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DURHAM, N.C. -- Development of drugs to treat a broad array
of diseases -- including cancer, hypertension, diabetes,
inflammation and infectious diseases -- could become enormously
more effective through the process of "proteome mining,"
according to a Duke University Medical Center
pharmacologist.

Just as the genome is the cell's entire set of genes, the
proteome is the set of the cell's proteins. Many of these
proteins are the molecular switches called enzymes that
catalyze the cell's biological processes. As such, they are
prime targets for drugs to manipulate cellular function -- from
jamming enzymes that cancer cells need to proliferate, to
killing pathological microbes by selectively attacking enzymes
they need to live.

According to pharmacologist Tim Haystead, Ph.D., among
researchers developing the approach, proteome mining involves
isolating the hundreds of enzymes that control key cellular
processes and performing mass screening for potential drugs to
affect those switches. From this screening -- which is
relatively quick and inexpensive -- new drugs to treat disease
can be rapidly identified and progressed to animal testing,
said Haystead, who is an associate professor of pharmacology
and cancer biology.

In a talk delivered Aug. 23, 2004, at the national meeting
of the American Chemical
Society in Philadelphia, Haystead described the current
process of proteome mining. He also explained how he and his
colleagues are using the approach to identify new drugs to
treat malaria without the serious side effects of current
drugs. Malaria affects some 5 to 10 percent of the world's
population, with some 300 million people currently infected by
the malaria parasite. Malaria kills more than 1 million people
-- mostly children -- every year.

"The approach we've been using enables us to mine en masse
large combinatorial chemical libraries that contain drug-like
molecules for novel target associations," said Haystead in an
interview. "And these become starting points for iterative
chemistry and improved selectivity, depending on the protein
targets."

Haystead and his colleagues concentrate on cellular proteins
that bind molecules called purines, because the cell
machinery's principal control switches are purine-binding
protein enzymes called kinases. Such kinases are activated by
the purine adenosine triphosphate (ATP). Thus, reason the
pharmacologists, sifting through the many hundreds of
purine-binding proteins to find drugs that bind and jam such
enzymes constitutes an excellent start to identifying drugs
that affect cellular processes.

"The purine-binding proteome represents proteins coded by
some 2,000 genes, including all protein kinases," said
Haystead. "These proteins represent half or more of the
'druggable genome,' that is, the enzymes that can be targeted
by drugs to affect cellular function."

In their proteome mining, Haystead and his colleagues first
isolate the collection of purine-binding proteins from specific
cells -- including the brain, testes, lung and liver -- that
hold a diverse array of such proteins.

To capture these proteins, they create "affinity arrays" --
passing the complex mix of cellular proteins through a column
containing plastic beads to which are attached immobilized ATP
or similar purines. This column thus captures hundreds of
proteins that have a particular affinity for ATP.

Once they have this captured mixture of proteins, the
researchers can then do proteome mining by individually
treating a series of such columns with each of hundreds of
chemical compounds that make up the libraries of drug-like
compounds created by chemists.

When a given compound interacts strongly with specific
purine-binding proteins, it pulls those proteins from the
column, isolating them. The researchers can then analyze this
sample to determine the proteins' structure. Thanks to advanced
analytical techniques such as "microsequencing" and mass
spectrometry, said Haystead, it is now possible to identify any
protein in a complex mixture, even with exceedingly small
samples.

With the proteins' structures, the researchers can use
database searches to determine whether they play a role in a
disease-related cell signaling pathway. The researchers can
then refine the structure of the potential drug molecule to
make it more selective for one protein and test it on the
affinity array. Such studies of "structure-activity
relationships" reveal how alterations in the drug's structure
changes its effects. This information also enables further
searches of drug databases to find existing compounds that
might be effective.

Finally, the researchers can perform animal studies of the
potential drug's effects to explore its value in treating the
target disease or battling a particular pathogenic
organism.

Importantly, said Haystead, because a given compound usually
pulls more than one protein from the affinity array, the
researchers can also easily get a preview of whether a given
compound might produce side-effects by interacting with other
components in the cell.

To provide such proteome mining services to the
pharmaceutical industry, Haystead and his colleagues have
founded Serenex, a
Durham-based company.

At Duke, Haystead and his colleagues are using proteome
mining to identify new antimalarial drugs that do not have the
eye-damaging side effects of current drugs such as chloroquine.
In these studies, they isolated from proteomes of human cells
those proteins that interact with antimalarial drugs. This
screen revealed that the drugs' effects on a particular enzyme
called aldehyde dehydrogenase appears to be central to the
blindness-causing retinopathy that is a side effect of such
drugs.

However, the researchers have also discovered that another
target of the chloroquine, a human enzyme called quinone
reductase 2 found in blood cells appears to play a key role in
its antimalarial action. This enzyme appears to be part of a
mechanism to protect red blood cells against stress, said
Haystead.

"We believe that the drug inhibits the human enzyme, which
the malaria parasite is essentially using to protect itself
inside the blood cell," said Haystead. "And we believe that if
you inhibit the enzyme then the parasite can't survive, so
drugs that target it will confer resistance to malaria."

Thus, the researchers are now developing and animal-testing
antimalarial drugs that target only this enzyme and not
aldehyde dehydrogenase. They are also developing mice that lack
the gene for the enzyme and studying malaria-resistant people
with mutations in the gene for quinine reductase 2 that give
them resistance.

"What's extraordinary about proteome mining is that, even
though it begins like many discovery processes as a fishing
expedition, it can very quickly and efficiently get down to the
level of one protein target that can be iteratively tested
against libraries of compounds," concluded Haystead.