Synthetic biology meets medicine: "programmable molecular scissors" may help fight COVID-19 infection

Scientists at the University of Cambridge have used synthetic biology to create artificial enzymes that target the genetic code of SARS-CoV-2 and destroy viruses, a method that could be used to develop a new generation of antiviral drugs
.

Enzymes are naturally occurring biocatalysts that enable the chemical transformations our bodies need to function — from converting the genetic code into proteins to digesting food
.
Although most enzymes are proteins, some of these key reactions are catalyzed by RNA (a chemical relative of DNA), which can fold into ribosases
.
Some types of ribozymes are able to target specific sequences in other RNA molecules and precisely cut them
.

In 2014, Dr.
Alex Taylor and his colleagues discovered that artificial genetic material known as XNA — in other words, synthetic chemical substitutes for RNA and DNA that don't exist in nature — could be used to create the world's first fully artificial enzyme, which Taylor named XNAzymes
.

In the beginning, XNAzymes was inefficient and required unrealistic laboratory conditions to function
.
Earlier this year, however, his lab reported a new generation of XNAzymes, which was engineered to be more stable and efficient
under intracellular conditions.
These artificial enzymes can cut long, complex RNA molecules so precisely that if the target sequence differs by just one nucleotide, the basic structure of RNA, they will recognize not to cut it
.
This means they can be programmed to attack mutated RNAs associated with cancer or other diseases without interfering with normal RNA molecules
.

Now, in the study, published today in Nature Communications, Taylor and his team at the University of Cambridge's Institute of Therapeutic Immunology and Infectious Diseases (CITIID) report how they used this technique to successfully "kill" the live SARS-CoV-2 virus
.

Taylor said: "Simply put, XNAzymes are molecular scissors that recognize specific sequences in RNA and then cut
them.
As soon as the scientists published the RNA sequence for SARS-CoV-2, we began scanning for sequences that our XNAzymes could attack
.
”

While these artificial enzymes can be programmed to recognize specific RNA sequences, XNAzyme's catalytic core — the mechanism by which the scissors operate — hasn't changed
.
This means that the creation of new XNAzymes can be done
in much less time than is typically developed for antiviral drugs.

Taylor: "It's like a pair of scissors, the overall design remains the same, but you can change the blade or handle
depending on the material you want to cut.
The power of this approach is that even though I was working alone in the lab at the beginning of the pandemic, I was able to generate and screen small amounts of this XNAzymes
in a matter of days.
”

Taylor then teamed up with Dr.
Nicholas Matheson to demonstrate his XNAzymes' activity against the coronavirus, leveraging CITIID's state-of-the-art tertiary containment laboratory, the country's largest academic facility
for studying high-risk biologics such as the coronavirus.

Dr.
Pehuén Pereyra Gerber, who conducted experiments on SARS-CoV-2 in the Matheson lab, said: "It's really encouraging, it's the first time, we're actually getting them to work as enzymes inside cells and inhibit the replication of live viruses, which has been a big goal
in the field.
"

Matheson added: "What we are showing is a proof of principle, which is still in its early stages
.
However, it's worth remembering that Pfizer and Moderna's highly successful COVID-19 vaccine is itself based on synthetic RNA molecules, so this is a very exciting and rapidly evolving area with great potential
.
”

Taylor compared the target viral sequences to a database of human RNA to make sure they didn't appear in
our own RNA.
Because XNAzymes is highly specific, it should theoretically be possible to prevent some of the "off-target" side effects that similar, less precise molecular therapies can cause, such as hepatotoxicity
.

SARS-CoV-2 has the ability to evolve and alter its genetic code, leading to new variants
of vaccines that are ineffective against it.
To solve this problem, Taylor not only targeted regions of the viral RNA that mutate less frequently, but also designed three XNAzymes to self-assemble into a "nanostructure" that cuts different parts of
the viral genome.

"Our goal is multiple sequences, so for the virus to evade treatment, it has to mutate
at multiple sites at the same time," he said.
In principle, you can combine a lot of these XNAzymes into a cocktail
.
But even if new variants emerge that can bypass this hurdle, because we already have a catalytic core, we can quickly make new enzymes to get ahead of it
.
”

XNAzymes may be used as a drug to protect people exposed to COVID-19, prevent viral infections, or treat infected patients to help clear the virus
from the body.
This approach may be particularly important
for patients who have difficulty clearing the virus on their own due to a weakened immune system.

The next step for Taylor and his team is to make XNAzymes more specific and robust — "bulletproof," he says — so that they stay in the body longer, act as more effective catalysts, and use smaller
doses.

Pehué n Pereyra Gerber, Maria J.
Donde, Nicholas J.
Matheson, Alexander I.
Taylor.
XNAzymes targeting the SARS-CoV-2 genome inhibit viral infection.
Nature Communications, 2022; 13 (1)