For centuries, certain red seaweeds were used to treat intestinal worm infections in Japan. And neuroscientists have used the active ingredient from those plants—a molecule known as kainic acid—to study epilepsy, Alzheimer’s disease, and other neurological conditions. But in the past couple decades, there has been a global shortage of kainic acid, making those experiments expensive to perform.
Researchers have now sequenced the genome of one species of red seaweed and discovered the enzymes that synthesize kainic acid, using them to make the molecule in gram quantities in the lab. The results offer a route to large-scale, biosynthetic production of kainic acid, which could lower the cost of important neuroscience experiments (Angew. Chem. Int. Ed. 2019, DOI: 10.1002/anie.201902910).
Since 1950, researchers have known that kainic acid injected into the brain binds to glutamate receptors and kills nerve cells, making the molecule a valuable tool to study injuries in specific brain regions. In the past, researchers sourced the chemical from drug companies, which extracted kilograms of kainic acid from red seaweeds to produce deworming drugs. But that source dried up about 20 years ago, perhaps because other deworming drugs became popular.
While chemists have devised more than 70 different ways to make kainic acid, these synthetic reactions are complex—the shortest involves six steps—because of the compound’s ring structure and intricate stereochemistry. As a result, synthetic kainic acid is expensive.
To search for a more efficient solution, Bradley Moore of the University of California, San Diego and his colleagues turned to the red seaweed itself, a species named Digenea simplex, to determine how the plant makes the molecule. The team started their search by piecing together the plant’s genome. But seaweed genomes are notoriously tricky to sequence because they’re filled with repetitive sequences. Much like assembling a blue sky in a jigsaw puzzle, it’s difficult to piece together many similar-looking DNA sequences in the correct order. So, to assemble the D. simplex genome, the researchers turned to newer technology that yields DNA sequences that are a thousand times as long as those from traditional sequencers. Then they looked for sequences similar to those of algal genes for enzymes that produce domoic acid, a compound similar to kainic acid. They identified two genes and found similar-looking sequences in several other red seaweeds and algae.
“It’s a very elegant piece of work,” says Claudia Schmidt-Dannert of the University of Minnesota, who was not involved with the study. “People normally focus on plants, bacteria, and fungi for the discovery of new compounds,” but the sequencing strategies used here open up the possibility of studying seaweeds.
The researchers expressed the seaweed genes in Escherichia coli, and found the purified enzymes could form kainic acid in solution. When incubated with the right starting materials, E. coli carrying the genes for these enzymes could produce kainic acid in a fermentation-type reaction with a 40% yield. “Finding that the enzymes were so efficient at this catalysis was a game changer,” Moore says. “Nowhere did we anticipate that we’d so quickly be able to make grams of kainic acid. That’s when it went from being simply an academic exercise to making productive amounts of material.”
Compared to other complex natural products that have been synthesized in labs, “kainic acid is actually quite a simple molecule,” says chemical biologist Richard Chamberlin of the University of California, Irvine, who was not involved in the study. “But that simplicity raises expectations of brevity.”
While chemists theoretically could produce kainic acid in a one-step reaction, there’s no efficient chemical way to form the necessary bonds, Chamberlin explains. The new study “is by far the closest to that theoretical, one-step synthesis,” he says. “It’s a great example of the power of modern molecular biology to solve recalcitrant problems in synthetic organic chemistry.”