A renewed scientific campaign against this devastating disease is offering humanity new hope.

There are parasites – smaller than human cells – that have an unquenchable appetite for human haemoglobin, the bright-red, life-giving molecule that carries oxygen in our blood.

Transmitted by mosquito bites, these microbial parasites cause malaria, which annually afflicts millions of people through debilitating fever. Every year, the disease kills about a million people – mostly children and mostly in Africa.

Despite malaria’s grim status as one of the planet’s most devastating diseases, infection rates declined by 25 per cent between 2000 and 2012. A combination of drugs, bed nets and indoor spraying with insecticides has helped keep malaria at historically low levels.

But for doctors, researchers and communities in malaria-prone regions, the respite was always going to be short-lived. The parasite’s relentless ability to acquire resistance to drugs is well known, which is why there has been mounting dread as humanity’s medicine cabinet comes down to its last effective class of antimalarial compounds – the artemisinins. But now, clinics in Thailand and Cambodia report that even this last drug defence may have been breached.

Should resistance to artemisinin spread – as has resistance to every other antimalarial drug – the consequences could see life expectancy in the tropics once again start to fall, dragged down especially by rising infant mortality rates.

Science alert

This time, however, there is a difference. The loss of this drug defence was predicted, and an unprecedented philanthropic bequest has driven one of the most concerted scientific assaults on the disease ever seen.

Mosquitoes at the pupa stage of their life cycle.Mosquitoes at the pupa stage of their life cycle.
Photo: 123rf.com

More than a decade ago, the World Health Organization, knowing time was ticking on another malarial pandemic, initiated a pre-emptive strike – the Medicines for Malaria Venture (MMV). The funding for this global research effort has come from a range of donors, including government aid agencies in Australia, the US and Europe, private-sector corporations such as Newcrest Mining and ExxonMobil, and the non-profit sector, particularly the Bill and Melinda Gates Foundation.

The outcome 15 years later is being described as one of the most successful drug-development initiatives of the modern era – and one of the centres where some of the most promising drugs have been optimised for clinical use is an inconspicuous laboratory in the leafy Melbourne suburb of Parkville.

There you will find Professor Susan Charman, director of the Centre for Drug Candidate Optimisation, a key component of the Monash Institute of Pharmaceutical Sciences.

Research led by Professor Charman – in collaboration with researchers around the world – has been internationally acclaimed for its pivotal role in the development of some of the most advanced new antimalarial drugs so far – Synriam™ and yet-to-be-named OZ439 and DSM265.

Approved in 2012 and now marketed in India, Synriam™ borrows its anti-parasite chemistry from artemisinin but is much cheaper and easier to make.

Taking antimalarial drugs to the next level, OZ439 reduces treatment times from three days to one, thereby achieving an MMV “holy grail” – a drug that can be administered as a single-dose treatment that will cost less than one US dollar. It is now in advanced clinical trials.

Then comes DSM265, which is in early clinical trials. This new drug introduces an entirely new and targeted way to attack the parasite.

Another drug candidate, MMV390048, the first developed in Africa, will soon enter clinical trials and a further two drug candidates are in pre-clinical development.
All of these compounds have at one point in their development passed through Professor Charman’s laboratory and, in the process, earned her five MMV Project of the Year awards.

MMV CEO Dr David Reddy says that the work MMV does to develop and deliver the next-generation medicines would not be possible without the expertise of partners such as Professor Charman.

“Sue has provided incredible scientific support right across our portfolio of medicines,” Dr Reddy says. “In particular, her group has supported the development of our lead candidate for a single-dose cure, which could be a real game changer for the treatment of malaria.”

Surviving the body

Professor Charman explains that her research at Monash University specialises in optimising the way a drug is processed inside the human body.

It is an area of expertise called pharmacokinetics and recognises, clinically, that the body is not a passive recipient of drugs but rather views a drug as something foreign that it can chemically modify and eliminate at will.

“Our aim is to optimise a compound early in its development, well before the compound reaches clinical trials,” says Professor Charman, whose team works with drug-discovery groups all over the world on many diseases, including cancer.

Professor Charman explains how, once swallowed, drugs must be released from the formulation in the stomach, pass into the intestine, dissolve in the intestinal fluids and be absorbed into the bloodstream. That blood is taken directly to the liver and filtered before it is allowed access to the rest of the body. Enzymes in the liver can “detoxify” (chemically neutralise) drugs before they reach their intended targets.

“We know a lot about the chemical characteristics a drug needs to have to ensure good absorption from the intestine and low metabolism in the liver, both of which are needed to allow it to reach its target in the right concentration and remain there for the right duration of time,” Professor Charman says.

For more than a decade she has used that expertise to identify pharmacokinetic problems with compounds that have promising antimalarial activity, and has worked with chemists to improve them.

While there are many malaria research groups around the world, few have an embedded pharmacokinetic team the way Monash does. As a result, Professor Charman collaborates with a vast network of malaria researchers both within Monash and worldwide, putting her at the front row in the global malaria drug-discovery effort.

In 2014, she described the drug-development pipeline as being in the best condition of its history.

Nonetheless, researchers are acutely aware that malaria has developed resistance to every drug ever produced.

“You always need new drugs for malaria,” Professor Charman says. “That means new compounds coming through the pipeline continuously.”

The malaria box

Four years ago, the quest for novel antimalaria compounds received a massive boost when pharmaceutical companies – primarily GlaxoSmithKline (GSK) and Novartis – screened their entire compound libraries for their ability to kill malaria parasites.

The GSK data is especially valuable as all active compounds were also tested for activity against a multi-drug-resistant parasite strain and their molecular structures made publicly available. The work was done in Spain by the GSK malaria unit led by Associate Professor Jose Garcia-Bustos, now at Monash.

The GSK team screened more than two million compounds – mostly without the benefit of high-throughput robotics – in a project that took five years to complete.
“In all, we identified 13,500 molecules that are capable of killing the malaria parasite in test-tube assays,” Associate Professor Garcia-Bustos says.

Despite including many proprietary molecules owned exclusively by GSK, the company has made all the compounds available for use by researchers.

“There have been few media reports about it but companies are finding ways to contribute to these public-good ventures,” Associate Professor Garcia-Bustos says.

In 2011, MMV brought together a representative set of about 400 molecules to produce the “malaria box”.

“To date, more than 160 physical copies of the box have been delivered to researchers around the globe in a bid to stimulate malaria and neglected disease drug discovery,” MMV’s Dr Reddy says.

Professor Charman says that while none of the compounds are drugs in their own right yet, they are a good starting point because they all have reasonable pharmacokinetic properties.

“A good medicinal chemist can optimise the molecules, including the interaction with the target in the parasite – if it is known,” she says. “Unfortunately, with malaria we often do not know the identity of the drug targets, even in the case of artemisinin.”

That, however, is something that scientists at the Monash Department of Microbiology are looking to change.

Malaria as a molecule

The malaria parasite can be viewed simply as an assembly of molecular-driven biochemical processes. Biologists find this perspective helpful because it brings into focus molecules that control either processes essential to the parasite’s survival or processes that cause disease.

Knowledge of such key “regulatory” molecules provides the ability to scan their physical structure for weaknesses and to design small, molecular assassins – usually in the form of inhibitors – to attack them and trigger a domino effect that brings down the parasite.

In his next blockbuster project, Associate Professor Garcia-Bustos is attempting to identify all parasite targets attacked by the GSK antimalarial compounds.

One strategy stands as a masterclass in biomolecular deviousness. First, he helps the parasite to acquire resistance to his compounds. He then scans the parasite genome to identify which genes mutated to create resistance.

“This can often identify the molecule most under pressure by each compound, and so reveals the likely drug targets,” Associate Professor Garcia-Bustos says.

That project is starting at Monash, where he was recruited by the director of the Microbiology Department, Professor Christian Doerig, who is also an accomplished malaria researcher with a reputation for game-changing, big-picture projects.

Drug targets

Professor Doerig’s focus when it comes to drug targets is a class of molecules called kinases. These are regulatory molecules that cells in all organisms use to relay important signals, such as the command to replicate.

Unlike kinase researchers of the past, Professor Doerig does not work on one such molecule. Instead he has mined the entire parasite genome for all such molecules.

“We found 85 genes that encode kinases and that together make up the parasite’s ‘kinome’,” he says. “Importantly, we found that some have no counterpart in any other species and are so different from all other known kinases that we cannot predict their function in the parasite’s life cycle; working on them is like doing exobiology [extraterrestrial biology].”

These differences, however, are a superb quality to have in a drug target because it means a greater likelihood that the drug will selectively inhibit the parasite and not the infected human.

The 85 regulating kinases are being systematically analysed and categorised at Monash on a spectacular genome-wide scale. “These proteins sit at key regulatory junctions in the parasite’s biology,” Professor Doerig says. “By characterising all of them we can assemble a map from which drug targets clearly stand out.”

In the process, the project is creating invaluable research materials – such as genetically modified parasite lines – that are of use to malaria researchers all over the world.

Cancer ally

Causing particular excitement is the discovery that to survive and proliferate in humans, the malaria parasite is capable of hijacking human kinases – the same kinases already targeted for drug discovery by cancer researchers. When Professor Doerig tested these potential anti-cancer compounds against malaria-infected red blood cells, the chemotherapy drugs were found to kill the parasite.

“This is interesting for two reasons,” Professor Doerig says. “First, targeting a human enzyme will make it much more difficult for the parasite to become resistant to the drug. Secondly, we can piggyback on the huge investment the pharmaceutical industry has made in the past decade targeting human kinases for cancer chemotherapy.”

A view of the surface of a malaria-infected red blood cell at the highest resolution ever achieved.A view of the surface of a malaria-infected red blood cell at the highest resolution ever achieved.
Photo: Professor Brian Cooke and Steven Morton

Another subset of unique kinases are of particular interest to Professor Brian Cooke, deputy head of the Monash Department of Microbiology and a 25-year veteran of pioneering malaria research, whose primary interest is the surface membrane of infected red blood cells.

He brings up an image (see image) on his desktop computer that he took with an atomic-force microscope. It shows, with unprecedented detail, the outer red cell membrane’s exquisite architecture but pricked and marred by molecules and structures inserted there by the parasite.

“The parasite alters the membrane’s properties causing the infected blood cell to become unusually stiff and sticky,” Professor Cooke says. “These disruptions are responsible for the most lethal consequences of being infected with malaria.

“There have been efforts to target these molecules for drug and vaccine development in the past but these efforts were thwarted by the parasite’s ability to switch and change these molecules to avoid detection.”

However, Professor Cooke has identified some of the kinases that regulate the parasite’s membrane-disrupting biology. “If we could inhibit these particular kinases, I strongly believe the inhibitors offer real possibilities for new drugs,” he says.

Additionally, the membrane studies have spurred advances in diagnostic medicine through collaborations with physical chemist Associate Professor Bayden Wood from the Monash Department of Chemistry.

Star Trek diagnostics

Associate Professor Wood confesses that his quest to use light as a diagnostic tool in medicine was based on the same science-fiction series that inspired the smartphone.

“All the great ideas come from Star Trek,” he says. “Dr McCoy’s medical tricorder was the first time I saw someone point a handheld device and use light in diagnostic medicine.”

That light has diagnostic applications in the real world is due to a quirk of matter. When any atom or molecule changes energy state it does so by emitting and absorbing light (or more accurately, electromagnetic radiation, which includes visible light, but also gamma rays, X-rays, microwaves and ultraviolet, infrared and radio waves). Each type of molecule has a unique, telltale way of doing this, which scientists can analyse. This is how astronomers know the composition of matter in distant stars.

The instruments that can “read” light’s telltale signatures are called spectrometers. While spectroscopy has found important applications in astrophysics, chemistry and forensics, Associate Professor Wood is pioneering uses in diagnostic medicine, describing himself as a “biospectroscopist”.

To find an infrared signature typical of malaria, Associate Professor Wood analysed all the different parasite life stages at the single-cell level, initially using the infrared light source at the Australian Synchrotron.

Malaria signal loud and clear

“The breakthrough came when we identified a unique infrared signal associated with the fatty acids that constitute the parasite’s membranes,” Associate Professor Wood says.

In terms of malaria, we might be unique at Monash in that we can go from basic research all the way through to biomedical engineering, clinical applications and drug delivery.
- Professor Brian Cooke

The “malaria signal” came through loud and clear even when the parasite was tested in the presence of blood and even at early stages of infections. This is significant because it is currently difficult to diagnose malaria during its early stages.

“We were then able to detect that light signature using a small, cheap spectrometer – a malaria tricorder, so to speak – that can be used in remote locations without the need for healthcare professionals,” he says. Coupled with software that can automatically detect and quantify the presence of malaria parasites in a single drop of blood, the patented technology is extraordinarily sensitive.

With improved diagnostics, antimalarial drugs could be taken sooner after infection and the disease treated more effectively, Associate Professor Wood says.

The new technology would also allow clinicians to identify carriers of the parasite who do not show malaria symptoms. “These people pose a serious risk to communities because as they go about their daily business they pass on the parasite to others via mosquitoes moving from person to person,” he says.

“It is these ‘carriers’ that the medical tricorder hopes to identify so they can be isolated from their communities and treated.”

A pilot study with the device is scheduled for late 2014 in Thailand.

Like all the Monash malaria researchers, Associate Professor Wood attributes his success in part to an extensive network of collaborators across disciplines and institutions, including Professor Leanne Tilley (University of Melbourne) and Professor Cooke.

“In terms of malaria, we might be unique at Monash in that we can go from basic research all the way through to biomedical engineering, clinical applications and drug delivery,” Professor Cooke says.

“That makes sense when you recall that Australia only eradicated malaria in 1981 and that all the vectors are present for malaria to make a comeback. That is why Australia generally, and Monash specifically, never dropped its guard when it came to our antimalaria R&D capacity.”

Why malaria kills

Five microorganism species, all from the Plasmodium genus, can cause malaria in humans. These microorganisms invade and take over red blood cells to reproduce. In the process, they vandalise the host cell, making it unfit for human purposes. Within days, the infected cell bursts to release up to 50 new parasites. The resulting biochemical debris induces inflammation that the patient experiences as fever. With each round of parasite reproduction, the fever recurs and people do not acquire long-lasting immunity. The parasite also causes the red blood cells to become stiff and sticky. The cells clump together in the capillaries, where the parasite can hide from the human immune system. When this clumping takes place in the capillaries of the brain the result is cerebral malaria, which causes 80 per cent of malaria deaths.

Know the target – the HIV lesson

The importance of understanding an intended drug's target was made clear in the fight against HIV/AIDS and the breakthrough discovery that the AIDS virus relies on a protease (a molecule that cuts up other proteins) to replicate. The drugs that work are small molecules that inhibit the HIV protease.

Malaria too has been found to require proteases. The 3-D atomic structure of three such molecules has been ascertained by Dr Sheena McGowan, who runs a laboratory at the Monash University Department of Biochemistry and Molecular Biology.

"My strategy is to starve the malaria parasite by inhibiting specific proteases (called aminopeptidases) that the parasite uses to digest human haemoglobin, which it uses as food," Dr McGowan says.

She adopted an approach called structure-based drug design that was pioneered in Australia with the development of the anti-flu drug Relenza® by scientists from Monash, CSIRO and the Australian National University. It involves crystallising the protease and using a synchrotron's X-ray beam to decode the atomic structure of the protease as it interacts with various potential drugs.

Although the drug-development project is just beginning, she has already characterised an inhibitor to each of the targeted proteases.

"We have compounds that inhibit two of the targeted proteases and that work at concentrations that have no toxic effect on human cells in preliminary toxicity studies," she says. "That makes for a good start."

Integral to that progress, she says, has been access to the different scientific disciplines she needs at Monash, in particular the Australian Synchrotron next to Monash University's Clayton campus and the research team at the Monash Institute of Pharmaceutical Sciences (MIPS).

"MIPS makes it possible to move research findings from 'bench to bedside'," she says. "It means we can move the project forward and manage all the complexities and subtleties of getting compounds to clinical trials."