Mining Microbes for New Medicines

From Minnesota Alumni Magazine Winter 2016

Breakthrough scientist Michael Smanski

By Deane Morrison


Returning from a vacation in 1928, English chemist Alexander Fleming checked cultures of infectious Staphylococcus bacteria growing in petri dishes and noticed that the bacterial colonies were thriving—except in a clear space around a blob of mold. Fleming realized that the mold, named Penicillium, had released a chemical that inhibited bacterial growth. Thus the story of penicillin began.

It was a monumental stroke of luck. Molds, bacteria, and other microbes make many molecules useful to humans, but they don’t do it 24/7. Fleming caught that Penicillium specimen in the act of fending off other microbes, when the genes needed to produce penicillin were turned on. There’s no telling how many other potentially life-saving products lie dormant in microbial genes that rarely, if ever, see action.

Scientists like Michael Smanski are out to find those hidden treasures and turn them into new antibiotics, anticancer agents, and other critical products. Smanski, 31, an assistant professor in the University of Minnesota’s Department of Biochemistry, Molecular Biology, and Biophysics (BMBB), is a miner of microbial genomes. He searches them for clusters of “silent” genes, each of which could potentially direct one step in a biochemical pathway leading to a product, just as an architect, carpenter, and electrician each perform one step in building a house.

“Our approach to finding novel molecules is to mine sequenced genomes for biosynthetic pathways that have never been studied,” he explains. “For example, the majority of anticancer drugs were originally derived from natural products made in plants or microorganisms, and we are applying our technology to accelerate the discovery of new natural products.”

Smanski’s work has attracted international attention. He held a highly competitive Damon Runyon Fellowship for cancer researchers from 2012 to 2014, and in January 2015 he was among only six fellowship holders to win a $100,000 Damon Runyon–Dale F. Frey Breakthrough Scientist award, given to the scientists whose work showed the most promise for producing paradigm-shifting breakthroughs.

Awakening silent genes

In October, three researchers won the Nobel Prize in Medicine for discovering treatments for two ancient, intractable foes: the nematodes that cause river blindness and other diseases, and the malarial parasite. Both treatments involved products from natural sources: The sweet wormwood plant made the malaria drug, and Streptomyces bacteria made the nematode killer.

The nematode work was possible because soil bacteria like Streptomyces constantly wield chemical weapons in a war for resources against other microbes. But, as with penicillin, no discovery would have happened if the bacteria hadn’t been caught making a nematodicidal product first.

“We now know that only a small fraction of the genes required for making these drug-like molecules are naturally turned on when we grow the organisms in the lab,” Smanski notes. “For the rest, we need to go in and artificially turn them on using genetic engineering.”

He begins by peering into known bacterial genomes. Using computers, he identifies DNA sequences that resemble those for known drugs or other products, which makes them likely candidates to produce new types of drug-like molecules.

With relevant genes identified, he begins waking them up—a complex and daunting task he likens to directing an orchestra. “Dozens of genes are needed to make one drug-like molecule,” he explains. “The timing of when we turn genes on or off, and whether some genes are turned on very strongly or just a little, can make a huge difference. If everything isn’t working together just right, you won’t make the product.”

The need for work like Smanski’s has never been greater, because the pipeline that used to turn natural products into new drugs has all but dried up.

Smanski snips the genes, DNA sequences that switch them on or off, and any other desired genetic elements cleanly out of a bacterial chromosome. He sends the DNA sequence of each element to a company that “prints” numerous copies of them and sends them back in two days. He then recombines the elements into new clusters and splices them into circular pieces of DNA called plasmids. In each plasmid he varies the elements in a different way—for example, the order of the genes or the strength of the various switches. With a starting cluster of, say, two dozen genes plus switches, tens of thousands of plasmid variants are possible.

As a Runyon Fellow, Smanski developed a DNA assembly pipeline technology that allows him to quickly build as many variants as he wants, each in a single test tube. After all plasmids are built, he puts them back into cells of Streptomyces, like “installing a new app in your smart phone.” Next, the engineered bacteria are grown to see what product is made and which variant is most efficient.

“Our technology allows us to engineer these complex biological capabilities by building new plasmids at a speed and scale not possible before,” Smanski says. “We can build thousands of alternative designs at the same time and test them all, then use computers to identify the rules that explain why some designs work and others do not.”

The need for work like Smanski’s has never been greater, because the pipeline that used to turn natural products into new drugs has all but dried up. Analysts have blamed, among other factors, corporate structures and policies that inhibit innovation. Christine Salomon, assistant director of the University’s Center for Drug Design, offers another perspective.

“Even though historically natural products were so successful, major drug companies abandoned them when, about 20 years ago, the combinatorial chemists came along,” she says. “These chemists took pieces of synthetic molecules, recombined them in new ways, and made huge libraries [of molecules] that were useless. Now the focus is on making large libraries of small molecules that are more like natural ones.” Which comes much closer to Smanski’s approach.

After Smanski has transferred the synthetic gene clusters into Streptomyces bacteria and harvested their products, Salomon will screen them. For potential anticancer agents, she will first test them against a fast-growing cell line derived from human colon tumors. If a compound should kill those cells, she will test it against noncancerous cell lines to see if it is likely to spare healthy cells. If so, a bigger challenge looms: determining whether the product acts against cancer via a novel mechanism.

“We want to . . . make sure it’s different from other known drugs, so it won’t [run up against] the same drug-resistance strategies as other compounds do, and also so that we can anticipate possible side effects,” she says. Products that show promise may later be tested in lab animals and, eventually, clinical trials.

Besides potential anticancer agents, microbes harbor genes that may give rise to products that can counter other threats to health and even the food supply. For example, chemicals made by soil microbes may be harnessed to wage war on pathogens that attack crop plants. “[What we want] is to get bacteria that are already in the soil and not harming plants to kill the bacteria that do,” says Will Harcombe, assistant professor in the University’s BioTechnology Institute and Department of Ecology, Evolution, and Behavior. “Mike can give us a lot of insight into the chemicals that mediate microbial interactions—microbes are super social organisms. He can rapidly modify bacteria to excrete large amounts of chemicals of interest. Once we know what the chemicals are and how they work, we can figure out how to manage the communities of soil microbes to optimize production of compounds with natural disease-suppressive activity.”

Smanski also applies his technology to non-microbial organisms. He and Wei-Shou Hu, a professor in the U’s Department of Chemical Engineering and Materials Science, collaborate to engineer mammalian cells to produce natural disease-fighting proteins like antibodies and erythropoietin, a hormone that stimulates red blood cell production.

But in order to work, many therapeutic proteins, including erythropoietin, must be chemically modified with sugar molecules added to the protein spine. A different enzyme must perform each of the dozens of steps in this pathway. Smanski and Hu are orchestrating genetic changes they hope will not only alter the chemical structure of the added sugars, but also improve the proteins’ therapeutic performance.

“We do mathematical modeling to predict which enzymes should be changed,” Hu explains. “Mike is developing experimental tools to change them quickly by adding different combinations of genes to [cultured cells]. We seek better quality and higher production of protein drugs. Now, we’re at the mercy of whatever sugars the cells want to add to the proteins.”

For Smanski, the work is its own reward. But there are also others, such as when, as part of his Damon Runyon fellowship, he took part in a 5K run/walk in Yankee Stadium to raise money for cancer research.

“As a Damon Runyon Fellow, I got to wear the bright orange shirt that said ‘Scientist’ on the back,” he recalls. “People, including some battling cancer themselves, would come up and pat you on the back and say ‘good work, keep it up.’ That’s the kind of encouragement and inspiration you don’t get when you’re sitting at a lab bench.”


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