|New Paradigm Will Help Identify Leads for Drug Discovery
NIH Roadmap Initiative Develops More Precise Method for Rapidly Screening Chemical
A new screening approach can profile compounds in large chemical libraries
more accurately and precisely than standard methods, speeding the production
of data that can be used to probe biological activities and identify leads for
drug discovery, the National Institutes of Health (NIH) Chemical Genomics Center,
part of the NIH Roadmap for Medical Research’s Molecular Libraries and Imaging
Initiative, reported today.
“We are excited by the power of this approach, developed through the NIH Roadmap
for Medical Research, to generate new chemical ‘tools’ for biological exploration.
These tools will help researchers in both the public and private sectors unlock
the mysteries of gene function and signaling pathways throughout the human body,
opening the door to the development of new drugs,” said NIH Director Elias A.
In a paper published online in the Proceedings of the National Academy of
a team from the NIH Chemical Genomics Center demonstrates the feasibility of
a new paradigm for profiling every compound in chemical libraries, which are
large collections of chemicals. Traditional high-throughput screening measures
the biological activity of chemical compounds at just one concentration. In contrast,
the new approach, called quantitative high-throughput screening, or qHTS, tests
the biological activity of chemical compounds at seven or more concentration
levels spanning four orders of magnitude. The multi-concentration screen produces
a pharmacological characterization of all the compounds that is far more complete
and reliable than traditional methods.
“This advance is crucial to NIH’s goal of efficiently profiling the range of
biological activities associated with large chemical libraries and making that
data swiftly available to the worldwide research community,” said Francis S.
Collins, M.D., Ph.D., director of the National Human Genome Research Institute
(NHGRI). “Broad adoption of this paradigm should provide robust databases of
chemical activity information that will be suitable for accelerating the early
phase of the drug discovery process.”
The NIH Chemical Genomics Center, which is based in NHGRI’s Division of Intramural
Research, is part of an NIH-supported nationwide research consortium of 10 groups,
called the Molecular Libraries Screening Centers Network. The network has established
a collection of 100,000 chemicals from a class of compounds known as small molecules.
Such chemicals can serve as valuable probes in molecular, cellular and whole
organism studies of biological functions. Furthermore, most medications used
today are small molecules, and this class of chemicals is likely to offer attractive
targets for future drug development.
Christopher P. Austin, M.D., the center’s director and senior author of the
study, explained what motivated his team to develop the new approach. “Traditional
high-throughput screening frequently produces false positives and false negatives,
and requires extensive follow-up testing. Furthermore, traditional methods often
fail to detect compounds that exhibit partial activity or low efficacy, even
though such compounds may represent important modulators of biological activity,” Dr.
Austin said. “To achieve our aim of speeding the discovery of biological probes
and drug targets, we needed a method that offered far greater precision coupled
with the capacity to identify chemicals with a wide spectrum of biological activities.”
In their study published in PNAS, researchers from the NIH Chemical Genomics
Center used quantitative high-throughput screening to test the activity of varying
concentrations of more than 60,000 chemical compounds against pyruvate kinase,
a well-characterized enzyme involved in energy metabolism that is deficient in
a form of anemia and also implicated in cancer. The compounds were classified
as either activators or inhibitors of the enzyme, with the degree of potency
and efficiency associated with the various concentrations of each compound being
noted in extensive detail.
Of particular importance, the team was able to take advantage of the new approach
to elucidate relationships between the biological activity of a compound and
its chemical structure directly from the initial screen — a feat not possible
with the traditional method. “This new approach produces rich datasets that can
be immediately mined for reliable relationships between chemical structure and
biological activities. This represents a very significant savings of time and
resources compared with current iterative screening methods,” said the study’s
lead author James Inglese, Ph.D.
For most of scientific history, researchers discovered new chemical compounds
with medicinal qualities through a labor-intensive, time-consuming process that
involved manually testing the compounds on tissue samples or laboratory animals.
About 15 years ago, researchers in the pharmaceutical industry developed high-throughput
screening systems that tested large numbers of compounds on engineered cell lines
and proteins. Still, due to technical demands and limitations, such screening
generally has remained focused on a single concentration of each compound.
To address the limitations of traditional high-throughput screening, the NIH
Chemical Genomics Center set about developing a titration-based screening approach
that combines a variety of advanced technologies, including microfluidics, low-volume
dispensing, high-sensitivity detectors and robotic plate handling. In an experiment
designed to test the feasibility, accuracy and efficiency of the new approach,
the NIH researchers used sophisticated robotic systems to prepare 60,793 chemical
compounds at seven or more concentrations across 368 plates, each containing
1,536 microwells. Over the next 30 hours in an automated format, the plated compounds
were exposed to pyruvate kinase, and their biological activities were carefully
When the NIH research team compared their quantitative high-throughput screening
results with those generated by screening the same chemical compounds with traditional,
single-concentration methods, they found the new approach produced a much lower
prevalence of false negatives. “Upwards of half of the compounds identified as
active using the new approach were missed by the traditional screening method,” said
Doug Auld, Ph.D., co-author of the study and a group leader at the NIH Chemical
Genomics Center. “This tells us that quantitative high-throughput screening is
much more sensitive in uncovering chemicals with the potential to be used as
biological probes or leads for drug development.”
The researchers emphasized that miniaturization is essential to the efficiency
and cost-effectiveness of their new approach. They noted that their miniaturized,
seven-point concentration screen consumed less chemicals, used the same amount
of enzyme and required only 1.75-times the number of plates as a traditional
single-point concentration screen. Furthermore, the additional plate handling
was offset by the elimination of the need to “cherry pick” and re-test compounds
in separate experiments, which conserved time and chemical compounds.
In addition to its potential for identifying new biological probes and drug
targets, the NIH Chemical Genomics Center will be using the new paradigm as a
platform for its contributions to PubChem, the Molecular Libraries Roadmap’s
publicly available database of chemical compounds of relevance to genomic research.
For more information on PubChem, go to http://pubchem.ncbi.nlm.nih.gov/.
For more information about the NIH Chemical Genomics Center, go to http://www.ncgc.nih.gov/.
For more information on the Molecular Libraries Small Molecule Repository, go
to http://mlsmr.discoverypartners.com/MLSMR_HomePage/. To download photos of
the robotic system used in quantitative high-throughput screening, go to http://www.genome.gov/pressDisplay.cfm?photoID=79 and http://www.genome.gov/pressDisplay.cfm?photoID=10003.
The Molecular Libraries Screening Centers Network is guided by the National
Human Genome Research Institute and the National Institute for Mental Health.
For more information about this nationwide consortium and other components of
the Molecular Libraries and Imaging Initiative, go to http://nihroadmap.nih.gov/molecularlibraries/.
NHGRI is one of the 27 institutes and centers at NIH. The NHGRI Division
of Intramural Research develops and implements technology to understand, diagnose
and treat genomic and genetic diseases. Additional information about NHGRI
can be found at www.genome.gov.
The NIH Roadmap is a series of far-reaching initiatives designed to transform
the nation’s medical research capabilities and speed the movement of research
discoveries from the bench to the bedside. It provides a framework for the
priorities the NIH must address in order to optimize its entire research portfolio
and lays out a vision for a more efficient and productive system of medical
research. Additional information about the NIH Roadmap can be found at http://www.nihroadmap.nih.gov/.
The National Institutes of Health (NIH) — The Nation's Medical Research
Agency — includes 27 Institutes and Centers and is a component of
the U.S. Department of Health and Human Services. It is the primary federal
agency for conducting and supporting basic, clinical and translational medical
research, and it investigates the causes, treatments, and cures for both common
and rare diseases. For more information about NIH and its programs, visit www.nih.gov.