With the emergence of small molecule screening as a powerful research tool
in biology, biomolecular screening has arrived in the laboratories of academe.
More and more, researchers in universities and hospital research institutes are
recognizing the power of small molecules as probes of biochemical and
biological systems. At McMaster University in Hamilton, ON, we have established
a state-of-the-art small molecule screening laboratory that became fully
operational a little more than two years ago (http://hts.mcmaster.ca). It's
with considerable enthusiasm, as the founding director of that laboratory, that
I offer the following perspectives on screening in an academic setting and on
my own experiences in setting up such a facility.
There has been a groundswell of interest among academic researchers in high
throughput screening. It began with the establishment of the first academic
screening operations--including that of the Harvard Institute of Chemistry and
Cell Biology in the late 1990s. Today, biological researchers in most
research-intensive academic institutions are, at the very least, considering
the establishment of capabilities and a presence in small molecule screening in
order to fuel research activities in the emerging field of chemical biology.
Nevertheless, the implementation of a reasonably capable screening facility
with its associated liquid handling, instrumentation, compound and information
management systems is a complex, costly, and energetic undertaking.
In setting up a state-of-the-art screening laboratory, it has been
instructive for me to reflect on how advances in high throughput screening in
the private sector have exerted recent influence on research directions in
biological research at universities and research institutes. This trend contrasts
with the conventional academic view of innovation, which has emerging
technology moving from university to industry. Advances in biological research
have, of course, been among the most celebrated university-based innovations.
The once purely academic pursuits of biological chemistry and cell biology have
slowly but firmly established themselves in the research paradigm of formerly
chemistry-centred pharma, beginning with revolutionary advances in molecular
biology in the late 1970s. It is perhaps ironic, if not remarkable, then that
similarly revolutionary progress made by high throughput screeners in the
pharmaceutical sector has impacted on the technology now available to chemical
biologists in academe.
Equipped with robust robotics, information systems and well-established
screening methodologies, all developed by and large in the biotechnology and
pharmaceutical sector, biochemists and cell biologists in academe are turning
in earnest to small molecule screening as a fresh approach to discovering molecular
probes of systems under their study. With the freedom to innovate and publish,
academic screeners will now surely be in a position to return the favour to
their private sector colleagues with new discoveries and new approaches.
Our own HTS Lab was founded by three principle investigators at McMaster
whose research interests include antimicrobial research (Gerry Wright and I)
and materials science (John D. Brennan). The genesis and funding for the
laboratory came as part of a province-wide initiative in genomics. It included
close partnerships with combinatorial chemistry laboratories at York University
and the University of Toronto. The thinking was that the chemists and screeners
could work together, for example, in lead optimization activities. Indeed, the
practicality of attracting the interest of collaborators in synthetic chemistry
for downstream optimization of hits from commercial libraries is frequently a
concern among academic researchers considering screening projects. In practice,
we've been very pleasantly surprised by the interest of colleagues in synthetic
chemistry and the ease with which meaningful collaborations have arisen.
Among the primary considerations in setting up the McMaster HTS Lab was to
clearly define our goals. We wanted to establish a facility that would be in a
position to lead in academic screening in Canada and elsewhere. Therefore, in
addition to servicing the research needs of the principle investigators, the
McMaster HTS Lab has aspired to provide a service to the biological research
community in Canada and beyond. Those objectives have required the
establishment of capable research, service, and training components that can be
tapped into on an ad hoc basis. As a result, the McMaster HTS Lab has
participated in collaborative projects with researchers from across the
country. It has provided advice and training resources for researchers setting
up screening operations in the public and private sectors in Canada and the
U.S.
In setting up the screening infrastructure, we needed to make some
important philosophical choices. In screening circles, opinions on
instrumentation, informatics and compound collections border on religion.
Having spent three years in the private sector in Boston, MA, working in
antibacterial lead discovery, I developed some strong thoughts of my own.
Nonetheless, we consulted widely with colleagues in the private sector and
visited screening labs in pharmaceutical companies in Boston and Montreal, QC.
Those consultations were invaluable and our most important philosophical
decision was to concentrate on the biological research capabilities of our
facility. That meant de-emphasizing the technology of screening and choosing
"off-the-shelf" technology where possible. We have not, for example,
allocated funds to programming, engineering, or instrumentation development. We
have not elected to push the limits of throughput. The result is a screening
operation that is flexible, user-friendly, and small in scale. It functions
with a highly trained but skeleton crew of just three full-time researchers,
including a lab manager and two research scientists.
Our compound collection is consistent with this user-friendly philosophy.
The core of the collection is a couple of milligrams each of 50,000 diverse
molecules from Maybridge, an organic compound producer in the U.K. This
collection is recognized in screening circles for its quality and for ease of
re-supply. The latter is particularly important to the academic biological
screener who is typically without resources for re-synthesis. In our
experience, molecules can be re-ordered cost-effectively from Maybridge with
quick turnaround to verify structure and activity and to make headway on
mechanism of action. This additional data is very helpful in solidifying downstream
research activities and may provide preliminary results to secure funding and
collaborations for those efforts. In addition to our core collection of 50,000
Maybridge compounds, we have lesser quantities of Chembridge molecules (50,000)
and 10,000 proprietary molecules under agreement with Crompton Corporation. We
have found that the core collection provides a good first pass that fits with
most academic goals and finances, where the latter is a reality of academic
research budgets, particularly due to the high costs of disposables in
screening. For high priority screens and targets, we screen our entire
collection.
For our screening instrumentation, we chose an integrated screening system,
the SAGIAN Core System from Beckman equipped with a three metre rail, ORCA
robotic arm, Biomek FX liquid handler (96-tip and span eight pipettors), and
SAMI integration software. For instrumentation on the rail, we have an LJL
Analyst fluorescence reader, Molecular Devices Spectra Max plus absorbance
reader, C[O.sub.2] incubator, etc.--all components that Beckman had
successfully integrated before with the SAMI software. The goal here was to
create a system that worked with little development of fiddling. In addition to
the integrated Core System, we also have a complement of off-line readers and
instrumentation, including a Biomek FX liquid handler equipped with a single
pod 96-tip pipettor/gripper that is frequently used for plate replication and
as general liquid handling capacity to assuage the screening queue.
For informatics we have likewise chosen "off-the-shelf" solutions
with ActivityBase by IDBS and DecisionSite by Spotfire. Again, the goal was to
streamline our operation with little or no informatics development. Here,
ActivityBase is a highly functional relational database system and Decision
Site serves as a data visualization and analysis tool. Together these programs
have been particularly up to the service challenges of the McMaster HTS Lab
where meaningful data and queries must be delivered to users not trained on the
software.
The McMaster HTS Lab became fully operational in April 2002. Since that
time, despite our "off-the-shelf" approach, we've experienced delays
and down time amounting to about 20 percent due to instrumentation,
informatics, and user difficulties. Even so, the growing pains appear to be
behind us now. To date, we've collected millions of data points on more than a
dozen screening campaigns. The first screens were of the principle
investigators here at McMaster, the lion's share of those currently underway
are screens for researchers from other institutions across Canada. Of the
assays completed some were cell-based and many were biochemical, that was among
the first published (Bioorganic & Medicinal Chemistry Letters 2003, 13:2493).
It has formed the basis of an international data-mining and docking competition
with the involvement of computational chemists from around the world (Nature
Reviews Drug Discovery 2004, 3:6). Virtually all of our screens have produced
molecules worthy of ongoing study and have spurred significant collaborations
with synthetic chemists and structural biologists. Among the most important
lessons learned: devote quality time to assay development and run screens in
duplicate.
In closing, it's a great time to be a small molecule screener in academe.
Thanks mostly to more than a decade of development directed by the
pharmaceutical and biotechnology sectors, screening technology is now available
in sophisticated and user-friendly solutions. Furthermore, thanks to
organizations such as the SBS, and its associated journal, screening approaches
and methodologies are maturing and becoming more accessible to public domain
researchers. Establishing a reasonable scale screening laboratory, however,
remains a complex undertaking requiring investment and strategies for operation
that are uncommon among facilities traditionally used by academic researchers.
Regardless of the challenges, small molecule screening is very likely to find
an enduring home in academe as biologists in universities and research
institutes are increasingly recognizing the utility of small molecules as
probes of their experimental systems.
Acknowledgements
The author would like to acknowledge the staff at the McMaster HTS
Laboratory, Jan Blanchard, ACIC, Jonathan Cechetto, and Nadine Elowe for their
efforts. And my colleagues John Brennan, MCIC, and Gerry Wright for their
thoughts and insights. I am also grateful to the Ontario Research and
Development Challenge Fund for infrastructure and operating funds. Thanks also
to the Canada Research Chairs program for a salary award.
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