Feature: Banking on nature

Nearly all front-line antibiotics from the past half century have lost efficacy with the emergence of multi-resistant strains of pathogenic bacteria like methicillin-resistant Staphylococcus aureus (MRSA) and Vancomycin-resistant Enterococci (VRE) and Mycobacterium tuberculosis (TB) that now haunt the world’s hospitals.

So it was a rare piece of good news when Griffith University’s Eskitis Institute announced last year that it had licensed Swedish biotechnology company Creative Antibiotics to take a natural compound from a Papua New Guinea rainforest plant into development as a novel antibiotic that might break through the stubborn resistance of some of these belligerent pathogens.

The Swedish biotech is taking a softly-softly route to antibiotic development: it aims to develop compounds that will not kill bacteria, as such.

Rather it seeks to neutralise the virulence factors that transform passive bacterial cells into deadly pathogens that proliferate rapidly, and can overwhelm the immune system before it can mount an effective response. Creative Antibiotics hopes to effectively buy time for patients by preventing the Jekyll-to-Hyde transition.

The company is planning to develop a compound identified by the Eskitis Institute, INP11252, as a virulence blocker for a particularly troublesome pathogen: Pseudomonas aeruginosa, nemesis of cystic fibrosis patients, and a cause of severe urinary tract infections.

The Eskitis Institute identified the compound by screening samples stored in Nature Bank, its repository of more than 45,000 plants and marine organisms, including over 11,500 plant species from Queensland, Papua New Guinea and China, and 4000 species of marine organisms from the Great Barrier Reef.

Nature Bank is the brainchild of Eskitis Director Professor Ron Quinn, who has decades of experience in natural-product drug discovery, and in synthetic and medical chemistry and pharmacology. It was established in 1993 in collaboration with AstraZeneca as a national resource, accessible to drug researchers in academia, and also to industry on a fee-for-service basis.

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The Eskitis Institute can supply screen-ready plates of Nature Bank fractions to research institutes around the world to examine on their own high-throughput screening facilities, and offers a follow-up service to identify individual compounds in any extract that records a “hit.”

Its huge repository of biological samples has been refined to produce more than 200,000 lead-like enhanced (LLE) fractions, which have been processed to remove non-drug-like components. High Pressure Liquid Chromatography is used to identify individual compounds within the LLE fractions, which typically contain up to five drug-like molecules.

The institute recently installed Australia’s largest robotic system of its kind to screen compounds from Nature Bank for biological activity against new therapeutic targets. These targets have been identified by publicly funded and private research programs across Australia or, as in the case of Creative Antibiotics, by overseas outfits.

Natural automation

Nature Bank fractions are stored in the Queensland Compound Library (QCL), which is Australia’s only integrated compound management and logistics facility, and provides a crucial link between Australia’s chemists and biologists.

The QCL is a national facility, jointly funded by Griffith University, the Queensland State Government’s Smart State program and the Commonwealth’s Super Science Initiative – a four-year, $1.1 billion program announced in 2009 to contribute to priority areas of Australian research until 2013. “The QCL is a major piece of infrastructure that can underpin the development of proprietary, unique molecules made by the chemistry community around Australia,” says Quinn. “For example, a biologist in a university laboratory in Adelaide might ask us to deliver samples of Compound X in Format B to a particular laboratory for testing.

“The Cooperative Research Centre for Cancer Therapeutics does that: it chooses the target it wants to screen, has plates made up, and sends them to screening centres. One is located at Brisbane’s Eskitis Institute, the other is at the Walter and Eliza Hall Institute for Medical Research in Melbourne.

“An individual researcher may have only a small number of compounds, which makes it rather difficult to get someone in the pharmaceutical industry to screen for ligands.

“It’s an advantage to be able to accumulate the output around Australia, and allow it to be used for biological testing by academia, or by academia-industry collaboration. It’s a matter of scale, and the ease with which we can align and array samples in any format a researcher wants.”

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Quinn says the 200,000 Nature Bank lead-like fractions are kept in solution in small, barcoded canisters. The canisters are loaded into pneumatic tubes and propelled by compressed nitrogen gas to an automated workstation, where syringes are inserted through their caps to withdraw small volumes for testing.

The samples are made up into microtitre plates; depending on requirements, 96, 384 or 1536-well plates can be used. Typically, the volume of solution delivered into each well is around 1 microlitre, but can be as little as 2.5 nanolitres.

The microtitre plates can also be replicated in multiples for different assays. “We can plate out in any format, because our clients usually want their own particular kinds of assays,” says Quinn.

He says the Institute’s Fourier Transform Mass Spectrometer (FTMS) represents an exciting new tool in the search for new drugs.

The Institute developed the revolutionary, high-throughput screening technology, which that uses mass spectrometry to detect weak binding interactions between a pool of proteins and a library of known fragments, or between individual proteins and components of a crude extract. Eskitis researchers can then observe and identify compounds binding to proteins in real time.

Another of Nature Bank’s marquee projects is funded by a Bill and Melinda Gates Foundation Grand Challenge Explorations grant. It has Eskitis researchers using FTMS to identify compounds binding to potential protein targets in the malaria parasite, Plasmodium falciparum. It has also been used to screen target proteins for African sleeping sickness, caused by the tsetse fly-transmitted parasite Trypanosoma brucei.

The robotic system has proven instrumental to the success of Nature Bank, and enables screening of a far greater number of compounds than by hand. The collaboration with Creative Antibiotics is only one of the projects underway, although this alone could provide a breakthrough in the treatment of stubborn pathogens that prove the benefit of combining the latest technology with nature’s own products to advance human health.