Combinatorial
Chemistry & High Throughput Screening
ISSN: 1386-2073
Combinatorial Chemistry &
High Throughput Screening
Volume 11, Number 3, March 2008
Contents
“Spirit” of High Throughput Screening
Guest Editors: Holger Wesche, Shou-Hua (Josh) Xiao and
Steve Young
Editorial Pp.174
Discovery of Novel Targets with High Throughput RNA Interference
Screening Pp. 175-184
Paul D. Kassner
[Abstract]
Impact of Novel Screening Technologies on Ion Channel
Drug Discovery Pp. 185-194
Qiang Lü and W. Frank An
[Abstract]
High Throughput Screening for Orphan and Liganded
GPCRs Pp. 195-215
Shou-Hua Xiao, Jeff D. Reagan, Paul H. Lee, Angela Fu,
Ralf Schwandner,Xiaoning Zhao, Johannes Knop, Holger Beckmann
and Stephen W. Young
[Abstract]
High-Content Analysis in Preclinical
Drug Discovery Pp. 216-230
Philip Denner, Janine Schmalowsky and Stefan Prechtl
[Abstract]
Back to Basics: Label-Free Technologies for Small
Molecule Screening Pp. 231-237
Andrew K. Shiau, Mark E. Massari and Can C. Ozbal
[Abstract]
High Throughput Screening for Neurodegeneration
and Complex Disease Phenotypes Pp. 238-248
Hemant Varma, Donald C. Lo and Brent R. Stockwell
[Abstract]
High Throughput Screening Informatics Pp.
249-257
Xuefeng Bruce Ling
[Abstract]
Recent Advances in High Throughput Screening
for ADME Properties Pp. 258-264
Timothy J. Carlson and Michael B. Fisher
[Abstract]
Meet
the Guest Editors Pp. 265
Abstracts
[Back to top]
Editorial
The last two decades have seen the rapid and extensive
adoption of an increasingly diverse portfolio of automated
high throughput technologies by the pharmaceutical and biotechnology
industries. Such approaches are now established as a ubiquitous
and integral component of modern drug discovery.
From the inception of high throughput screening up until the
early 90s’, such techniques were predominantly applied
to facilitate rapid high volume evaluation of low molecular
weight chemical libraries. These early screening campaigns
were performed primarily by the pharmaceutical industry with
the goal of identifying small molecule modulators for novel
drug targets.Today the preponderance of chemical drug leads
are derived from high throughput screening, the success of
which has resulted in over a hundred candidates in clinical
trials or approved for marketing.
At the beginning of the new millennium, sequencing of the
human genome marked the beginning of what has popularly been
termed the “genomic revolution”. High throughput
technologies were enthusiastically adopted by biotechnology
companies and applied to many aspects of modern biomedical
research enabling systematic research endeavors on a scale
not previously possible. Notable examples include expansive
campaigns to sequence genomes or ESTs, automated gene expression
profiling programs and protein/protein interaction mapping
projects etc. This new target discovery paradigm generated
many potential drug targets, which in turn needed to be screened
against compound libraries to identify new drug candidates.
In consequence, the demand for more, better,faster, more flexible
and cost-effective technologies grew and was eagerly addressed
by an ever growing field of equipment manufacturers and service
companies. These new machines increasingly opened the world
of high throughput research to ever more scientists across
a broadening and increasingly diverse catalogue of disciplines.
Consequently, high throughput approaches are no longer limited
to industry, as they largely were in the early days; many
academic institutions have established screening and technology
centers. In addition, the application of high throughput techniques
has expanded far beyond pharmaceutical and genomics laboratories
and is revolutionizing all aspects of biology and drug discovery.
Inevitably, new opportunities have brought new challenges.
In particular, the enormous quantity of data now being routinely
generated has driven the rapid development of new data capture,
analysis and storage capabilities. This has been, and remains,
critical in overcoming persistent limitations in the timely
and effective utilization of the new data.
This special issue of Combinatorial Chemistry & High
Throughput Screening was conceived with the objective
of bringing together leading scientists from diverse fields
to give a broad overview of the impact of modern high throughput
approaches on the whole process of drug discovery from target
identification to lead identification and lead optimization.
Holger Wesche, Shou-Hua (Josh) Xiao and Steve Young
Amgen Inc.
120 Veterans Blvd.
South San Francisco
CA 94080
USA
E-mail: hwesche@amgen.com
[Back to top]
Discovery of Novel Targets with High Throughput
RNA Interference Screening
Paul D. Kassne
High throughput technologies have the potential to affect
all aspects of drug discovery. Considerable attention is paid
to high throughput screening (HTS) for small molecule lead
compounds. The identification of the targets that enter those
HTS campaigns had been driven by basic research until the
advent of genomics level data acquisition such as sequencing
and gene expression microarrays. Large-scale profiling approaches
(e.g., microarrays, protein analysis by mass spectrometry,
and metabolite profiling) can yield vast quantities of data
and important information. However, these approaches usually
require painstaking in silico analysis and low-throughputbasic
wet-lab research to identify the function of a gene and validate
the gene product as a potential therapeutic drug target.Functional
genomic screening offers the promise of direct identification
of genes involved in phenotypes of interest. In this review,
RNA interference (RNAi) mediated loss-of-functionscreens will
be discussed and as well as their utility in target identification.
Some of the genes identified in these screens should produce
similar phenotypes if their gene products are antagonized
with drugs. With a carefully chosen phenotype, an understanding
of the biology of RNAi and appreciation of the limitations
of RNAi screening, there is great potential for the discovery
of new drug targets.
[Back to top]
Impact of Novel Screening Technologies on Ion Channel
Drug Discovery
Qiang Lü and W. Frank An
Ion channels are a large superfamily of membrane
proteins that pass ions across membranes. They are critical
to diverse physiological functions in both excitable and nonexcitable
cells and underlie many diseases. As a result, they are an
importanttarget class which is proven to be highly “druggable”.
However,for high throughput screening (HTS), ion channels
are historically difficult as a target class due to their
unique molecular properties and the limitations of assay technologies
that are HTS-amendable. In this article, we describe the background
of ion channels and current status and challenges for ion
channel drug discovery, followed by an overview of both conventional
and newly emerged ion channel screening technologies. The
critical impact of such new technologies on current and future
ion channel drug discovery is also discussed.
[Back to top]
High Throughput Screening for Orphan and Liganded
GPCRs
Shou-Hua Xiao, Jeff D. Reagan, Paul H. Lee, Angela Fu,
Ralf Schwandner,Xiaoning Zhao, Johannes Knop, Holger Beckmann
and Stephen W. Young
GPCRs had significant representation in the drug
discovery portfolios of most major commercial drug discovery
organizations for many years. This is due in part to the diverse
biological roles mediated by GPCRs as a class, as well as
the empirical discovery that they have proven relatively tractable
to the development of small molecule therapeutics. Publication
of the human genome sequence in 2001 confirmed GPCRs as the
largest single gene superfamily with more than 700 members,furthering
the already strong appeal of addressing this target class
using efficient and highly parallelized platform approaches.
The GPCR research platform implemented at Amgen is used as
a case study to review the evolution and implementation of
available assays and technologies applicable to GPCR drug
discovery. The strengths, weaknesses, and applications of
assay technologies applicable to Gα
s, Gα
i and Gα
q-coupled receptors are described and their relative
meritsev aluated. Particular consideration is made of the
role and practice of “de-orphaning” and signaling
pathway characterization as a prerequisite to establishing
effective screens. In silico and in vitro
methodology developed for rapid,parallel high throughput hit
characterization and prioritization is also discussed extensively.
[Back to top]
High-Content Analysis in Preclinical Drug Discovery
Philip Denner, Janine Schmalowsky and Stefan Prechtl
High-Content Analysis (HCA) has developed into an
established tool and is used in a wide range of academic laboratories
and pharmaceutical research groups. HCA is now routinely proving
to be effective in providing functionally relevant results.
It is essential to select the appropriate HCA application
with regard to the targeted compound’s cellular function.
The cellular impact and compound specificity as revealed by
HCA analysis facilitates reaching definitive conclusions at
an early stage in the drug discovery process. This technology
therefore has the potential to substantially improve the efficiency
of pharmaceutical research. Recent advances in fluorescent
probes have significantly boosted the success of HCA. Autofluorescent
proteins which minimally hinder the functioning of the living
cell have been playing a decisive role in cell biology research.
For companies the severely restricted license conditions regarding
auto-fluorescent proteins hamper their general use in pharmaceutical
research. This has opened the field for other solutions such
as self-labeling protein technology,which could potentially
replace the well established methods that utilize auto-fluorescent
proteins. In addition, direct labeling techniques have improved
considerably and may supersede many of the approaches based
on fusion proteins. Following sample preparation, treated
cells are imaged and the resulting multiple fluorescent signals
are subjected to contextual and statistical analysis. The
extraordinary advantage of HCA is that it enables the large-scale
and simultaneous quantification and correlation of multiple
phenotypic responses and physiological reactions using sophisticated
software solutions that permit assay-specific image analysis.
Hence, HCA once more has demonstrated its outstanding potential
to significantly support establishing effective pharmaceutical
research processes in order to both advance research projects
and cut costs.
[Back to top]
Back to Basics: Label-Free Technologies for Small
Molecule Screening
Andrew K. Shiau, Mark E. Massari and Can C. Ozbal
Small molecule high-throughput screening in drug discovery
today is dominated by techniques which are dependent upon
artificial labels or reporter systems. While effective, these
approaches can be affected by certain experimental limitations,
such as conformational restrictions imposed by the selected
label or compound fluorescence/quenching. Label-free approaches
potentially address many of these issues by allowing researchers
to investigate more native systems without fluorescence or
luminescence-based readouts. However, due to throughput and
expense constraints, label-free methods have been largely
relegated to a supporting role as the basis of secondary assays.
In this review, we describe recent improvements in impedance-based,
optical biosensor-based,automated patch clamp and mass spectrometry
technologies that have enhanced their ease of use and throughput
and,hence, their utility for primary screening of small- to
mediumsized compound libraries. The ultimate maturation of
these techniques will enable drug discovery researchers to
screen large chemical libraries against minimally manipulated
biological systems.
[Back to top]
High Throughput Screening for Neurodegeneration and
Complex Disease Phenotypes
Hemant Varma, Donald C. Lo and Brent R. Stockwell
High throughput screening (HTS) for complex diseases
is challenging. This stems from the fact that complex phenotypes
are difficult to adapt to rapid, high throughput assays. We
describe the recent development of high throughput and highcontent
screens (HCS) for neurodegenerative diseases, with a focus
on inherited neurodegenerative disorders, such as Huntington’s
disease. We describe, among others, HTS assays based on protein
aggregation, neuronal death, caspase activation and mutant
protein clearance. Furthermore, we describe high-content screens
that are being used to prioritize hits identified in such
HTS assays. These assays and screening approaches should accelerate
drug discovery for neurodegenerative disorders and guide the
development of screening approaches for other complex disease
phenotypes.
[Back to top]
High Throughput Screening Informatics
Xuefeng Bruce Ling
High throughput screening (HTS), an industrial effort
to leverage developments in the areas of modern robotics,
data analysis and control software, liquid handling devices,
and sensitive detectors, has played a pivotal role in the
drug discovery process, allowing researchers to efficiently
screen millions of compounds to identify tractable small molecule
modulators of a given biological process or disease state
and advance them into high quality leads. As HTS throughput
has significantly increased the volume, complexity, and information
content of datasets, lead discovery research demands a clear
corporate strategy for scientific computing and subsequent
establishment of robust enterprise-wide (usually global)informatics
platforms, which enable complicated HTS work flows,facilitate
HTS data mining, and drive effective decision-making.The purpose
of this review is, from the data analysis and handling perspective,
to examine key elements in HTS operations and some essential
data-related activities supporting or interfacing the screening
process, and outline properties that various enabling software
should have. Additionally, some general advice for corporate
managers with system procurement responsibilities is offered.
[Back to top]
Recent Advances in High Throughput Screening for ADME
Properties
Timothy J. Carlson and Michael B. Fisher
With the increase in the numbers of molecules synthesized
in a typical drug discovery program, as well as the large
amount of information utilized in the selection of a drug
candidate, there is a need for a plethora of drug metabolism
and pharmacokinetic (DMPK) information to be regularly generated
in discovery.Over the past decade, many in vitro,
and even in vivo, DMPK screens have been developed
and routinely deployed to generate this information in support
of drug discovery efforts. In the past few years, newer methods,
or adaptations to methods,have been published, and this review
attempts to summarize these advances. In particular, advances
have been reported for experimental approaches to metabolic
clearance, CYP inhibition, in vivo exposure, and
distribution, as well as in silico determinations
of absorption, distribution, metabolism, and excretion (ADME)
properties. Bioanalytical approaches aimed at optimizing analyte
method development, sample preparation, and analyte detection,
have also been reported. Future advances will further improve
the ability to make decisions on molecules earlier in drug
discovery.
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