Laboratory evolution of virus-like protein cages for eukaryotic mrna delivery
Nucleic acids are promising candidates for treating disease by stimulating, inhibiting, or replacing other nucleic acids or proteins inside of eukaryotic cells—a process known as “gene therapy.” However, methods to efficiently and safely deliver genes into cells are still lacking. The problem is that nucleic acids are not cell permeant and degrade before reaching the cytosol. One way to transport oligonucleotides into cells is by packaging them into hollow containers made of proteins, a method that has been successfully hijacked by viruses for a long time.

Here, we propose to design and engineer an artificial proteinaceous container that (1) selectively encapsulates ribonucleic acids (RNAs) using a known RNA recognition tag and (2) delivers this RNA into the cytosol of mammalian cells. Protein engineering, which embodies both rational design and computational modeling, will be used to create the starting design of this artificial protein container. The initial design will be based on the protein lumazine synthase from the bacterial organism Aquifex aeolicus (AaLS), which forms small but highly symmetrical nanocompartments in bacteria and is very tolerant to genetic changes. To optimize this design, we will use directed evolution to induce an artificial selection pressure on a large population of distinct capsid variants, allowing us to obtain only the best-performing capsid variants: those that can enter and disassemble selectively inside of mammalian cells, thereby releasing the enclosed RNA molecules into the cytosol. New AaLS containers will be thoroughly characterized using cutting-edge technologies, such next-generation sequencing and cryo-electron microscopy.

The ultimate goal of LEVERAGE mRNA is to use the designed and evolved capsids to deliver messenger RNAs (mRNAs) into cells that encode missing or dysfunctional proteins, for example in enzyme replacement therapies. If successful, this action will have lasting positive impacts on human health.