Mining fungi: a fountain of new medicines?

While fungi are a rich source of natural molecules, it has historically been hard to identify and capture these in a systematic way. Now a new technology platform, developed by researchers at Northwestern University and their partners, promises to speed up the process dramatically. Could this lead to a gold rush of drug discoveries? Abi Miller finds out.

Professor Neil Kelleher, a chemical biologist at Northwestern University, is a man who loves his fungi. As one of the authors of Nature Chemical Biology’s August cover story – headlined ‘scouting the fungal jungle’ – he has spent the last five years developing a platform called FAC-MS (Fungal Artificial Chromosomes with Metabolomic Scoring). This technology has huge potential for drug discovery, allowing scientists to quickly home in on promising new molecules in mould.

It’s a complex process, involving elements of genomics, molecular biology, mass spectrometry and data analytics. But when asked what’s so exciting about fungi, Kelleher’s answer is simple.

“One word – penicillin,” he says. “The natural world has been evolving chemistries to impact biology for a lot longer than humans have been on the planet. It’s not such a heretical statement to say that natural products can provide major value to the pharmaceutical industry – they already have!”

‘Prospecting for gold’

Penicillin, the first true antibiotic, was famously discovered by Alexander Fleming in 1928 when he found a blob of mould on a petri dish. The petri dish was being used to grow colonies of the Staphylococcus bacteria, but an exclusion zone had formed around the mould, as though it was secreting something that killed bacteria (or at least prevented its growth). By the 1940s, penicillin was being synthesised on an industrial scale, and touted as a ‘miracle drug’.

While there have been other drugs derived from fungi (not least the immunosuppressant cyclosporine, first isolated in 1971, and certain types of statins), the last few decades have not seen much activity in this space. Kelleher believes this stems from two factors: a lack of investment and a lack of strategy.

"The researchers applied their method to 56 fungal gene clusters."

“For the past 20 or 30 years, fungi and bacteria haven’t been much sought out in the main funding lines of drug discovery in private industry. That’s because synthetic molecules and antibodies have become the major source of drug discovery leads,” he says. “Looking for natural molecules has been like prospecting for gold in the Wild West of America – it’s a one-off affair where you find a gold nugget. But how do you strip-mine the natural world, how do you set up a mechanised industrial scale process? There have not been good answers to that.”

An amazing hit rate

Kelleher and his collaborators believe their technique provides just such an answer. FAC-MS – which was developed in collaboration with colleagues at Northwestern University, Nancy Keller’s lab at the University of Wisconsin-Madison and the biotech company Intact Genomics – could be used to unearth new molecules in a scalable fashion.

As reported in the Nature paper, the researchers applied their method to 56 fungal gene clusters. They discovered 17 new natural products, a hit rate of around 30%, which Kelleher calls ‘amazing’.

“In this field, finding one new gene cluster and its metabolite is normally what’s reported as a new gold nugget, a good paper,” he explains. “But we have 17 of them in one paper, and these are dropping out of the sky now. Imagine instead of attempting it 56 times, we attempted it 560 times – well, that should give 10 times more hits, or 170 new, possibly bioactive drug leads. The word ‘scalable’ is a signal that if you put in resources, you will get out a defined return.”

Three-step process

The technology has three parts. First, the researchers use genomics and molecular biology to capture chunks of the fungal genome. Next, they drop the gene clusters into a host fungus, the widely-studied Aspergillus nidulans. Finally, they use mass spectrometry and analytics to find the appropriate fungal compounds.

Kelleher says this final part of the process is comparable to finding needles in a haystack.

"Each chunk of fungal DNA has genes on it that encode proteins."
“There are tons of molecules in there – primary metabolites, secondary metabolites, all sorts of things,” he says. “But what we’re after is a very specific type of molecule. Each chunk of fungal DNA has genes on it that encode proteins, and those proteins make the natural products we’re looking for. So we go from capturing the DNA all the way through to the detection of the small molecule – that’s the FAC-MS platform.”

The technology isn’t foolproof – sometimes the DNA doesn’t express within the host, and sometimes the metabolites can’t be detected – but its 30% success rate is unprecedented. Kelleher’s paper mentions the ‘recalcitrant genetics, cryptic expression and unculturability’ of fungi, all of which have prevented scientists from harvesting these products in the past.

The next penicillin?

If utilised on an industrial scale, the implications of this technology could be staggering. Of the metabolites discovered, it seems likely that a proportion would have therapeutic benefits.

“These are complex natural products with potent biological activity – the simplest way to think about it is, here’s how a fungus would kill a bacteria, or a fungus would kill another fungus, or a fungus would secrete toxins,” says Kelleher. “Now we have the technology that unearths a bunch of these chemicals, the next step is to put them into screening programmes, using them as drug leads. That puts us at the door of the big pharmaceutical companies.”

In the short term, his team is taking a closer look at two of their 17 metabolites, which seem to have particularly interesting properties. This will provide the basis for a follow-up paper.

In the longer term, though, Kelleher hopes that pharma companies will place a renewed focus on the natural world. As technologies like FAC-MS become available, making the search for compounds easier and more financially viable, companies seeking the next penicillin or lovastatin will have far greater odds of success.

“In academia, we’ve long been hoping for a renaissance in natural products, and with the new technologies combining genomics and metabolomics, I think it’s ready to become mainstream,” he says.

As Kelleher sees it, there is no time to waste. Given the looming threat of antimicrobial resistance – which could kill 10 million people a year by 2050 – the need for solutions is pressing. It could well be that the natural world is replete with such solutions – as-yet-unknown compounds in fungi or bacteria that could do for the world what penicillin did in the 1940s.

Clearly, government funding and philanthropy play important roles in addressing this crisis – Kelleher says his own work would not have been achievable without funding from the National Institutes of Health. However, he believes future progress will depend to a large degree on industry investment.

“Really we need the industry to get back on board and fund such work,” he says. “Sure, small companies like ours are one part of it, but you’ve got to get the big players to re-engage, re-invest. With our technique, the idea is that they can go after the gold of all these natural products in a systematic way.”