New Protein Delivery System Developed Using AI Tool AlphaFold

KEY TAKEAWAYS
Researchers have developed a novel protein delivery method using a natural bacterial system that can deliver gene-editing tools and cancer therapies to different cell types.
The use of AlphaFold, an AI tool, allowed the team to engineer the syringe structures to deliver a range of useful proteins to human cells and live mice, demonstrating the potential of protein engineering as a tool in bioengineering and creating new therapeutic systems.
The system has the potential to overcome the delivery challenges in gene editing applications, particularly for brain or kidney diseases, where efficient delivery systems are currently lacking.
Researchers manipulated a syringe-like system in a bioluminescent bacterium to recognize human cells by modifying the tail fiber using AlphaFold.
The successful delivery of Cas9 protein, which is about five times larger than the syringes' usual cargo, demonstrates the technique's flexibility and has the potential to have a transformational effect on medicine.

Researchers from the McGovern Institute for Brain Research at MIT and the Broad Institute of MIT and Harvard have created a novel protein delivery method using a natural bacterial system. 

The technology can be programmed to deliver a variety of proteins, including gene-editing tools, to different cell types.

This method has the potential to be a safe and efficient way to deliver gene and cancer therapies.

Harnessing Bacterial Syringe-like Structures

The research team, led by MIT Associate Professor Feng Zhang, exploited a tiny syringe-like injection structure produced by a bacterium that naturally binds to insect cells and injects protein payloads into them.

The scientists employed the artificial intelligence tool AlphaFold to engineer these syringe structures to deliver a range of useful proteins to human cells and live mice.

This development demonstrates the potential of protein engineering as a tool in bioengineering and creating new therapeutic systems, according to Joseph Kreitz, the study’s first author and a member of Zhang’s lab.

 

Overcoming Delivery Challenges in CRISPR Applications

One of the main bottlenecks in gene editing is delivering the necessary components, such as the DNA-cutting Cas9 enzyme and a short piece of RNA that guides Cas9 to a specific region in the genome, into cells.

The limited options for delivery have restricted most clinical trials to editing genomes in liver, eye, or blood cells.

The lack of efficient delivery systems has hindered the tackling of brain or kidney diseases.

The successful delivery of the Cas9 protein, which is about five times larger than the syringes’ usual cargo, demonstrates the technique’s flexibility.

Learning from Bacterial Systems

Researchers turned to an unusual group of bacteria that use molecular spikes to pierce a hole in the membranes of host cells.

These bacteria then transport proteins through the perforation and into the cell, taking advantage of the host’s physiology.

The scientists successfully manipulated the syringe-like system in the bioluminescent bacterium Photorhabdus asymbiotica to load proteins of their choosing from mammals, plants, and fungi.

Kreitz and his collaborators at Zhang’s lab worked on engineering the P. asymbiotica molecular syringe to recognize human cells.

They focused on a region of the syringe called the tail fiber, which typically binds to a protein found on insect cells.

Using AlphaFold, the team designed modifications to the tail fiber so that it would recognize mouse and human cells instead.

With the help of the AI-generated protein structure prediction, they were able to easily modify the tail fiber for their purposes.

Afterwards, they loaded the syringes with various proteins, including Cas9 and toxins that could be used to kill cancer cells, and delivered them into human cells grown in the lab and into the brains of mice.

A Flexible System with Potential for Transformational Impact

Although the system was initially unable to transport the mRNA guide needed for CRISPR-Cas9 genome editing, the team is currently developing methods to achieve this.

The successful delivery of the Cas9 protein, which is about five times larger than the syringes’ usual cargo, demonstrates the technique’s flexibility.

This new approach, reminiscent of the early days of CRISPR-Cas9 research, has the potential to have a transformational effect on medicine.

The ability to engineer both the payload and the specificity of the bacterial syringes is a significant development.

As researchers continue to explore the roles of these syringes in microbial ecology, further advancements in protein delivery systems could be achieved, revolutionizing the field of gene editing and therapeutics.

Craig Miller

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