Taking the fight to the enemy’s door

ODT, 26.9.2006

UNDERNEATH, SOME of the most dangerous killers of our time are also very beautiful. Killers such as HIV and bird flu have at their heart delicate molecular structures of helix curls and suspended symmetries that would grace the foyer of any modern corporate headquarters.

University of Otago scientists have joined a small cadre of international researchers revealing those structures, but it is not an exercise in aesthetics.

They want to identify where the structures might be vulnerable, where a drug molecule might step in to neutralise them.

Biochemist Prof Kurt Krause and his collaborators at Otago have recently finished setting up a new million-dollar protein crystallography laboratory that can see down into the molecular structure of the protein-building blocks of killer viruses and other pathogens.

The lab, which forms the heart of the university’s Centre for Molecular Research in Infectious Diseases, uses robots and X-rays to reveal the forces at work.

“We are setting up shop here to try to design drugs to treat infectious diseases,” Prof Krause explained in an interview.

“The World Health Organisation’s recent warnings about the increasing spread in Africa of ultra-resistant tuberculosis underlines how absolutely vital it is to pursue new arsenals against a whole range of infectious diseases.”

Tuberculosis, HIV and pathogenic parasites such as toxoplasmosis are targets of Prof Krause’s own research.

Other pressing projects that centre scientists could tackle include the development of vaccines and diagnostics.

“New Zealand scientists could design vaccines for threatening diseases like bird flu, and not have to rely on other countries for these products,” Prof Krause said.

“We are trying to pull our research centre together to do just this type of work.”

By taking on the work of developing new drugs, Otago could with its interdisciplinary strengths stretching from chemistry to pharmacy and pharmacology fill an important role in the battle against infectious disease.

Many of the big international drug companies were backing off developing new antibacterial medicines because of the costs and risks involved, Prof Krause said.

Even where they came up with a new antibiotic, if bacteria developed resistance, their investment might be lost.

“My idea is that New Zealand scientists can get involved.”

In the lab, the work has already started.

“The laboratory’s work involves minutely probing the molecular structure of proteins inside infectious viruses and microbes to seek out weaknesses that can be exploited.”

Proteins are the engines that carry out the tasks of the body, but viruses and bacteria also contain proteins proteins that can spread infection and harm their human host.

Prof Krause said the majority of pharmaceuticals worked by targeting an essential function of the pathogen involved and interrupting it.

Once the shape and the charge of a protein’s “active site” was established, it was often possible to neutralise it by designing an inhibitor (or drug) to bind to and block access to this site.

The drug molecule would be built like a key to a lock, to precisely fit with the active site of the protein molecule within the bacteria or virus it was targeting.

“In order to fit, a potential drug compound has to have a complementary charge, shape and polarity when compared to the protein,” Prof Krause said.

Advances in equipment and knowledge in the past 25 years have made some of the work of identifying a protein’s molecular structure more straightforward, but the processes of purifying proteins for investigation and protein crystallography remain tough, uphill climbs.

There is a series of steps in the process.

Once a protein perhaps from a bacteria has been isolated for further investigation, a crystal has to be made.

“Almost anything you can purify, you can crystallise,” Prof Krause said.

“Even big things like huge viruses, if you can get them pure, you can crystallise them.”

A robot, in the centre’s lab, does that part of the process, making crystals 0.3mm across from small quantities of protein soup.

From there, a tiny loop made from a fibre the width of a human hair is used to scoop up a single crystal, which is placed in the laboratory’s X-ray generator the most advanced of its kind in New Zealand.

The machine produces two frequencies of X-ray, a feature usually available only from multimillion-dollar atomsmashing synchrotron facilities in the northern hemisphere.

Those X-rays are fired at the crystal, which is frozen to minus 180degC with liquid nitrogen processed directly from air in the lab, and the diffraction pattern of the rays is caught on a plate behind it.

The pattern, which accumulates over a day or so and might contain between 30,000 and 40,000 spots, is the starting point for some “quite sophisticated and difficult” calculations.

All going well, those calculations will produce a three-dimensional “glove“, giving the approximate shape of the molecule. Further work will reveal the atomic structure itself.

However, that again is only another step in the process.

“The goal is not to get the structure; it’s to figure out how it works,” Prof Krause said.

“You take your atoms and start interpreting them. That’s the interesting part.”

The pay-offs of this kind of inquiry have been many.

In the example of the HIV protease, or enzyme, eight new drugs have gone on the market in the dozen years since its structure was unlocked.

“Academic labs had a big role in that,” Prof Krause said.

The Dunedin facility is the third such lab Prof Krause has helped to set up a task made easier by a $166,000 gift from United States businessman, physician and philanthropist Dr John Thrash.

The gift was received under the university’s Leading Thinkers initiative and will attract matching funds from the New Zealand Government.

The lab was given an initial test drive on a difficult protein fragment containing several atoms of sulphur, Prof Krause said.

“And it worked, so we were very happy with what we have done.”

Having established that the equipment will do what it needs to, the centre can get on with the job of identifying and examining sites of interest within protein structures.

Prof Krause said the centre aimed to map up to 10 molecular structures a year for research teams both at Otago and around the country.

From that point, there are several more years of research and testing to put a new drug on pharmacy shelves.