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Imagine
a technology
that can test
thousands
of properties
of cells for faster discovery of better drugs
...
a n d i t ’s a v a i l a b l e n o w
There is a p r o b l e m
in drug
discovery: The economics and efficiency of the drug development process are more
important now than ever before, while at the same time that process is undergoing radical
change. With the advent of gene sequencing, gene expression analysis, and combinatorial
chemistry, a new problem has arisen.
Now there are too many unqualified targets and
leads. A critical need has developed for technologies that allow researchers to quickly,
efficiently, and accurately characterize and sort through these targets and leads.
Ta r ge t Va l i d a t i o n
is a key step in the drug discovery process.
Advances
in genomics have created an intensely competitive environment in which thousands of
genes are being mapped, proposed as important new targets, and patented. Selecting the
best target genes is difficult because the function of most of these genes is unknown.
Functional Genomics
technologies will provide the means to gain
understanding of the function of these important genes.
With such information
one can greatly speed up the selection or elimination of a particular gene as a drug target.
Therefore, rapid access to gene function information provides a competitive advantage in
t a rg e t v a l i d a t i o n .
It is also essential in gaining a strong patent position.
L e a d Va l i d a t i o n
follows the process of target validation. Companies now
have ready access to large chemical libraries either from natural product sources or from
With high-throughput robotic assays they can test these
libraries against their target gene/protein of interest. But these technologies provide only
part of the picture – major hurdles remain. Knowing that a chemical is active against its
target is the first of many steps. The ability to rapidly gain information on the specificity
of these drug leads is also of great value.
Technology that provides insight at the
cellular level about the interaction of a lead candidate with the thousands of other
cellular proteins, would offer significant benefits. Optimal drug candidates will have
specific effects on the target without causing undesired side effects.
NOW
t h e r e
i s
a
s o l u t i o n
combinatorial synthesis.
PHENOTYPE MICROARRAYS™
information at the cellular
sets of arrays. Each well of the
A MAJOR NEW TECHNOLOGY
level ... and much more.
array is designed to test a
P
different phenotype.
henotype MicroArrays
Phenotype MicroArrays are
(PMs) represent a breakthrough
comprehensive cellular profiles
Cells are tested after a genetic
in technology, alongside DNA
that can be used to identify
change or exposure to a drug
Microarrays and Proteomic
Technologies (Figure 1), to
complete the information
RNA
DNA
PROTEIN
PHENOTYPE
O’Farrel, 1975
Biolog, 2000
needed in the genomic era of
drug development.
Affymetrix, 1993
Just as DNA Microarrays and
Proteomic Technologies have
made it possible to assay the
expression level of thousands
Molecular Analyses
of genes or proteins all at once,
Phenotype MicroArrays make
Cellular Analysis
Figure 1
it possible to measure,
quantitatively, thousands of
gene function, validate targets,
lead, and the researcher can
cellular phenotypes all at once.
and assist lead validation and
directly evaluate cellular
optimization.
response to that change. The
DNA Microarrays and
scientist simply inoculates a
Proteomic Technologies allow
HOW THE TECHNOLOGY
standardized cell suspension
scientists to detect genes or
WORKS
into the MicroArray panels,
proteins that are coregulated
Phenotype MicroArray
thereby testing thousands of
and whose patterns of change
technology is an integrated
phenotypes at once. The
correlate with something
system of cellular assays,
MicroArray is then incubated,
important such as a disease
instrumentation, and
typically for 24 to 48 hours.
state. However, there is no
bioinformatic software. The
assurance that these changes
testing process is diagrammed
PMs use Biolog’s patented
are really significant to the cell.
in Figure 2.
redox chemistry, employing
Phenotype MicroArrays are a
cell respiration as a universal
complementary technology
Biolog preconfigures a wide
reporter. If the phenotype is
providing the needed
range of phenotypic tests into
strongly “positive” in a well,
Add
Cells
Add
Cells
a. PM Pattern
b. OmniLog PM System
c. PM Kinetic Result
d. Comparison
Figure 2
the cells respire actively,
phenotypes are monitored
reducing a tetrazolium dye and
simultaneously by the
forming a strong color (Figure
OmniLog and more than
2a). If it is weakly positive or
450,000 data points can be
nitrogen, phosphorus,
negative, respiration is slowed
generated in one 24-hour run.
and sulfur
or stopped, and less color or no
• cell surface binding and
transport functions
• catabolism of carbon,
• biosynthesis of small
color is formed. The redox
To compare the phenotypes of
assay provides for both
two cell lines, one is recorded
amplification and precise
as a red tracing and one as a
quantitation of phenotypes.
green tracing (Figure 2c).
These graphs can then be
molecules
• biosynthesis of polymeric
macromolecules
• formation of cellular
structures
Incubation and recording of
overlaid by the bioinformatics
• cellular respiratory functions
phenotypic data is performed
software to detect differences.
• stress and repair functions
by the patented OmniLog PM
Areas of overlap (i.e., no
• other cellular properties
instrument (Figure 2b). The
change) are colored yellow,
Currently, PMs are available
OmniLog captures a digital
whereas differences are
for use with bacterial and fun-
image of the MicroArray color
highlighted as patches of red or
gal cells. They are being devel-
change several times each hour,
green (Figure 2d).
oped also for mammalian cells.
values into computer files. The
Phenotype MicroArrays can
TARGET VALIDATION:
computer files can be displayed
monitor, either directly
Determining Gene Function
to the scientist in the form of
or indirectly, most aspects of
In many cases, researchers have
kinetic graphs. Thousands of
cell function. The range of
already determined genes they
™
and stores the quantitative
phenotypes includes:
believe may be good drug
TARGET IDENTIFICATION:
LEAD VALIDATION:
targets. As diagrammed in
Establishing New Drug Targets
Assaying Drug Candidates
Figure 2, a direct cell-to-cell
PMs have many other uses in
PM technology provides a
comparison can be made
cellular studies for
revolutionary new tool for
between a normal cell and a
characterizing and defining
evaluating drug leads. In this
cell with the gene of interest
phenotypic properties of cells.
application, testing is again
inactivated by a genetic
mutation (i.e., knocked out).
performed in a comparative
For example, PM cell line-to-
mode. A model cell line is
cell line comparisons can be
tested without drug exposure
Genetic changes result in
performed to identify new drug
(as a control) and then tested
phenotypic changes. Any gene
targets. Researchers may want
against a collection of drug
of unknown function can be
to find phenotypes that can be
leads of interest. The testing
procedure is the same, except
arginine
that the drug leads are added to
the cell suspension just before
ornithine
the cells are distributed into the
MicroArray wells (Figure 4a).
Here again, the OmniLog
instrument (Figure 4b)
MG1655
ynjB::Tn10
monitors, records and compares
the assays automatically.
Figure 3
The PM pattern that forms in
knocked out and the knockout
targeted by drugs toxic to:
the absence of drug is different
cells can be assayed for
• pathogenic bacteria, but not
than patterns formed with
phenotypic changes. An
their non-pathogenic relatives
various drugs added. From this
example is shown in Figure 3
• bacteria and fungi that infect
comprehensive cellular assay,
comparing the nitrogen
plants and animals, but not
data from the MicroArrays is
metabolism of a normal E. coli
the plant and animal hosts
analyzed by pattern recognition
strain and a mutant that has lost
• cancerous cells, but not their
and clustering software (Figure
function of a pathway for
non-cancerous precursors
metabolizing arginine and
• virus-infected cells, but not
ornithine as nitrogen sources.
PMs provide a direct cellular
assay of gene function.
uninfected cells
• diseased cells but not their
non-diseased neighbors
4c) to sort drugs based on
mode of action.
Add
Cells
Add
Cells
+Drug
a. PM Pattern
b. OmniLog PM System
c. Bioinformatics Analysis
Figure 4
PM technology allows
drug on non-target sites.
mammalian cell PM assays, it
researchers to analyze chemical
These effects can be critically
will be possible to assay drug
libraries in a rapid, high-
important if they result in
candidates against a battery of
throughput method with several
unacceptable side effects.
cell lines that represent the
major organs and tissues of the
unique and significant
Third, one can use PMs
body. This will permit rapid
containing other drugs as part
and cost effective screening to
First, it measures the effect of
of the overall phenotypic
help eliminate unsatisfactory
drugs on cells under thousands
analysis. This aspect of PM
drug candidates earlier in
of physiological states. When
technology allows you to test
development.
the cell changes its
the drug candidate’s interaction
physiological state it also
with other drugs. Normally,
The PM approach to assaying
changes its surface receptors
this would be done inefficiently
drug leads is unique and
and internal protein make-up,
as a separate study. Discovering
powerful. It provides a highly
in a sense becoming a different
an unexpected synergy or
efficient means to assay the
cell. Current assay technologies
antagonism with a known drug
effect of a drug on thousands of
using cells grown under one
early on can change the entire
cellular targets under thousands
condition give a very limited,
course of drug development.
of physiological states of
advantages.
the cell.
incomplete view of the range of
biological possibilities.
Soon, PM technology will also
be used as a basis for detailed
Second, PM technology allows
scientists to see the effect of a
toxicological studies. With
Benefits in Drug Discovery
Phenotype MicroArrays:
Complement DNA microarrays. DNA microarrays allow scientists
to measure the expression of thousands of genes of a cell under one
growth condition, whereas Phenotype MicroArrays allow scientists
to measure the effect of one gene in the cell under thousands of
growth conditions.
Provide rapid answers to critical questions about cellular properties
in a simple, rapid, efficient, and cost-effective process.
Provide rapid answers to how a gene of unknown function affects a
cell at a physiological level.
Provide cell-to-cell comparisons to find novel drug targets based on
in vivo physiological differences.
Provide
a means to assay the effect of a drug on thousands of
cellular targets under thousands of physiological states of the cell.
Provide rapid answers to questions about how a new lead affects a
cell at a biochemical level.
Provide information on how new drug leads compare to and interact
with existing drugs.
Reduce the time and cost of slow and cumbersome animal, plant, or
human studies in late development.
Eliminate unproductive leads and projects, saving substantial R&D
budget dollars that would be wasted in later development.
3938 Trust Way Hayward, CA 94545 Telephone: 510-785-2564 Fax: 510-782-4639 www.biolog.com
04/01