Synthetic biology meets medicine: ‘Programmable molecular scissors’ could help fight COVID-19 infection

Cambridge scientists used synthetic biology to create artificial enzymes programmed to target the genetic code of SARS-CoV-2 and destroy the virus, an approach that could be used to develop a new generation of antiviral drugs.

Enzymes are natural biological catalysts that enable the chemical transformations necessary for our body to function, from translating genetic code into proteins to digesting food. Although most enzymes are proteins, some of these crucial reactions are catalyzed by RNA, a chemical cousin of DNA, which can transform into enzymes called ribozymes. Certain classes of ribozyme are able to target specific sequences in other RNA molecules and cut them precisely.

In 2014, Dr. Alex Taylor and his colleagues discovered that the artificial genetic material known as XNA – in other words, synthetic chemical alternatives to RNA and DNA not found in nature – could be used to create the world’s first fully artificial enzymes, which Taylor named XNAzymes.

At first, XNAzymes were ineffective, requiring unrealistic laboratory conditions to work. Earlier this year, however, his lab reported a new generation of XNAzymes, designed to be much more stable and efficient under conditions inside cells. These artificial enzymes can cut long, complex RNA molecules and are so precise that if the target sequence differs by only one nucleotide (the basic structural unit of RNA), they will recognize that it should not be cut it. This means they can be programmed to attack mutated RNAs implicated in cancer or other diseases, leaving normal RNA molecules well on their own.

Now, in research published today in Nature CommunicationTaylor and his team at the Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, report how they used this technology to successfully “kill” the live SARS-CoV-2 virus.

Taylor, a Sir Henry Dale Fellow and Affiliate Researcher at St John’s College, Cambridge, said: “In simple terms, XNAzymes are molecular scissors that recognize a particular sequence in RNA and then chop it up. As soon as the scientists released the RNA sequence of SARS-CoV-2, we started scanning through the sequences looking for our XNAzymes to attack. »

While these artificial enzymes can be programmed to recognize specific RNA sequences, the catalytic core of the XNAzyme – the machinery that operates the “scissors” – does not change. This means that the creation of new XNAzymes can be accomplished in much less time than it normally takes to develop antiviral drugs.

As Taylor explained, “It’s like having a pair of scissors where the overall design stays the same, but you can change the blades or the handles depending on the material you want to cut. The power of this approach is that, even working alone in the lab at the start of the pandemic, I was able to generate and screen a handful of these XNAzymes within days.

Taylor then partnered with Dr. Nicholas Matheson to show that his XNAzymes were active against the live SARS-CoV-2 virus, leveraging the state-of-the-art containment Level 3 laboratory at CITIID, the largest academic institution for the study of high-risk biohazards. agents like SARS-CoV-2 in the country.

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

“What we’ve shown is proof of principle, and it’s still early days,” Matheson added, “It’s worth remembering, however, that the incredibly successful Pfizer and Moderna COVID-19 vaccines are themselves based on synthetic RNA molecules – so this is a really exciting and developing field with huge potential.”

Taylor checked the target viral sequences against human RNA databases to ensure that they were not present in our own RNA. Since XNAzymes are highly specific, this should in theory prevent some of the “off-target” side effects that similar, less precise molecular therapies can cause, such as liver toxicity.

SARS-CoV-2 has the ability to evolve and change its genetic code, leading to new variants against which vaccines are less effective. To circumvent this problem, Taylor not only targeted regions of the viral RNA that mutate less frequently, but he also engineered three of the XNAzymes to self-assemble into a “nanostructure” that cuts different parts of the genome. of the virus.

“We are targeting multiple sequences, so for the virus to evade therapy, it would have to mutate at multiple sites at once,” he said. “In principle, you could combine a lot of these XNAzymes together in a cocktail. But even if a new variant that can circumvent this appears, because we already have the catalytic core, we can quickly make new enzymes to keep a length of advance. this.”

XNAzymes could potentially be administered as drugs to protect people exposed to COVID-19, to prevent the virus from taking hold, or to treat infected patients, helping to rid the body of the virus. This type of approach could be particularly important for patients who, due to a weakened immune system, find it difficult to eliminate the virus on their own.

The next step for Taylor and his team is to make even more specific and robust XNAzymes — “bulletproof,” he says — allowing them to stay in the body longer and function as even more effective catalysts. , at lower doses.