medicines.
The Glamorous Life of Secondary Metabolites
Bachmann analyzes his samples from his 12th floor laboratory at Vanderbilt University overlooking Nashville, Tennessee. He is interested not only in what molecules the samples contain, but also in how cave-dwelling creatures manufacture those molecules.
Bachmann ignores the molecules known as primary metabolites—DNA, amino acids, simple sugars and vitamins—that all organisms need to live.
His focus is on secondary metabolites, which endow organisms with abilities like communication and weaponry. These natural properties can be adapted for human use—to kill bacteria or reduce inflammation, for instance. Because of this, secondary metabolites, or chemically modified versions of them, have the potential to become invaluable drugs.
All of the following are secondary metabolites: caffeine, penicillin, codeine, steroids, bacitracin (an antiseptic), artemisinin (for malaria) and atropine (for cardiac arrest). And that's just the tip of the metabolite iceberg. Between half and three-quarters of all drugs on the market today are based on secondary metabolites.
The search for new drug sources—either discovering organisms that make interesting metabolites or finding new uses for known metabolites—is what gets Bachmann excited about crawling around in the mud.
"I love science," he says, and has since childhood (see "A Born Chemist"). "I brush my teeth with vigor every morning thinking about a problem, a puzzle, in chemical biology. You might think it's an obsession."
So far, his "obsession" has steered him into quests for better malaria drugs, cheaper HIV drugs, new technologies for drug discovery and half a dozen promising drug candidates.
It may sound like a motley collection of projects, but as Bachmann explains, "They're all unified by chemistry—the chemistry of how life makes molecules."
The long-term goal, he says, is to "know the design rules across all orders of life." He wants to understand life's construction processes so well that he can modify those processes to suit human needs.
"If we can teach E. coli to make ibuprofen or an AIDS drug—[or any other] compounds they don't make naturally—that will be the ultimate proof that we really understand," he says.
Do Drugs Grow in Caves?
Some chemists on the hunt for completely new drugs investigate natural products—particularly secondary metabolites.
Rainforests rich in plant and animal life have yielded compounds that led to drugs such as the cancer fighter Taxol®.
Other drugs and drug precursors, like a painkiller discovered in the venom of a cone snail, come from the ocean (see "Secrets of the Killer Snails" in the September 2002 issue of Findings).
"I have a lot of colleagues who go diving off coral reefs in Jamaica, Papua New Guinea and Indonesia. They work very hard, but they always come back tanned," laughs Bachmann. "I come back covered in mud, bruised, with a busted ankle."
Perhaps the unglamorous conditions in caves kept other people away, because Bachmann thinks he's one of the first to go spelunking in search of drug-making organisms. He suspects that the secluded, nutrient-poor environments underground create unique collections of microorganisms that constantly churn out metabolites to stay alive and out-compete their neighbors.
Bachmann wants to identify those metabolites and find out which ones could help treat human disease. To do that, he not only collects his filter paper swabs, he also sets out collection traps he hopes will entice microorganisms to come inside and grow. He comes back to collect the traps about a month later.
With each trip below ground, Bachmann learns more about which areas of a cave are most likely to have new and exciting microbes.
"For instance, we've learned not to get samples from bat guano," he says. "That's the one place we've never found any kind of microorganisms we're interested in."
He also stays away from where humans have tread before, figuring that way he's more likely to find microorganisms no one else has discovered—and less likely to accidentally come back with microbes from some previous spelunker. Sometimes that involves convincing his caving partner to "Spiderman his way up a wall to get at some remote crevice."
In general, while collecting samples, he focuses on "being as creative as possible. We try to get as much diversity as we can."
And he's careful not to damage the caves or take more material than necessary. His team follows what he calls the caver's motto: "Take nothing but pictures, leave nothing but footprints, kill nothing but time." After a trip, "there is more soil on our boots than in our sample tubes," he says.
In the 4 years he's been searching, Bachmann has plucked more than 20 compounds from cave organisms. About half of them are new to science.
"That's actually a very high success rate," he says, since a typical natural product discovery rate is more like 1 in 20. "It seems there is something special about caves."
How to Spot a Drug Candidate
When Bachmann brings his samples back to Vanderbilt, he tries to grow the most promising microorganisms in his lab.
It's not easy. The microbes are far from home and don't always survive in their new surroundings.
But if they make it, they sometimes do so with a vengeance. They've subsisted on meager rations all their lives, like college students living on instant noodles. When Bachmann puts them in dishes coated with nutrients, their meta bolite production goes into overdrive.
"It's like they're at an all-you-can-eat buffet," says David Wright, a fellow chemist and one of Bachmann's collaborators at Vanderbilt. "They pump out all these potentially interesting compounds."
To find these compounds, Bachmann ferments the samples in a bacterial beer containing tens of thousands of compounds. Then he faces what he calls "the central question in natural product discovery: What's interesting in that broth, and how do you pull it out?"
He could run a test on the whole brew to look for a single, specific ingredient—say, a cholesterollowering enzyme. But that risks overlooking other compounds like potential antidepressants or bloodclot busters.
Another technique is to add a strain of bacteria to the culture dish. If the added bacteria die, Bachmann surmises there's an antibiotic in the broth.
To isolate the antibiotic molecule, he must analyze each ingredient separately. Then it's rinse and repeat with a different bacterial strain.
It's a tedious process, and screening every broth ingredient for every possible biological activity isn't practical. So Bachmann has partnered up with academic and industry colleagues to develop technology that searches faster and smarter.
One method, developed by Vanderbilt chemist John McLean, is called ion mobility mass spectroscopy—a technical way of saying it flags molecules with funky shapes. Because many drugs have unusual shapes that allow them to do specific jobs in the human body, the spectrometer helps Bachmann pinpoint compounds that may have drug-like activity.
Another program in progress goes by the nickname NELI (short for Natural Extract Lead Identification System). In this case, "lead" (pronounced "leed") refers not to the heavy metal but to a molecule that might lead to a new drug.
Usually, natural products themselves don't end up on pharmacy shelves, but rather serve as drug leads. Scientists like Bachmann chemically tweak them to make them more effective, less toxic or otherwise better suited to the human body.
NELI lets Bachmann compare different growth conditions to find those that encourage an organism to produce interesting compounds.
He and collaborator Wright use NELI to search for compounds that might treat malaria.
Beyond the search for new secondary metabolites, Bachmann is trying to unlock the secrets of how organisms make them in the first place.
Sometimes this involves analyzing the genome of a promising microbe and trying to predict what kinds of enzymes or compounds it makes. For example, he decoded the genetic "blueprints" for aking anthramycin, a kind of natural chemical equivalent to Valium® that came from an organism found in a rotting compost heap.
He uncovered the molecular structure of a compound called K-26 found in a soil sample next to a pond in Japan. K-26 contains a rare carbon-phosphorus bond and lowers blood pressure like a powerful ACE inhibitor. His work could provide insight into making a better blood pressure drug.
Bachmann is also working with Vanderbilt pharmacologist Tina Iverson to see if they can resuscitate a failed antibiotic called everninomycin.
It's critical to find new antibiotics because bacteria are becoming resistant to many existing treatments. Most new antibiotics "are really just modifications" of existing ones, says Iverson. She and Bachmann want to find truly new antibiotics.
Everninomycin could have been one, if it had worked better when it was tested in people.
Bachmann and Iverson believe that, by genetically "tweaking" the organism that makes everninomycin, they could coax it to produce a safer, more effective cousin—a potential new antibiotic.
Bachmann is also working with Iverson to genetically engineer E. coli bacteria to make affordable HIV drugs.
Drugs called nucleoside analogs make up about half our arsenal against tough viral infections like HIV and hepatitis. But manufacturing them is so expensive that people in developing countries can't afford them. If Bachmann and Iverson can co-opt E. coli into churning them out in large and cost-effective amounts, the drugs could fall to one-tenth of their current price.
"Right now, that's still a dream," says Bachmann. He compares the process to teaching organisms to make biofuel.
Still, if it takes years to pull off—or even if it never comes to fruition—the project is already contributing to basic science knowledge. And that knowledge has the potential to pay off in unforeseen ways.
In Search of Something New
In caves or at home, the search for the new extends throughout Bachmann's life.
He likes to use new power tools to fix up his family's 1940s-era home and dabbles in landscaping. He and his wife, Beth, an award-winning poet and English professor at Vanderbilt, experiment with new culinary techniques when they make their own Indian food. When he gets bored with his current music, he pumps his nieces and nephews for new bands.
"Basically, if I can find something that sounds new, I get pretty excited," Bachmann says.
He has also been engrossed in what he fondly calls his new "synthetic biology experiment": his 3-year-old daughter, Ilyana.
"She's teaching me a lot. I'm learning fundamental things about what it's like to be human, and consciousness, and identity...."
He brings that same thrill of insight to his professional life.
"It's amazing that we are now potentially going to be able to understand much of what it means to be human, through chemistry," he says. "Sometimes my head reels with the magnitude of the understanding we're gaining about the molecular basis of who we are and what we could become."
A hobbyist philosopher, Bachmann embraces the big questions in science and in life. He wants to know: "Why does a soil organism make a compound that lowers human blood pressure? How does life manage these small miracles of chemical synthesis?"
"Brian's not afraid to grapple with really big questions," says collaborator Wright. "It makes me not afraid to ask my own big questions."
Whether he's pondering the meaning of life or examining the structure of a single molecule, Bachmann never loses his enthusiasm for the potential of synthetic chemistry.
"It's like walking on the moon. Oftentimes you look down at your feet and think, 'Nobody else has stepped here before.' That's a wonderful feeling, when you think you're the first person to have seen a new way to make a natural molecule, or use life's design rules to build a molecule, or see a molecule no one else has described."
With a lot of hard work and a little luck, Bachmann's ventures into unfamiliar territory—whether in caves or in the lab—will yield new knowledge and new drugs to help improve people's health around the world.
A Born Chemist
You could say that Brian Bachmann was destined to be a chemist.
His parents met in an organic chemistry class in college.
A scientist, entrepreneur and inventor, Bachmann's father started a chemistry company in the basement of the family's Connecticut farmhouse.
Bachmann remembers that he loved working in the lab as much as other kids loved playing with toys. One Christmas Day when he was young, he set aside his newly opened presents and went into the lab with his father.
"It was something fun to do," he recalls. "And at the end of the day, we had a patentable invention."
He learned from his father about the scientific method—"knowing what's in your experiment, changing one thing at a time, having a hypothesis and testing it"—as well as the importance of thinking outside the box and deriving joy from science.
But like any teenager in the mood for rebellion, Bachmann decided he wasn't going to go into chemistry. In college, he took courses in physics, philosophy and English.
Then he took an elective in organic chemistry, and fell in love.
"It's such a beautiful system. You could come up with a theory on a piece of paper and test it the same day by mixing things in a flask, stirring and heating it and analyzing the results," he says.
A few years spent in industry taught Bachmann to look for practical applications, embrace useful technology and put together an interdisciplinary team.
Biochemists, synthetic chemists, microbiologists, molecular biologists, engineers and geneticists now work side by side in his lab to solve problems in innovative ways (see main story). The lab is set inside Vanderbilt's medical center and across the street from a hospital, so they never lose sight of their ultimate goal to help people.
Overlooking it all are magnetic puppets of Charles Darwin and Thomas Edison holding hands—the evolutionary biologist and the genius inventor, reminding Bachmann's team to work together —S.D.