DeepMind's AI used to develop tiny 'syringe' for injecting gene therapy and tumor-killing drugs
Researchers used the AI system AlphaFold to develop a tiny "syringe" that can inject proteins into cells.
Scientists have developed a molecular "syringe" that can inject proteins, including cancer-killing drugs and gene therapies, directly into human cells.
And the researchers did it using an artificial intelligence (AI) program made by Google's DeepMind. The AI program, called AlphaFold, previously predicted the structure of nearly every protein known to science.
The team modified a syringe-like protein naturally found in Photorhabdus asymbiotica, a species of bacteria that primarily infects insects. The modified syringe, which was described Wednesday (March 29) in the journal Nature, has not yet been tested in humans, only in lab dishes and live mice.
But experts say, eventually, the syringe could have medical applications.
"The authors show that this approach can be tuned to target specific cells and to deliver customized protein cargoes (payloads)," Charles Ericson and Martin Pilhofer, who study bacterial cell-cell interactions at ETH Zürich in Switzerland and were not involved in the research, wrote in an accompanying commentary. "These re-engineered injection complexes represent an exciting biotechnological toolbox that could have applications in various biological systems," they wrote.
Related: DeepMind scientists win $3 million 'Breakthrough Prize' for AI that predicts every protein's structure
P. asymbiotica bacteria normally grow inside roundworms called nematodes and use the worms as Trojan horses to invade insect larvae. It works like this: a nematode invades the larva's body and regurgitates P. asymbiotica; the bacteria kills the insect's cells; and the nematode feasts on the dying larva's flesh. Thus, the nematodes and bacteria enjoy a beautiful symbiotic relationship.
To kill the insect cells, P. asymbiotica secretes tiny, spring-loaded syringes, scientifically known as "extracellular contractile injection systems," that carry toxic proteins inside a hollow "needle" with a spike on one end. Small "tails" extend from the base of the syringe — imagine the landing gear of a space probe — and these tails bind to proteins on the surface of insect cells. Once bound, the syringe stabs its needle through the cell membrane to release its cargo.
In previous studies, scientists isolated these syringes from Photorhabdus bacteria and also discovered that some could target mouse cells, not just insect cells. This raised the possibility that such syringes could be modified for use in humans.
To test whether this idea might be feasible, the team first loaded the syringe's hollow tube with proteins of their choosing. Then, they used AlphaFold to better understand how the syringes hone in on insect cells, so they could be modified to target human cells instead. They used the AI system to predict the structure of the bottom of the syringe's landing gear — the part that first makes contact with the target cell surface. They then altered this structure so it would latch onto surface proteins found only on human cells.
Without AlphaFold, the researchers would have had to conduct this analysis using advanced microscopy techniques and crystallography, meaning detailed studies of the landing gear's atomic structure, Joseph Kreitz, a doctoral student at the McGovern Institute for Brain Research at MIT and first author of the study, told Live Science in an email.
"This could have taken many months," Kreitz said. "With AlphaFold, we were able to obtain predicted structures of candidate tail fiber designs almost in real-time, significantly accelerating our efforts to reprogram this protein."
The researchers then used their modified syringes to tweak cells' genomes in lab dishes. Specifically, they delivered components of the powerful CRISPR-Cas9 gene editing tool into cells to cut and paste sections of DNA into their genomes. The team also used the syringes to insert tiny DNA-snipping scissors called zinc-finger deaminases into cells.
They also used the system to deliver toxic proteins into cancer cells in lab dishes. And finally, they injected the syringes into live mice and found that their cargo could only be detected in the targeted areas and did not spark a harmful immune reaction. For this last experiment, the team used AlphaFold to design their syringes to specifically target mouse cells.
These experiments demonstrate that the syringes can serve as "programmable protein delivery devices with possible applications in gene therapy, cancer therapy and biocontrol," the authors concluded. In contrast to therapies that deliver genetic instructions, like DNA or RNA, into cells, these protein-carrying syringes could provide "better control over the dose and half-life of a therapeutic inside cells," Kreitz and the study's senior author Feng Zhang told Live Science in an email.
That's because genetic instructions prompt cells to build proteins for themselves, whereas the syringes would come with a premeasured dose of protein. This precise dosing would be useful for treatments involving transcription factors, which tweak a cell's gene activity, and chemotherapy, which has toxic effects at high doses, they said.
The tiny syringes could also potentially be programmed to fight disease-causing bacteria in the body, Ericson and Pilhofer wrote. And in the future, it may be possible for scientists to connect multiple syringes to form multi-barrelled complexes. "These might enable more cargo to be delivered per target cell than with a single injection system," they suggested.
"However, we note that this system is still in its infancy; further efforts will be required to characterize the behavior of this system in vivo before it can be applied in clinical or commercial settings," Kreitz and Zhang told Live Science. The team is now studying how well the syringes diffuse through different tissues and organs, and continuing to examine how the immune system reacts to the new protein delivery system.
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Nicoletta Lanese is the health channel editor at Live Science and was previously a news editor and staff writer at the site. She holds a graduate certificate in science communication from UC Santa Cruz and degrees in neuroscience and dance from the University of Florida. Her work has appeared in The Scientist, Science News, the Mercury News, Mongabay and Stanford Medicine Magazine, among other outlets. Based in NYC, she also remains heavily involved in dance and performs in local choreographers' work.
By Kiley Price