Scientists at Cambridge have used synthetic biology to make artificial enzymes that can be programmed or reprogrammed to attack the genetic code of SARS-CoV-2 and kill the virus. This method could be used to make a new generation of drugs that fight viruses.

Enzymes are biological catalysts that occur naturally and are essential for a wide variety of bodily processes, including protein synthesis and digestion. Even while proteins make up the majority of enzymes, some of these vital activities are also catalyzed by RNA, a chemical relative of DNA that may fold into an enzyme called a ribozyme. Certain kinds of ribozymes can precisely target and cut particular sequences in other RNA molecules.

2014 saw the discovery by Dr. Alex Taylor and colleagues that XNA, or synthetic chemical substitutes for RNA and DNA not present in nature, could be used to make the first wholly artificial enzymes, which Taylor called XNAzymes.

XNAzymes weren’t very effective at first and needed improbable lab settings to work. But earlier this year, his lab published research on a novel class of XNAzymes that had been specially designed to be considerably more effective and stable inside cells. These artificial enzymes can cut long, complicated RNA molecules. They are so accurate that if the target sequence differs by just one nucleotide, the basic building block of RNA, they will know not to cut it. This allows them to be targeted against specific RNA mutations associated with cancer and other disorders while sparing healthy RNA molecules.

Now, Taylor and his colleagues at the Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, describe using this approach to successfully “kill” live SARS-CoV-2 virus in research published today in Nature Communications.

St. John’s College, Cambridge Affiliated Researcher and Sir Henry Dale Fellow Taylor explained, “Put simply, XNAzymes are molecular scissors which recognise 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.”

Although these synthetic enzymes can be trained to recognize a certain RNA sequence, the ‘scissors’ operating machinery at their catalytic core, the XNAzyme, remains unchanged. This means that it is possible to produce new XNAzymes in a fraction of the time it usually takes to produce antiviral drugs.

As Taylor put it, “It’s 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.”

Using the state-of-the-art Containment Level 3 Laboratory at CITIID, the largest academic facility in the nation for researching high risk biological agents like SARS-CoV-2, Taylor and Dr. Nicholas Matheson then worked together to demonstrate that their XNAzymes were effective against live SARS-CoV-2 virus.

According to Dr. Pehuén Pereyra Gerber, who carried out the studies on SARS-CoV-2 in Matheson’s lab, “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.”

“What we’ve shown is proof of principle, and it’s still early days,” said Matheson, highlighting, “it’s worth remembering, however, 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.”

Taylor used human RNA databases to make sure the target virus sequences weren’t already present in our own RNA. The extremely specific nature of the XNAzymes should, in principle, prevent some of the “off-target” negative effects that related, less precise molecular therapies might bring about, such as liver damage.

SARS-CoV-2 has the capacity to adapt and mutate, giving rise to novel forms that vaccinations are less effective against. Taylor devised three of the XNAzymes to self-assemble into a “nanostructure” that cuts various portions of the viral genome in order to avoid this issue in addition to targeting viral RNA sections that mutate less frequently.

In order for the virus to evade the treatment, 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.”

XNAzymes may be given as medications to treat COVID-19 infections and help patients recover, or they may be used to protect those who have been exposed to the virus and stop it from spreading. This kind of strategy may be crucial for patients whose compromised immune systems make it difficult for them to get rid of the virus on their own.

Making XNAzymes that are even more specialized, strong, and “bulletproof,” as Taylor puts it, is Taylor and his team’s next step. This will enable them to stay in the body for longer and function as catalysts even more effectively in smaller dosages.

Source: 10.1038/s41467-022-34339-w

Image Credit: Win McNamee/Getty Images