Unlocking nature's secrets with A.I.

AMPLY Discovery has a fresh take on drug research

Hello there,

The only problem with calling a newsletter ‘PreSeed Now’ is that funding round stages are incredibly vague labels. For example, one startup founder I spoke to a while back told me they had raised a small ‘seed’ round and later rebadged it as ‘pre-seed’ because the optics were better.

Today’s startup, by its own description, is outside the usual remit of this newsletter because it’s already raised a ‘seed’ round. But their total funding to date is closer to what I’d describe as ‘pre-seed’ myself.

But hey - don’t let labels worry you. Take a look at what AMPLY Discovery is doing - it’s fascinating and could make a big impact as something of an IP factory in the field of drug development.

Of course, if you’re one of the increasing number of PreSeed Now members, you get the full version of the newsletter with details of their funding, future plans, and more. Not a member yet? You can upgrade here 👇

– Martin

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👀 Things to keep your eye on

• TECH COMPANIES TO WATCH: PreSeed Now is supporting a great event from the fine folk at Prolific North on 10 November in Manchester. If you’re going to be in the area, do come along to Tech Companies to Watch, a showcase of “ambitious early-stage tech companies that we think should be on everyone’s radar as we head into 2023.”

• PUBLIC SECTOR TECH: Amid the chaos in Westminster over the past week, a new Government unit has launched. Based in Salford, the Government Office for Technology Transfer’s task is to “ensure that the public sector is maximising the value of its knowledge and innovation assets estimated to be worth £104 billion - including intellectual property, software, processes and data”. There’s funding available to support this, which could open up some interesting opportunities for startups.

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AMPLY Discovery is unlocking nature's secrets with A.I.

AMPLY Discovery alongside Queen’s University Belfast staff.

The discovery of penicillin almost 100 years ago showed how we could take things like mould from the natural world and turn them into life-saving drugs. Now a Belfast-based startup is using modern A.I. techniques to apply a new level of intelligence to drug discovery.

A spinout from Queen’s University, it has developed software that can analyse digital biological data and identify compounds that could be useful for human and animal healthcare. They’re using it to identify new antibiotics, anti-cancer drugs, and anti-parasitic drugs among others. 

A.I.-based drug discovery is nothing new, but AMPLY Discovery sets itself apart with its unusual approach.

“Small organisms fight one another. Bacteria fight other bacteria for supremacy, larger organisms have to try to fight off smaller organisms. So what we're doing is we're finding those compounds that these creatures are already producing, shaped by years of evolution and appropriating them for human beings,” says CEO Ben Thomas.

And finding these compounds is just the beginning…

Drug discovery, the AMPLY way

AMPLY Discovery makes use of genetic sequencing data or protein and peptide analysis, either from publicly available sources or their own research. Their software then scans it, using A.I. techniques to identify potentially useful compounds.

Once they’ve found a likely candidate compound within the digital data, they can use 3D bioprinting to create a physical version of it to test in their lab. “It’s a real merging of modern technology and old school, tangible drug discovery,” Thomas says.

As an example, Thomas says AMPLY Discovery has scanned the digital sequencing data of a particular type of cannabis, identified a previously undiscovered compound, and printed that out into the form of powder to test in their lab. 

“We've taken this natural process of discovery, and accelerated and compressed it to an almost terrifyingly fast process… [It] can be done in days, whereas these procedures can be very, very slow.”

AMPLY Discovery aims to collect a library of the compounds it finds so that when drug companies come looking for solutions to problems, they might already have something ready to licence. The rapid arrival of Covid in 2020, and the sudden spread of monkeypox more recently, demonstrates why this could be a particularly valuable approach.

“We already have a large library of compounds that kill a lot of stuff that simply can't be killed by conventional drugs,” says Thomas.

We’re going on a compound hunt

So how does AMPLY Discovery go about figuring out what to investigate in the first place?

“We normally start from a position of ‘what do you want to kill?’,” Thomas says. “Let's say for example we're dealing with an antibacterial. So an example might be MRSA. So you have this staphylococcus, it's a bacteria and it's not touched by conventional antibiotics. It's a serious threat, you need to find something. We can then move into this sort of ‘digital prospecting’ phase”.

This “prospecting” might involve finding bacteria that live in environments where they have to compete with staphylococcus, or they might look at plants or animals that are known to be good at protecting themselves from bacterial and fungal strains. For example, in the case of MRSA, Thomas says they found interesting compounds in frogs from the Peruvian rainforest.

In this case, Thomas said they analysed the skin of a frog and put that data into their software. 

“One of the benefits of these digital technologies is that we're not limited by what you can culture in a lab or on a petri dish or anything like that. What we're looking at is literally every chemical that frog was expressing in its skin at the precise moment it was killed.” 

The software allows the team to highlight potentially interesting compounds that have the potential to be used in safe medication for a particular purpose, allowing them to then bioprint the most promising candidates for testing. The system learns from the results of its output, Thomas says, meaning it gets better at pointing out the best compounds over time.

As for the bioprinting itself, Thomas describes is as a bit link an inkjet printer that uses amino acids rather than ink, and can reconstruct the specific parts of a molecule that they’re interested in.

“There are different technologies to do this and, like in the body, sometimes we may like to modify these molecules post-printing beyond the sequence of amino acids by doing some chemical design on them, but fundamentally it’s possible to get a powder in a tube purely from a datafile fed into a biological printing machine,” Thomas says.

“There are many people who know and do this, but it’s the end-to-end stitching of the deep digging for novel compounds, the prediction and chopping out of the good bits and the fact we test, and can feed back our real world results into our virtual ones, which makes this a very powerful process.”

From pig farmer to tech entrepreneur

Thomas has a varied background. Having gained a degree in Biology, he worked as a tech consultant and then a pig farmer. He then did a PhD in Biomathematics, Bioinformatics, and Computational Biology at Aberystwyth University.

“I was looking to see if you can get good, interesting drugs from the stomachs of cows. And one day, I presented some of the data I'd done and it looked identical to one of the systems that I generated for fund managers to do stock picking. It was effectively stocks replaced by biological molecules with a series of metrics.”

From there he pivoted his PhD to a more commercial focus, and then moved to Queen’s University Belfast to work as a postdoctoral researcher. There he met Dermot Tierney from the university’s tech transfer team, who had previously nurtured startups at the Dublin Institute of Technology. 

After helping to shape AMPLY Discovery’s commercial model and spin out from the university in early 2021, Tierney came on board part time as a director, before joining full-time as chief commercial officer this summer.

At present, AMPLY Discovery is investigating compounds to treat animal and human conditions as it gears up for its next funding round (more on that below).

Who else is in this space?

There are hundreds of startups working in the field of A.I.-enhanced drug discovery, but only a handful who overlap with AMPLY Discovery’s approach.