How Designer Proteins Could Change Your Life

How Designer Proteins Could Change Your Life

By Melissa Pandika


Because skipping evolution could help solve some of medicine’s most pressing problems. 

By Melissa Pandika

Bread and pasta wreak havoc on Suzanne Dombkowski’s life. Her muscles ache and her memory lapses, so that she can’t remember simple names. The culprit is celiac disease, in which gluten — a protein in barley, rye and wheat — triggers a painful immune response. Ever since her diagnosis, the 24-year-old has gone out of her way to avoid encounters with the stuff. 

But one day, Dombkowski and the estimated 3 million Americans who suffer from celiac disease may be able to drop their guard, thanks to a new enzyme called KumaMax. Developed by University of Washington researchers, KumaMax digests gluten before it reaches the intestines, defusing the immune response before it has a chance to start.

More than that, the enzyme has enormous significance as a bioengineering standard bearer. It is one of the latest in what could emerge as an entirely new class of drugs: protein-based medicines that are built from scratch, not found in nature. Using sophisticated software, researchers are folding peptides and engineering amino acids to create drugs with a range of new capabilities. They might bind to a single type of molecule, thereby minimizing side effects. Or they might inoculate against many flu strains at once. “In the last four or five years, there’s been this flowering of de novo protein designs,” says David Baker, director of UW’s Institute for Protein Design.

Proteins allow cells to communicate, protect the body from disease and carry out other crucial functions that have evolved over more than a billion years. But “humans have changed the planet a lot, and there are a lot of new challenges,” Baker says. “To address those challenges, we need to make new proteins.” Traditionally, that required modifying the DNA encoding the amino acid building blocks of proteins, which govern how they fold into 3-D shapes, which, in turn, determines their function. Baker’s team initially used this approach — “Neanderthal protein design” — to reshape existing enzymes. But this sometimes caused them to fold in unpredictable ways. So they decided to circumvent evolution and build from scratch.

In 1998, they developed Rosetta, a software that predicts a protein’s structure based on its amino acid sequence, and have been building on it ever since. Founded on the principle that peptides — chains of amino acids — fold into the shape with the lowest energy, Rosetta twists peptides into a multitude of shapes, searching for the one with the lowest energy. But it works in reverse too. Rosetta can start with a desired structure and function, and then predict the amino acid sequence that’s needed. Over the years, Rosetta has only gained accuracy. Meanwhile, improvements in computing power have allowed Rosetta and other protein design software to run faster, while molecular biology advances have made synthesizing the genes and peptides needed to generate these designed proteins in the lab easier and cheaper than ever. “The potential for new proteins is really only limited by the imagination,” says Ingrid Swanson Pultz, chief scientific officer of PvP Biologics.

Ingrid swanson pultz

Ingrid Swanson Pultz

Source Courtesy of PVP Biologics

As a Ph.D. student, Swanson Pultz led a team of UW undergraduates in using a crowdsourced video game version of Rosetta — FoldIt — to build KumaMax as part of a competition. They used kumamolisin, an enzyme produced by bacteria that live in acidic conditions similar to the stomach, as a template. Then they used FoldIt to engineer it with the ability to digest gluten, substituting amino acids to remodel its active site — “the business end,” Swanson Pultz explains — so that gluten could fit inside. They produced the FoldIt-generated designs in the lab and tested their ability to break down gluten. In 2012, Swanson Pultz co-founded PvP Biologics to streamline KumaMax’s arrival to the clinic. So far, it can digest 99 percent of gluten in a test tube, and has shown promising results in rodents. Now Swanson Pultz and team are planning clinical trials of KumaMax, which would come in pill form.

Baker and collaborators have also designed a protein to prevent the flu. Many flu virus strains exist, and they mutate quickly. Flu vaccines typically attack only a few strains. But the new protein targets a segment of hemagglutinin, a protein found in many flu strains, important for infecting host cells. Last year, Baker and colleagues showed in PLOS Pathology that their protein prevented infection in mice injected with a variety of flu strains, and even reduced symptoms after infection.

Most protein design research nowadays focuses on developing the building blocks of proteins, says Dek Woolfson of the University of Bristol. His lab has designed self-assembling protein cages that could one day shuttle and release drugs, or act as broad-spectrum vaccines. Andrew Jamieson’s lab at the University of Glasgow has even engineered new amino acids to bridge, or “staple,” the loops of a spiral structure common in proteins, known as an alpha helix. The researchers stapled proteins based on a sea snail toxin that could offer a more targeted alternative to opioids for chronic pain. The network of chemical bonds that holds the toxic protein together is notoriously difficult to make, so they replaced them with peptide staples.

To be sure, it’s early days yet. Most designer proteins still resemble “large rocks,” Woolfson says. He and others want to move from these stable proteins to dynamic proteins that behave in more sophisticated ways, like recognizing tumor cells based on the complex pattern of molecular markers on their surface. And, of course, researchers still need to conduct clinical trials of designer proteins.

Even then, they might present limitations. KumaMax, for instance, wouldn’t cure celiac disease but instead offer a “safety net” for the inevitable slipup, says Jeff Mandel of San Diego, who suffers from the disease. Still, Dombkowski expresses optimism about KumaMax and other designer protein drugs. “I’m not scared of the fact that it’s engineered,” she says. “I’d definitely be willing to try.”