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Birth
of a drug-screening enterprise |
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Fast
forward to 2002. Fu, along with Emory pharmacology chair Raymond
Dingledine, Winship Cancer Institute associate director Fadlo
Khuri, and Emory chemists Dennis Liotta and James Snyder, set
their sights on securing drug discovery technology that previously
had been the exclusive purview of large pharmaceutical companies––robotics
equipment that could automatically handle thousands of liquids
and chemical assays in minute quantities, then compute and analyze
the resulting massive amounts of information. This powerful system
can quickly screen hundreds of thousands of molecular compounds
against protein targets.
Researchers at Harvard Medical School
had become the first academic scientists to venture into this
new frontier at the beginning of the 21st century. High-throughput
screening equipment was becoming more affordable, and a number
of chemical companies were offering large libraries of compounds
for sale.
In light of Harvard’s success
and Emory’s own experiences in drug development, researchers
here decided it was time to claim a spot for Emory as a national
drug-screening leader. Using existing research grants, combined
with funds from the Keck Foundation and Synaptic Pharmaceuticals,
the group began to piece together the necessary resources, including
a library of 100,000 molecular compounds purchased from ChemDiv.
The Georgia Research Alliance (GRA)
contributed $400,000 for high-throughput robotics screening equipment,
Amgen Corporation offered some planning funds, and the Emory University
Chemical-Biology Discovery Center was officially born.
The new drug discovery center placed
Emory squarely on the front lines of academic drug screening.
In 2005, when the NIH decided to fund a national network of molecular
screening centers, the Emory team was already up and running.
Emory was designated one of nine new centers in the NIH Molecular
Libraries Screening Center Network (MLSCN) and received a three-year
grant of $9 million dollars, including a library of 100,000 additional
compounds. Part of the NIH Roadmap’s “New Pathways
to Discovery” initiative, the network aims to build a better
toolbox for medical researchers and to serve as a resource for
academic researchers throughout the country. Scientists submit
suggested proteins to a national MLSCN peer-review process that
picks the most promising. Each center is expected to screen the
interactions of about 20 proteins a year.
Emory scientists now have two chances
to submit a protein for high-throughput screening—either
through Emory’s own drug discovery center or through the
national MLSCN. In some cases, proteins are being screened against
the compound libraries in both centers. |
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Protein
power |
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High-throughput
screening (HTS) technology is one way for scientists to capitalize
on the human genome project and venture into the realm of proteomics,
or the study of proteins that genes produce. Scientists originally
believed that each gene within the DNA sequence corresponded only
to one human protein. Now, however, they recognize that the 25,000
or 30,000 genes in our DNA may encode five to 10 times that many
proteins.
Because proteins play a part in
everything that happens inside living cells, they are the object
of intense study by scientists seeking to understand disease processes.
Drug compounds are aimed at either inhibiting or enhancing the
actions of proteins that are related to disease.
For example, Fu identified a tiny
fragment that serves as the “mouth” of his 14-3-3
protein and enables the cell-to-cell communication that triggers
cancer oncogenes. He designed an assay to connect the protein
fragment to a fluorophore, a chemical marker that lights up when
the protein binds to a molecule. Fu was the first Emory scientist
to use the new screening equipment to test his protein against
the entire library of 100,000 molecular compounds in Emory’s
drug discovery center, and his protein also was selected for testing
by the MLSCN network. He has identified several promising compounds
that may be inhibitors to his target protein.
In conventional laboratory experiments,
a researcher pipettes solutions from one test tube to another
and writes down in a notebook what was done and why.
The new robotics equipment automatically
pipettes liquids containing both a target protein and one of the
100,000 compounds into a tall stack of rectangular, 3x5-inch plastic
“plates” containing 384 tiny holes or “wells.”
A computerized plate reader analyzes the miniature chemical reactions
that occur when the compounds are combined with their targets
in the wells. An assay this small must elicit a simple on or off
reaction—either the compound has the desired effect or it
doesn’t. A program lists each of the compounds that reacted
with the protein target. These compounds can then be cherry picked
from the library for further study. It takes about one to two
weeks to screen the protein interactions with a library of 100,000
compounds using HTS equipment. |
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Using
the cherry-picked compounds from the initial screenings, scientists
like Fu then go back to their laboratories to perform a more “old-fashioned”
biological experiment that sorts out the false-positive hit compounds.
The end result can be up to 20 promising compounds. They then
relay these compounds to the chemistry department, where a bioinformatics
and modeling group directed by Jim Snyder combines its knowledge
of chemical compounds with specialized computer software to analyze
the detailed molecular structures of all the hit compounds. A
model of molecular activity called the QSAR, for quantitative
structure activity relationship, helps predict which structural
modifications of the compounds will be more active against a target.
This analysis is the first step in the “hit-to-lead”
process that puts a compound on the drug-candidate pathway.
Medicinal chemists use this information
as a guide to remodel the structures of the validated hits by
laboratory synthesis to improve the biological profiles. Fu’s
lead compounds, for example, are now being optimized by a chemistry
team led by Dennis Liotta. The gold standard is a compound that
exerts a strong and selective effect on a target protein at a
very low concentration. This means it is less likely to be toxic
than a less selective, less potent compound would be. Desirable
drug-like properties also include high solubility in water. “A
drug with zero solubility would be like ingesting a small rock,”
says Liotta.
Now the modeling group and the synthesis
group are developing their own small library of compounds. These
might include modified compounds from the screening-modeling-synthesis
process. Or they might be structurally similar compounds identified
by the researchers that are available for purchase but not yet
part of Emory’s library.
“This kind of work would be
almost impossible without our screening center,” says Fu.
“There is a huge difference between academia and industry
in screening target proteins. We design the screening assays in
our own laboratories, whereas many pharmaceutical companies often
purchase ready-made assays. Academic scientists know these targets
inside out because we’ve been studying them for years. Emory’s
screening centers, combined with the ability of our expert chemists
to modify compounds, can serve as the glue to enhance the interaction
between basic and clinical science and to promote the translation
of basic science to the bedside.”
“We are not competing with
pharmaceutical companies, although some of our findings may well
be useful to them on down the road,” Dingledine says. “We
intentionally are not looking for the next blockbuster antidepressant
or antireflux drug. That’s not our ball game. We are trying
to identify targets that are not being pursued by major pharmaceutical
companies yet might have real research value or clinical impact.
Academic medical laboratories like ours have a Zen-like focus
on understanding the properties of proteins.” |
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Why
Emory got the grant |
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Emory’s
history in successful AIDS drug discovery and its track record
of collaboration between the medical school and the college’s
chemistry department gave it a leg up in the selection process
for the new NIH screening centers.
“When we went up against some
of the biggest-name universities in the country, we were very
competitive,” says Liotta. “This was because we had
ongoing collaborations between chemistry and the School of Medicine
that we could point to as real examples of our expertise and our
desire to move in that direction. It wasn’t a forced interaction––it
is what we’ve done for years.
“Drug discovery is an intimate
partnership between biologists and chemists,” Liotta continues.
“In most places, there is little or no interaction between
those two groups, which means that each group is by definition
limited in terms of the kinds of questions they can ask and the
kinds of answers they can get. Emory’s screening center
allows for a smooth interface between these two critical groups
that enables us to ask and answer the bigger questions. We hope
this will make Emory more competitive for external funding and
may lead to alternative revenue sources such as drug royalties.
Overall, it’s an opportunity for us to pool our complementary
skill sets and do important work. We hope this also will enable
us to recruit the best people, because this extra opportunity
is something they don’t have at other research institutions.”
Former Emory faculty member Jeffrey
Conn, now professor and director of Translational Neuropharmacology
at Vanderbilt, heads another of the newly designated NIH Molecular
Libraries Screening Centers. “Emory is in an excellent position
to play a major leadership role in what may be the early stages
of a major shift in biomedical research,” said Conn. “Because
of its culture of strong collaborations between clinical and basic
scientists, I see a translational mindset of scientists across
Emory. The Department of Pharmacology has an uncommon combination
of strength in classical pharmacology, and the chemistry department
is world-class—in fact one of the rare chemistry departments
with an established track record in discovery of marketed drugs.”
Carson Loomis, program director
of the NIH Molecular Screening Libraries Division of Extramural
Research at the National Human Genome Research Institute, says
Dingledine’s leadership in assay-development and high-throughput
screening helped Emory capture the molecular libraries designation.
“The award was based on the quality of his scientific staff,
his development plan, and the proven record of scientific success
at Emory,” he says. |
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Cooperation
versus competition |
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The MLSCN has a really nice feature that’s different from
any other NIH award with which I have been involved,” says
chemistry’s Jim Snyder. “There are ten centers around
the country, one of which is at the NIH, and this network is meant
to be collaborative. We all get on the phone once a month and
share information. We try to lower the cost of software and pool
ideas about how we can more efficiently do the tasks of molecular
screening.”
Emory will continue screening proteins
identified by its own faculty members in the Emory Chemical-Biology
Discovery Center at the same time it screens the NIH-identified
proteins. A great deal of the equipment and personnel in the two
centers will overlap. Intellectual property issues have required
complex negotiations between the NIH and Emory’s Office
of Technology Transfer. The NIH wants all results of the MLSCN
to be transferred quickly into the publicly accessible PubChem
database. After much debate, however, it agreed to allow the screening
centers and investigators a short time to file patent applications
on their discoveries. Compounds not immediately patented will
go into PubChem. Many Emory scientists feel strongly that protecting
intellectual property is critical for the future of therapeutic
development and for the ultimate good of patients.
“If the targets are important
and if we discover novel modulators of those targets, then it’s
our responsibility to file patent applications on them,”
says Liotta. “If we don’t, and they get into the public
domain, no one will ever develop them commercially. It would be
terrible if we found something that was potentially an important
therapy but no one would spend the money to develop it because
we didn’t patent it. That’s when the public loses.
It’s not about money; it’s about getting these discoveries
into the marketplace for the benefit of patients.”
“This screening center is
going to have a huge impact on tech transfer for a number of reasons,”
says Todd Sherer, director of technology transfer at Emory. “Venture
capitalists and large pharmaceutical companies are not as interested
in commercializing early-stage technologies and target proteins
as they were five years ago because of changes in patent laws.
That means we have to find ways to move target technology further
down the innovation pathway and create better investment opportunities.
“This screening center will
help us cross the ‘valley of death’ that stands between
many laboratory research discoveries and getting drugs into the
marketplace. This ability to create more compelling intellectual
property technology is a crucial part of our ability to be successful
in the future.” |
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A
winning combination |
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Two
of the first three proteins selected by the NIH MLSCN for screening
at Emory included Fu’s 14-3-3 protein and a protein called
BAP-1, identified in 1998 by Emory biochemists Keith Wilkinson
and Frank Rauscher. BAP-1 interacts with the BRCA1 protein, which
is a product of a breast cancer suppressor gene that when mutated
promotes the growth of breast cancer. Wilkinson and Rauscher hope
they may be able to slow the growth of breast tumor cells by finding
a compound to inhibit this protein. After first screening the
BAP-1 protein in Emory’s library of compounds, they now
are screening it through the MLSCN library.
“Before these centers existed,
we would have been reduced to trying to talk a drug company into
doing this kind of screening,” says Wilkinson. “That
is difficult if you can’t point to the disease and to the
nature of a drug that might develop from such a screening. Pharmaceutical
companies are not in the business of generating reagents for curious
biologists.”
Scientists from throughout the School
of Medicine are beginning to use the Emory Chemical-Biology Center
to advance their research. Neurologist Jonathan Glass is looking
for compounds that might inhibit a protein that causes toxic nerve
reactions to the anti-cancer drug taxol. Microbiologists Richard
Plemper and Richard Compans, along with Jim Snyder and Dennis
Liotta, are trying to develop an antiviral drug for measles. In
the first round of high-throughput screening based on a cell fusion
assay, they identified more active and promising compounds than
they had identified in the past two years working with conventional
chemical synthesis. Biochemist David Lambeth is studying a target
protein related to the inflammation involved in cardiovascular
disease and cancer. Stem cell expert Marie Csete and Dingledine
are planning to look for compounds that would reduce the ability
of cultured stem cells to differentiate in the laboratory or direct
them to differentiate into specific types of cells.
“Emory recognized the opportunity
for this kind of high-throughput molecular screening earlier than
most academic institutions and was fortunate to receive the support
to move forward,” Dingledine says. “Others are now
recognizing the advantages of combining chemistry and biology
and pharmacology. The national network will move us in exciting
new directions, with expertise and interests that by design are
complementary rather than competing. No individual center could
do all this on its own, but together we can accomplish a great
deal.” |
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