Programmable ‘molecular scissors’ are capable of chopping up the Covid-19 virus, University of Cambridge researchers show

University of Cambridge scientists have identified a potential new weapon in the fight against Covid-19 – ‘molecular scissors’ called XNAzymes that can be programmed to chop up the virus.

This exciting synthetic biology approach has been shown to ‘kill’ the live SARS-CoV-2 virus in experiments at the country’s largest academic facility for studying high-risk biological agents.

Dr Alex Taylor at the Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) created artificial enzymes to target the virus’ genetic code.

The SARS-CoV-2 virus that causes Covid-19.  Image: Alissa Eckert, MS;  Dan Higgins, MAMS;  CDC
The SARS-CoV-2 virus that causes Covid-19. Image: Alissa Eckert, MS; Dan Higgins, MAMS; CDC

Enzymes are natural biological catalysts, enabling chemical reactions throughout our bodies, such as translating genetic code into proteins, or helping to digest food.

But in 2014, Dr Taylor and his colleagues discovered that artificial genetic material known as XNA could be used to create the world’s fully artificial enzymes, which Dr Taylor named XNAzymes.

XNA, which is not found in nature, is a synthetic chemical alternative to DNA and RNA, its chemical cousin.

While most enzymes are proteins, some are formed from RNA, which can fold into a type of enzymes called ribozymes. Some of these ribozymes have an important and interesting property – they can target specific sequences of RNA molecules and cut them with great precision.

When Dr. Taylor and his team first created their artificial version of these, they were inefficient and required unfeasible laboratory conditions. But his lab reported a new generation of XNAzymes earlier this year that were engineered to be much more stable and efficient under conditions inside cells.

They can cut long, complex RNA molecules with such precision that if the target sequence differs by a single nucleotide – the basic structural unit of RNA – they recognize that it should not be cut. This creates the opportunity to program them to attack mutated RNAs, such as those involved in cancer or other diseases, without interfering with normal RNA molecules.

Dr Taylor, a Sir Henry Dale fellow and affiliated researcher at St John’s College, Cambridge, said: “Put simply, XNAzymes are molecular scissors which recognize a particular sequence in the RNA, then chop it up.

“As soon as scientists published the RNA sequence of SARS-CoV-2, we started scanning through looking for sequences for our XNAzymes to attack.”

The catalytic core of the XNAzyme is the machinery operating these ‘scissors’ and does not change however it is programmed, meaning it takes much less time to create new ones than it would to develop antiviral drugs.

Dr Taylor said: “It is like having a pair of scissors where the overall design remains the same, but you can change the blades or handles depending on the material you want to cut. The power of this approach is that, even working by myself in the lab at the start of the pandemic, I was able to generate and screen a handful of these XNAzymes in a matter of days.”

Dr Taylor teamed up with Dr Nicholas Matheson to demonstrate the XNAzymes were active against live SARS-CoV-2 virus, using CITIID’s state-of-the-art Containment Level 3 Laboratory. They reported the findings in Nature Communications.

Dr Pehuén Pereyra Gerber, who performed the experiments on SARS-CoV-2 in Dr Matheson’s lab, said: “It’s really encouraging that for the first time – and this has been a big goal of the field – we actually have them working as enzymes inside cells, and inhibiting replication of live virus.”

Much more work is required.

Dr Matheson said: “What we’ve shown is proof of principle, and it’s still early days. It’s worth remembering that the amazingly successful Pfizer and Moderna Covid-19 vaccines are themselves based on synthetic RNA molecules – so it’s a really exciting and rapidly developing field, with enormous potential.”

A key safety component of the work was to check the target viral sequences against the human RNA database to ensure they were not naturally present in our bodies.

The specificity of XNAzymes, it is hoped, could prevent any off-target side-effects found in similar but less accurate molecular therapeutics, such as liver toxicity.

But how would XNAzymes fare as SARS-CoV-2 evolves and changes its genetic code to form new variants?

The team is confident. Dr Taylor targeted regions of the viral RNA that mutate less frequently, and also designed three of the XNAzymes to self-assemble into a ‘nanostructure’. cutting different parts of the virus genome.

He explained: “We’re targeting multiple sequences, so for the virus to evade the therapy it would have to mutate at several sites at once.

“In principle, you could combine lots of these XNAzymes together into a cocktail. But even if a new variant does appear that is capable of getting round this, because we already have the catalytic core, we can rapidly make new enzymes to keep ahead of it.”

With further work, there is the potential for XNAzymes to be administered as drugs to prevent Covid-19 taking hold, protect people exposed to the virus or to treat patients with infection by helping rid the body of it. That could prove particularly valuable to those patients who, because of a weakened immune system, struggle to clear the virus on their own.

Now Dr Taylor and his team want to create ‘bulletproof’ XNAzymes – ones that are even more specific and robust, which will allow them to remain in the body for longer, work as very effective catalysts in smaller doses.

The research was funded by the Wellcome Trust, the Royal Society, the Medical Research Council, NHS Blood and Transplant, and Addenbrooke’s Charitable Trust.


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