Learning from vaccines: the race to make antiviral drugs

It took just days for Pfizer and Moderna to design an effective mRNA vaccine against COVID-19 – a breathtaking display of the power of this state-of-the-art mRNA technology.

By contrast it took years to design the first effective antiviral drugs against COVID-19, paxlovid and molnupiravir – a dismal display of how very yesteryear drug development is.

The only reason these drugs appeared in the clinic within two years of the COVID-19 outbreak rather than ten was because they were salvaged from existing pipelines: paxlovid from a compound targeted against the SARS virus of 2002 and molnupiravir from a compound to target influenza. The normal timeframe of drug development is usually greater than ten years.

It’s slow because it involves screening ‘libraries’ for promising compounds and tweaking their chemistry to turn them into well-behaved drugs – years of work before they can even begin to be tested in clinical trials.

Now, by taking a leaf from the mRNA vaccine playbook, that first phase of antiviral drug development – the design – might become lightning fast.

Last July Mohammed Fareh, a cancer researcher at Melbourne’s Peter MacCallum Cancer Institute (the ‘Peter Mac’) and Sharon Lewin, director of the Peter Doherty Institute, delivered a proof of concept. They made an RNA-based drug that killed SARS-CoV-2 in the culture dish – all within a few weeks.

“It could be a gamechanger,” believes Lewin.

“The big question is how to turn it into a treatment,” says Melanie Ott, director of the Gladstone Institute of Virology in San Francisco, who was not involved in the research. Nevertheless, she shares the excitement. “There is no shortcut when it comes to classical drug chemistry, so this is an opportunity to rethink our approach.”

If the vision pans out, this could mark the dawn of an era where we beat viruses at their own evolutionary game. Designer drugs could be deployed within weeks to demolish new SARS-CoV-2 variants and other emerging viruses.

RNA therapeutics: from cancer to COVID

Prior to the pandemic, Fareh’s day job didn’t revolve around shifty viruses but shifty cancers. Some cancer patients show an initial response to a drug. But within months the cancer cells evolve survival strategies, such as learning how to spit out toxic drugs, and resume their unbridled growth.

A diverse arsenal of weapons is needed to tackle these evaders.

In 2017, Feng Zhang at the Broad Institute in Massachusetts found such an arsenal: CRISPR-Cas13. Like CRISPR-Cas9, it is a customisable weapons system that bacteria use to defend themselves from even tinier invaders: the virus-like bacteriophage.

Because it can selectively snip DNA, scientists adapted CRISPR-Cas9 to ‘edit’ the DNA of plants, animals and even people. Jennifer Doudna and Emmanuelle Charpentier won the 2020 Nobel Prize in Chemistry for those efforts, but Zhang was also a pioneer. Returning to fossick around the bacterial arsenal, he found another tool, CRISPR-Cas13, lurking in a species called Leptotrichia wadei.

But while Cas9 targets DNA, Cas13 targets RNA.

That opened up a new universe of possibilities. You wouldn’t use Cas9 as a drug because you don’t want to be messing with human DNA, except for the rare case of trying to correct a genetic illness like cystic fibrosis. On the other hand, Cas13 could be the basis of a powerful new class of drugs that target RNA, particularly the type known as messenger RNA (mRNA), which is crucial to executing the business of the cell.

If DNA is the leather-bound manual containing all the instructions for how to operate a cell, mRNA is a flimsy photocopy of just the page that is needed at any one time on the factory floor.

Messenger RNA is a highly strategic target if you want to interfere with what a cancer cell is doing. For Fareh and his lab head Joe Trapani, Cas13 offered the chance to target the instructions that were helping cancer cells escape drug treatments.

That’s because Cas13 operates like scissors that snip away at the photocopied page of instructions represented by mRNA. Just which page is snipped is determined by a smart guide: a small, customisable piece of RNA that is able to seek out matching mRNA and is attached to the scissors. For every new page of mRNA instructions, a new guide could be quickly designed and attached.

In early tests, Cas13 was able to selectively destroy mRNA produced by the cancer cell lines. Buoyed by their success, Fareh and Trapani were embarking on a collaboration with the Children’s Cancer Institute in Sydney when COVID-19 struck. Like many researchers who were not mobilised to the COVID offensive, they had to down tools.

Until they realised: Cas13 could easily be adapted to fight SARS-CoV-2.

Antiviral drugs to target COVID

All that was needed was the genome sequence of the virus. Fareh had that by 10 January 2020, when the data was released by Chinese researchers – led by Yong-Zhen Zhang at Fudan University, China – who had isolated and fully sequenced the virus. (This was also the moment Moderna and Pfizer started designing their vaccines.)

What Fareh didn’t have was a way to test the Cas13 scissors on the virus. But the Peter Mac is in striking distance of the Doherty Institute, the major nerve centre of Australia’s COVID response. So in May 2020 Fareh and Trapani walked across the road to chat with Doherty head, Sharon Lewin.

Within a week, Fareh and his lab had decked out the Cas13 scissors with a guide that could seek out the SARS-CoV-2 mRNA instructions for manufacturing the spike protein. This is the bit that gives the virus access to cells. Because the virus can mutate its spike, Fareh’s team used a computer to predict the least-changeable part of the spike mRNA instructions as their target.

Working with Lewin’s team, they tested the tool on SARS-CoV-2 growing in green monkey kidney cells and human lung cells in culture dishes.

Cas13 obliterated the spike protein message and stopped the virus from proliferating.

Better yet, the shifty virus could not easily evade Cas13. When Fareh’s team mutated the virus by introducing single letter changes, Cas13 with its attached RNA guide continued to seek and destroy them. The tipping point was when the virus accrued three mutations.

But vanquishing a virus in culture dishes is just the first step.

Delivering Cas13 to clinical trials

The next step is to test Cas13 in mice that have been bred to be susceptible to COVID-19. It will also be tested in infected human cells washed from the nose, and in infected lung organoids: ‘mini organs’ grown from human stem cells.

A crucial issue is how to turn Cas13 into a drug. Cas13 itself is a protein, but its all-important guide is made of flimsy RNA.

This is where the Melbourne team plan to leverage off the global RNA revolution. Thirty years ago, the idea that RNA could be used as a drug was laughable. Its fragility was only the beginning – researchers also knew that injecting large amounts of it could trigger dangerous immune reactions.

But dogged pioneers engineered workarounds, substituting the RNA code letter uridine for ‘pseudouridine’, an alternative naturally-occurring code letter, which calmed the stormy immune response. And to protect the RNA, they packaged it in fatty capsules known as lipid nanoparticles.

These are the steps the Melbourne team will not have to reinvent. But still, the question remains: how can Cas13 be delivered into the body?

“A nasal spray,” says Lewin.

Used early in the infection or as a preventive treatment, the spray could stop the virus gaining a foothold in nasal cells before it invades the lungs, where the real damage is done.

Lewin’s group already has years of experience packaging drugs in lipid nanoparticles, as part of a strategy to target drugs to reach the HIV virus hiding deep inside some cells. “The team aims to use this technology to deliver Cas13,” says Lewin.

Despite borrowing from the RNA revolution, there’s no doubt that developing the Cas13 delivery technology will take years.  

But more funding will speed its passage. To that end, Lewin has wasted no time, weaving together a collaboration of several Australian groups – as well as those in Israel, the US and Denmark – to submit a proposal to a US$3 billion fund for COVID antivirals announced by the Biden administration on 17 June 2021.

It may well take years for the first Cas13 antiviral nasal spray to run the gauntlet of development pipelines and prove itself in the clinic.

But it will take weeks for the second.

“We’ll be ready for the next pandemic,” says Fareh.