Australian scientists, including at the Charles Perkins Centre, University of Sydney, have successfully developed a research system that uses ‘biological artificial intelligence’ to design and evolve molecules with new or improved functions directly in mammal cells. The researchers said this system provides a powerful new tool that will help scientists develop more specific and effective research tools or gene therapies.

Named PROTEUS (PROTein Evolution Using Selection) the system harnesses ‘directed evolution’, a lab technique that mimics the natural power of evolution. However, rather than taking years or decades, this method accelerates cycles of evolution and natural selection, allowing them to create molecules with new functions in weeks.

This could have a direct impact on finding new, more effective medicines. For example, this system can be applied to improve gene editing technology like CRISPR to improve its effectiveness.

“This means PROTEUS can be used to generate new molecules that are highly tuned to function in our bodies, and we can use it to make new medicine that would be otherwise difficult or impossible to make with current technologies.” says co-senior author Professor Greg Neely, Head of the Dr. John and Anne Chong Lab for Functional Genomics at the University of Sydney.

“What is new about our work is that directed evolution primarily work in bacterial cells, whereas PROTEUS can evolve molecules in mammal cells.”

PROTEUS can be given a problem with uncertain solution like when a user feeds in prompts for an artificial intelligence platform. For example the problem can be how to efficiently turn off a human disease gene inside our body. 

The findings were reported in Nature Communications, with the research performed at the Charles Perkins Centre, the University of Sydney with collaborators from the Centenary Institute.

PROTEUS then uses directed evolution to explore millions of possible sequences that have yet to exist naturally and finds molecules with properties that are highly adapted to solve the problem. This means PROTEUS can help find a solution that would normally take a human researcher years to solve if at all.

The researchers reported they used PROTEUS to develop improved versions of proteins that can be more easily regulated by drugs, and nanobodies (mini versions of antibodies) that can detect DNA damage, an important process that drives cancer. However, they said PROTEUS isn’t limited to this and can be used to enhance the function of most proteins and molecules. 

The original development of directed evolution, performed first in bacteria, was recognised by the 2018 Noble Prize in Chemistry.

“The invention of directed evolution changed the trajectory of biochemistry. Now, with PROTEUS, we can program a mammalian cell with a genetic problem we aren’t sure how to solve. Letting our system run continuously means we can check in regularly to understand just how the system is solving our genetic challenge,” said lead researcher Dr Christopher Denes from the Charles Perkins Centre and School of Life and Environmental Sciences

The biggest challenge Dr Denes and the team faced was how to make sure the mammalian cell could withstand the multiple cycles of evolution and mutations and remain stable, without the system “cheating” and coming up with a trivial solution that doesn’t answer the intended question.

They found the key was using chimeric virus-like particles, a design consisting of taking the outside shell of one virus and combining it with the genes of another virus, which blocked the system from cheating.

The design used parts of two significantly different virus families creating the best of both worlds. The resulting system allowed the cells to process many different possible solutions in parallel, with improved solutions winning and becoming more dominant while incorrect solutions instead disappear.

“PROTEUS is stable, robust and has been validated by independent labs. We welcome other labs to adopt this technique. By applying PROTEUS, we hope to empower the development of a new generation of enzymes, molecular tools and therapeutics,” Dr Denes said.

“We made this system open source for the research community, and we are excited to see what people use it for, our goals will be to enhance gene-editing technologies, or to fine tune mRNA medicines for more potent and specific effects,” Professor Neely said.

Declaration:  Alexandar Cole, Christopher Denes, Daniel Hesselson and Greg Neely have filed a provisional patent application on this technology The remaining authors declare no competing interests. 

Main image: Artist's impression of mRNA. Credit: Nick Hoskin