Miracles happen: Synthetic biologists tap into ancient herbal pharmacy to cure malaria and AIDS
story by David Pescovitz
photos by Bart Nagel
For 3.6 billion years, evolution has governed the biology of this planet. Molecular biologists can now shift bits of DNA from one organism to another, but the parts they play with are limited to what Mother Nature provides. Recently, Mother Nature teamed up with a handful of researchers whose aim is nothing short of reengineering life. UC Berkeley is a core center of this new discipline called synthetic biology, where genes, proteins, and cells are snapped together like Tinkertoys to build living systems.
Sweet wormwood, or Artemisia annua, used by Chinese herbalists since A.D. 150 to treat fevers, today holds promise of a cure for malaria, a disease that kills one African child every 30 seconds.
BART NAGEL PHOTO
Already, synthetic biology projects are under way at Berkeley to convert bacteria into chemical factories that produce anti-malaria treatments for pennies instead of dollars. Similar microbial factories could crank out the costly anti-cancer drug Taxol, synthesized from the Pacific yew tree, or produce a promising anti-AIDS drug derived from the Samoan mamala tree.
See related story about Keasling's work on an anti-AIDS drug derived from the Samoan mamala tree.
“The idea of synthetic biology is to do for biology what electrical engineers have done for circuit design and chemists have done for the synthesis of chemicals,” says Jay Keasling, professor in the Departments of Chemical Engineering and Bioengineering. “We’re turning biology into an engineering field.”
Keasling is the hub of UC Berkeley’s pioneering synthetic biology breakthroughs. In December, the Institute for One World Health—the first nonprofit pharmaceutical company in the United States—received a windfall $42.6 million grant from the Bill & Melinda Gates Foundation to support Keasling’s development of a microbial factory to cure malaria—one of the world’s deadliest diseases.
A parasitic blood disease, malaria claims more than one million lives each year in developing nations. Most are children under five and pregnant women from the poorest parts of rural Asia or Africa, where people live without access to insecticides, protective netting, or glass windows to keep mosquitoes at bay. Synthetic quinine, once hailed as malaria’s cure-all, is now considered largely ineffective because the disease quickly mutates into drug-resistant strains.
Ironically, the solution has been available for millennia. Since A.D. 150, Chinese herbalists have used an extract from Artemisia annua, the sweet wormwood plant, to treat fevers. Chinese researchers isolated the drug artemisinin 40 years ago to treat Vietnamese troops. Used in the early 1990s during a malaria epidemic, it cut the death rate by 97 percent. As other anti-malarials rapidly began to fail, world health authorities embraced artemisinin as the best first-line defense against the disease. The problem is that there’s just not enough of it.
Currently, the drug is extracted from wormwood cultivated in China and Vietnam. The plant takes eight months to mature, and drug companies have heard of Asian speculators hoarding what little remains of the herb. Last fall, the shortage caused artemisinin’s price to quadruple. Even if farmers dramatically stepped up production, harvesting the plants and extracting the chemical component that resides in its leaves is difficult, labor intensive, and costly. As a result, the price of the drug is $2.40 per treatment course, far too expensive for patients in developing nations. Keasling’s technology would reduce the cost of treatment tenfold to as little as 25 cents a treatment course.
“We need a sea change in the way drugs are produced,” Keasling says. “The cost of biopharmaceutical research, development, and production is pricing us out of medicine in this country. Now think about the developing nations where they spend less than $4 per person on health care annually. How can we ever make enough affordable drugs for the diseases that are really killing most of the people on the planet?”
The synthetic biology approach is to build more factories, albeit unusual ones—chemical factories inside bacteria. For several years, Keasling and his colleagues—including postdoctoral microbiology fellows Vincent Martin and Jack Newman and chemical engineering graduate students Doug Pitera and Sydnor Withers—labored in the wet lab to build a working microbial factory from just 12 genes borrowed from three organisms: bacteria, yeast, and wormwood.
The human gut bacterium E. coli was the laboratory host of choice because it grows so quickly. “We can engineer the bacteria we’re working with, in this case E. coli, to produce artemisinin,” says Dae-Kyun Ro, a research scientist in Keasling’s lab. “E. coli takes just 20 minutes to double in size under laboratory growth conditions."
Fifth-year chemical engineering doctoral students Doug Pitera (right) and Sydnor Withers (left) are key members of the 20-person multidisciplinary artemisinin project in Keasling's synthetic biology lab. "My dream is to see my laboratory's technology producing inexpensive drugs for the Third World," says Keasling (center).
BART NAGEL PHOTO
It’s also a very well studied organism, Pitera adds. “Think of the system we’re building as if it were a tree,” says Pitera. “We constructed the trunk of this tree, an eight-enzyme process, taking us from the base metabolites, or chemicals, in E. coli to the precursors we needed to create an isoprenoid, the large family of natural products, of which artemisinin is one. Now, we’re moving from those precursors down one branch of the tree to artemisinin,” he says. “We could just as easily have taken the branch that leads to the anti-cancer drug Taxol, or the anti-HIV compound prostratin, even carotenoids or natural rubber—all isoprenoids, and only available in small quantities from natural sources.”
Over the last few years, Keasling’s team has stepped up production inside the microbial factory a millionfold. They are in the process of identifying a few more genes in wormwood that, if transplanted into E. coli, could enable the bacterium to go a few extra steps in the chemical process and actually produce artemisinic acid. “We’ve added a ninth enzyme that directed us down the path toward artemisinin, and we now expect that three more enzymes will be needed,” says Pitera. “Once we have all the artemisinic acid we need, we’ll be ready for industrial production of the drug.”
Unique partnership accelerates production
As part of the Gates Foundation grant, startup Amyris Biotechnologies in Albany, founded by several of Keasling’s former postdocs, will scale up the process and produce artemisinin at cost. OneWorld Health, headquartered in San Francisco, will then spearhead the regulatory work necessary to bring the drug to market.
“This is an extraordinary partnership between public and private institutions,” says Regina Rabinovich, director of infectious diseases at the Bill & Melinda Gates Foundation. “I hope that Berkeley’s participation will serve as a model for other academic institutions to apply their scientific knowledge and resources to critical global health problems.”
While Keasling has focused his research on the grand challenges of global disease, synthetic biology spans many application areas. Currently, Keasling heads the Lawrence Berkeley National Laboratory’s Synthetic Biology Department, the first of its kind in the country. The multidisciplinary department has prototyped a bacteria that eats toxic waste, such as heavy metals, and hopes to design an organism that can ferment cellulose into hydrogen as a source of renewable energy. Keasling is also leading the charge to engineer a single-cell soil microorganism, Pseudomonas putida, that would swim into a pool of pesticides or nerve agents and degrade the chemicals.
New Center—first of its kind—opens its doors
This spring, the Berkeley Center for Synthetic Biology opened its doors just a few miles west of campus. The Center, Keasling says, will draw researchers from multiple campus departments. In one multidisciplinary project, Keasling is collaborating with EECS/ME professor Roger Howe to build nanoscale structures modeled after the ornately complex shells of brown algae. The biomimetic diatoms could be employed as filtration systems or self-contained catalysts in future nanodevices. Meanwhile, bioengineer Adam Arkin is writing software for the design of living systems from a library of validated interoperable genetic “parts” with specific functions, such as Keasling’s metabolic pathways. Indeed, one of the long-term goals of synthetic biology is to create a library of interoperable genetic circuits that can be assembled into myriad devices.
Trichomes like this magnified cluster of oil-producing cells contain the artemisinin made by the plant. Trichomes are purified in Keasling's lab to obtain the genes that encode artemisinin's biosynthetic pathway.
KARYN LYNN NEWMAN PHOTO
“When Jay first started his research, he didn’t have the mathematical models to guide him,” Arkin says. “Our aim is to make the process orders of magnitude more efficient. So we’re trying to develop a principled approach to creating a store of parts that we can then use much like the electronics industry uses transistors and capacitors.“
Continuing the metaphor, Arkin is pushing ahead on the development of Berkeley BioSPICE, software that represents and simulates cellular processes such as gene expression and cell division. Think of it as CAD (computer-aided design) for genetic circuits. A project of the California Institute for Quantitative Biomedical Research (QB3), Berkeley BioSPICE is analogous to SPICE (Simulation Program Integration Circuitry Evaluation), the industry-standard tool invented at Berkeley for integrated circuit design. The BioSPICE project’s motto, “open source biology,” refers to the fact that the fruits of the research are freely available for anyone to use and improve. It’s a concept that comes from open source software, a paradigm pioneered at Berkeley where the source code, the raw programming behind the software, is accessible for anyone to build upon and change for free.
Someday, “open source” biology could result in a new business model for the biopharmaindustry. One reason many therapeutics are so expensive today, Keasling explains, is that drug companies spend huge sums researching patentable parts, ballooning the overall price of drug development. Open source biology would change that.
“I’d like to see the parts become inexpensively available for anyone to pull together and use,” Keasling says. “If biopharma companies could draw from open source parts to begin with, they could then patent their process to make the drugs. We’re certainly not trying to put them out of business. We just want to provide a cheap way for them to make the active pharmaceutical ingredients they need.”
To that end, Berkeley hopes to bring together the academic leaders in synthetic biology from Harvard, MIT, and UCSF in a consortium that would ensure that the component parts each group develops are standardized and meet an agreed-upon set of specifications.
While progress is rapidly accelerating, synthetic biology is still in its infancy. In many ways, it’s where genetic engineering was before the launch of the Human Genome Project. And the public fear surrounding genetic engineering is not lost on Keasling. Ideally, synthetic biology will be self-regulated, he says, without the need for government intervention. But before scientists can convince the public that the field is safe, they themselves have to be sure that it is safe. As a step in that direction, Keasling and his colleagues have initiated discussions with Michael Nacht, dean of Berkeley's School of Public Policy, to consider the bioethics of their breakthroughs.
Keasling needs two more years before his lab and Amyris Biotechnologies can synthesize the drug at the high levels necessary to begin producing the treatment pharmaceutical. “In a couple of years, we’ll be producing the end product in E. coli’s growth medium,” he says. Add in two years of clinical trials, and this takes production to 2009-2010. Then the bacteria-produced artemisinin drug must still await approval from the Food and Drug Administration. It won’t be a vaccine, says Keasling, but rather a drug akin to an antibiotic taken for infections, to kill the malarial parasite once the disease has been contracted.
“It’s a very long haul,” says Keasling. “Still it’s getting easier to engineer life, and synthetic biology will make it simpler still. If the public doesn’t realize you can use it to make new drugs or renewable energy, it will look like we’re tinkering with biology. As scientists, it’s our responsibility to prove that synthetic biology has tremendous potential to save lives.”
DAVID PESCOVITZ writes Lab Notes, the College’s award-winning online research digest, and is co-editor of the popular blog BoingBoing.net. Pescovitz’s writing on science and technology has been featured in Wired, Scientific American, IEEE Spectrum, and the New York Times.