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A new vision of strategic collaborations
However, there is a new vision where strategic
collaborations between pharmaceutical
companies, government agencies, venture
capital-backed biotechnology companies and
academic medical centres will create a new
breadth of approaches that have a good chance
of increasing the innovation that has been
stagnant in recent years5-8. Government funding
agencies are increasing the emphasis on
translational research, even in a period of
funding pressures. Academic medical centres
are also increasing their efforts in translational
science, while continuing to create new tech -
nologies and basic knowledge. Life sciences
and diagnostic companies have recognised
the emergence of personalised or precision
medicine and have begun commercialising
the ‘omics’ platforms required for realising
personalised (precision) medicine. There is also a
heightened focus on coupling diagnostic /
prognostic tests with new therapeutics to
identify the patient sub-populations that will
benefit from a treatment. This evolution of the
pharmaceutical industry offers opportunities
and challenges to the potential partners.
It is necessary to harness the expertise of the
collaborating partners and to be innovative in
focused efforts in order to gain the advantage of
collaboration. All potential partners must be
willing to negotiate terms of agreements that
benefit all partners. In many cases, this will
require modifications of institutional policies
created in a very different era. In a new
environment of collaboration, each potential
partner must also identify and optimise the
strengths of their organisation to make it a good
complementary fit for potential partners.
Academic medical centres are in a great position
to take part in the collaborative business model
of drug discovery and development, clinical
trials and diagnostics, if they are willing to
negotiate mutually beneficial terms, including
ownership / licensing of intellectual property
arising from the collaboration.
The importance of adopting the collabor -
ative business model to increase the potential
for innovation is reflected in the fact that the
dominant paradigm in drug discovery for
the last 25 years has been the target-centric
model or the one gene, one target, one New
Chemical Entity (NCE) approach. Most
pharmaceutical companies embraced this
philosophy due to the expectation of a near-
term impact of the human genome project,
technological advances in screening auto -
mation, creation of large chemical libraries,
increases in the number of solutions to protein
The pharmaceutical industry has experienced a decade of turbulence driven by the
‘patent cliff’ as major revenue generators are lost to generic status, coupled to
the absence of a sustainable pipeline of drug candidates in development that have
a good chance of being approved and launched1,2
. It is generally agreed that the
lowest hanging drug discovery ‘fruit’ has been harvested and the industry is
addressing diseases that are more complex. The current one target, one drug
discovery and development paradigm continues to exhibit more than 90 per cent
attrition mainly due to the lack of success in translating preclinical efficacy and
safety data into successful human trials1
. It has also become clear that efficient
drug discovery and development requires a deeper understanding of the complexity
of human biology early in the process3
. The high attrition rates increase the costs
and with the science indicating that precision therapeutics will replace the
blockbuster model4
, the challenge of drug discovery and development is even
greater. The traditional business model of pharmaceutical companies working in
silos is no longer sustainable.
A new vision of drugdiscovery and development
D. Lansing Taylor
Director, University of Pittsburgh Drug Discovery Institute and Allegheny Foundation Professor of Computational and Systems Biology, University of Pittsburgh School of Medicine
DRUG DISCOVERY
European Pharmaceutical Review
Volume 17 | Issue 6 | 2012 20
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structures and the creation of in silico software tools. A major
challenge has been the slow and incomplete determination of the
relationship between the disease genotype and the phenotype. It is
now clear that putting most of the intellectual and experimental
‘eggs’ in this one basket has not produced the predicted productivity1.
A road to higher innovation
High Throughput Screening (HTS) had become the standard in
target-centric discovery programs by the early 1990s, but in the late
1990s, High Content Screening (HCS) was introduced as an
alternative or at least a complement to HTS9,10. The concept of HCS
was to fully automate fluorescence microscopic analysis of cells and
later small experimental organisms, allowing the creation of deeper
biological knowledge based on the physiological disease relevance
to better guide decisions on the progression of compounds.
HCS offered the opportunity to initiate discovery based on a disease
phenotype and not a specific molecular target. However, most
discovery programs in the early days used HCS only in secondary
assays and to follow a specific molecular target activity, since the
speed of reading primary assays using HTS was viewed as paramount.
However, given the late-stage failure of drug candidates, especially in
phase II clinical trials1, the speed of reading a plate in discovery is
insignificant compared to the time to make good decisions on
progressing candidates based on the necessary biological and
chemical knowledge11. Importantly, it has been demonstrated
that phenotypic discovery was the most successful approach for
first-in-class small molecule drugs approved by the US Food and Drug
Administration (FDA) between 1999 and 200812,13.
Combining the application of multiplexed HCS to more disease
relevant (and more complex) biological screening models such as
mixed cell cultures, 3D human tissue engineered models of organs
and small experimental organisms such as yeast, C. elegans, and
zebrafish should have a major impact in the early discovery
process14,15. Especially promising for the future is the potential of
human induced pluripotent stem cells (iPSCs) from patients with a
range of genomic backgrounds to serve as the source for disease
relevant human tissue models to be used in discovery and early
development16. Success here could have a major impact in optimising
efficacy, as well as pharmacodynamics (PD) and pharmacokinetics
(PK) and could minimise animal studies in pre-clinical trials after
proper validation. It will also be critical to expand the use of
computational chemistry and biology together with systems biology,
in parallel with the improvement of the experimental systems used in
phenotypic discovery17-19. Generation of complex data sets
integrating the available ‘omics’ information requires computational
methods to reduce the data to knowledge.
A critical role for quantitative systems pharmacology
Quantitative systems pharmacology (QSP) is an emerging field that
integrates experimentation, including screening data, with
computational tools to define the actions of drugs across multiple
scales of biological complexity from molecules to cells, tissues, organs
and organisms for a ‘systems’ level perspective20-22. QSP is the merger
of pharmacology, especially pharmacokinetics (PK) and
pharmacodynamics (PD) with the field of systems biology23.
European Pharmaceutical Review
Volume 17 | Issue 6 | 2012
DRUG DISCOVERY
taylor_Layout 1 03/12/2012 09:12 Page 2
The promise of QSP also includes the ability
to understand the interaction of drugs in indi -
vidual patients.
We view QSP as involving Inputs, as well as
the application of the elements of experi -
mentation and computational methods of QSP
and finally Outputs that result from the
approach (Figure 1). The Input (disease-
associated genotypes and phenotypes) of the
QSP approach includes all of the available
‘omics’ generated on the disease model systems
and patient samples including multiplexed
fluorescence-based pathology. Disease relevant
pathways are inferred from the ‘omics’ data to
guide the development of the optimal
phenotypic screen. The best possible pheno -
typic disease model is then validated as a High
Content Screen (HCS) assay. The disease
model/assay can range from multiplexed cells to
engineered human tissue to experimental
organisms. QSP integrates the data from the
phenotypic discovery approach (see Figure 3,
page 23) and applies a range of computational
chemistry, computational biology and systems
biology software tools to reduce the large
screening/experimental data sets to functional
knowledge, including polypharmacology24,25.
Furthermore, a number of machine learning
approaches have the potential to reduce the
amount of screening measurements required26.
Mathematical models of refined pathways, as
well as PK and PD, are developed and then
extended to define the complex processes of
living systems23,27. The Output from this
approach is expected to yield advanced
functional knowledge on the pathways,
including potential feedback loops between
pathways, as well as physiological processes
interrogated experimentally and compu -
tationally. Additionally, the output will identify
any ‘emergent properties’ or properties of
the system not predicted from investigating the
components, such as heterogeneity of system
responses22. Another important output should
be improved and predictive drug efficacy and
safety as a ‘knowledgebase’ of information as
QSP is applied. The major output should be
novel drugs, including drug combinations
working on connected pathways28. There
will be ‘feedback loops’ between input,
QSP and output. For example, the QSP results
will help build new hypotheses in regards
to pathways and MOA that could feedback to
input to perform new assays. Likewise,
the outputs (e.g. drugs, combination therapies
or polypharma cological strategies) would also
be tested against HCS assays and newly
collected omics data (e.g. from patients
that have received treatment). QSP will also
help to understand side effects, or mechanisms
of drug resistance.
European Pharmaceutical Review
Volume 17 | Issue 6 | 2012 22
DRUG DISCOVERY
Figure 1 QSP in drug discovery and development in the UPDDI begins with Inputs of ‘omics’ data, the developmentof inferred pathways involved in the disease and a phenotypic disease model for the screen. The application of QSPinvolves the phenotypic discovery approach using HCS and computational and systems biology, as well asmathematical modeling. The outputs of QSP include functional knowledge including any emergent properties,improved drug efficacy and safety and most importantly, novel drugs
Figure 2 Starting discovery campaigns with computational chemistry and biology allows the integration of existingknowledge of the targeted pathway(s) and the identification of predicted binding of existing drugs to pathwaycomponents that could identify useful ‘probes’ of pathway modulations, as well as starting points for rational drugdesign. Some of the databases used in target prediction include: STITCH – chemical-protein interactions,http://stitch.embl.de/ . DrugBank – approved/experimental drugs with target information from literature,http://www.drugbank.ca/ ,SIDER – drug side effects database, http://sideeffects.embl.de/ , ChEMBL – chemical-protein interactions from bioassays/literature, https://www.ebi.ac.uk/chembl/ , Target Hunter-identify possibletargets of small molecules, http://www.cbligand.org/targethunter, and MDDR – chemical bioactivity databasehttp://accelrys.com/products/databases/bioactivity/mddr.html
‘‘It is necessary to harness the expertiseof the collaborating partners and to beinnovative in focused efforts in order to
gain the advantage of collaboration’’
taylor_Layout 1 03/12/2012 09:13 Page 3
The University of Pittsburgh
Drug Discovery Institute (UPDDI)
as an example
The University of Pittsburgh Drug Discovery
Institute (UPDDI) has embraced a two-fold
strategy in creating an environment for the new
vision of drug discovery and development
(www.upddi.pitt.edu): Collaboration – through
integrated activities across internal depart -
ments, centres and institutes, along with
collaborations with other academic centres,
government agencies and commercial partners;
and Innovation – by developing and practicing
new approaches and technologies to comple -
ment the present paradigm of discovery.
Technologically, the UPDDI has key strengths in
HCS and phenotypic discovery, chemistry /
medicinal chemistry and molecular biophysics
applied to target-centric discovery and is
investing heavily in the implementation of QSP.
The focus of this discussion is on QSP coupled
to phenotypic discovery, but the power of
molecular biophysics in target-centric programs
is evident when applied to the right target and
can be performed subsequent to an initial
phenotypic discovery step when a target is
identified29. The University of Pittsburgh has the
depth and breadth to support a major effort
in drug discovery and development and in
cooperation with the University of Pittsburgh
Medical Center (UPMC), the ability to translate
basic research to clinical trials and clinical
practice. Ready access to clinician scientists,
patients and patient samples is crucial to the
success of this new paradigm.
A major advance in computational
chemistry and computational biology in recent
years has been the harnessing of genomics and
proteomics databases and sophisticated
algorithms to infer pathways responsible for cell
functions as a starting point for defining the
actual pathways (Figure 2, page 22). It is also
now possible to harness drug and target protein
databases to predict drug interactions with
specific target proteins. Positive ‘hits’ from the
in silico profiling can be used to identify useful
‘chemical probes’ of pathways and cellular
functions, as well as a starting point to design
a phenotypic screening strategy for drug
discovery and/or as a reference point for
pursuing a molecular biophysics / target-centric
approach to drug discovery30,31.
Critical role of HCS in QSP
The UPDDI is applying QSP in the drug discovery
and development process starting with the
application of phenotypic screening using
HCS11,14,15. Figure 3 shows the steps in performing
a phenotypic screen. In phenotypic drug
discovery, the detailed, basic and clinical science
is a critical component, as in target-centric
discovery. However, a functional, disease
relevant phenotype is selected, validated
and profiled by HCS rather than selecting and
validating a single molecular target. This
broadens the potential molecular targets that
can be modulated by compounds and puts the
initial focus on functions and pathways. This is
very different from applying hypothesis driven
research to follow a single molecular target, but
allows an unbiased, physiological profile to
define the cellular functions and pathways
directly involved in the disease. Optimally, one
or more biomarkers can be identified in the
process, quantified in the HCS assay and carried
through the whole discovery-development
process. A critical step is the selection of
compound libraries based on both diversity and
novelty. In addition, exploring existing drugs for
repurposing and natural products for added
diversity has great promise. The screening
campaign is performed identifying ‘hits’ and lead
generation and lead optimisation is subse -
quently performed. An optimally designed HCS
assay can be used to guide the structure activity
relationship (SAR) in lead optimisation15,32,33.
In fact, the FDA does not require molecular
target identification for approval13. Extensive
data mining on 890 approved drugs demon -
strated that on average, each of the analysed
drugs interact with six known molecular
targets34. This latter fact gives promise to the
drug repurposing efforts now underway35.
However, when optimised leads are
identified, it is important to apply chemical
proteomics approaches to try to identify
potential molecular target(s)36,37. Identification
of molecular target(s) allows the application of
mechanism of action (MOA) studies that might
involve multiple molecular targets across
multiple pathways. Furthermore, one or a
combination of identified molecular targets
could be useful as biomarkers. In vitro early
safety assessment can also be performed using
HCS at this stage to help guide the prioritisation
of leads38,39. The pre-clinical and clinical stages
are the same functionally, as with the target-
centric approach, but with the addition of
computational and systems biology that
permits quantification and modelling of
the data. The phenotypic drug discovery-
development approach allows the application
of QSP from early discovery on a range of
scales of biological complexity from molecules
to mammalian models to human patient
DRUG DISCOVERY
European Pharmaceutical Review
www.europeanpharmaceuticalreview.com 23 Volume 17 | Issue 6 | 2012
‘‘The phenotypic drug discovery-development approach allows
the application of QSP from earlydiscovery on a range of scales of biological complexity from
molecules to mammalian models to human patient cohorts’’
Figure 3 Phenotypic drug discovery and development using HCS is a major commitment of the UPDDI. Theimplementation of QSP involves the best experimental methods, including HCS screening data, coupled withcomputational chemistry and biology, as well as systems biology. Although not required by the FDA, theidentification of the molecular target(s) is investigated by chemical proteomics. The goal is to integrate and toanalyse data across the complete discovery-development continuum from early discovery to clinical data
taylor_Layout 1 03/12/2012 09:13 Page 4
cohorts. The phenotypic approach can be
extended from early discovery through pre-
clinical and clinical trials and represents a natural
path to the development and use of biomarkers
using multiscale imaging modalities40.
Conclusion
A new vision of drug discovery and develop -
ment is based on collaborations between
pharmaceutical companies, government
agencies, venture-backed biotechnology
companies and academic medical centres to
expand the potential for innovation, while
sharing the complexity and technologies
involved in discovering and developing novel
therapeutics. Quantitative systems pharma -
cology coupled with high content screening is
being developed as one innovative path at the
University of Pittsburgh Drug Discovery
Institute. Personalised / precision medicine is
dependent of the development of diagnostic
tests to guide the optimal delivery of thera -
peutics to patient sub-populations.
Acknowledgements
I would like to thank my colleagues for valuable
discussions on how to harness the new vision of
drug discovery and development including
Mark Schurdak, Bert Gough, Andy Stern,
Andreas Vogt, Dutch Boltz, Ivet Bahar, Jeremy
Berg, Ahmet Bakan, Tim Lezon and Bob Murphy.
European Pharmaceutical Review
Volume 17 | Issue 6 | 2012 24
DRUG DISCOVERY
Dr. D. Lansing Taylor began his academiccareer at Harvard University developing andapplying novel fluorescence-based reagentsand imaging technologies to investigatefundamental cellular processes. He thenmoved to Carnegie Mellon University andbecame the Director of the National Science
Foundation, Center for Light Microscope Imaging and Biotechnology,and in 1995 was named Vice Dean of CMU’s Division of MolecularSciences. Together with his students, post-docs and collaborators, Dr. Taylor developed reagent and imaging technologies includingfluorescent analog cytochemistry, ratio imaging, fluorescenceanisotropy imaging microscopy, the multimode light microscope andstanding wave fluorescence microscopy. Dr. Taylor co-founded and led a series of biotechnology companies including BiologicalDetection Systems (cyanine dyes with Alan Waggoner), Cellomics(High Content Screening), Cellumen (predictive early safetyassessment) and Cernostics (tissue systems pathology). Dr. Taylor is aco-inventor on more than 25 US patents, including six focused oncell-based imaging. He was the recipient of an NIH MERIT award anda Pioneer Award from the NSF. Dr. Taylor returned to academia at theend of 2010 to continue his academic interests which now link large-scale cell, tissue and experimental organism profiling withcomputational and systems biology to optimise drug discovery anddevelopment. As the Director of the Drug Discovery Institute, he isfocusing on the application of Quantitative Systems Pharmacology inorder to change the paradigm in drug discovery and development.
Biography
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24. Pujol A, Mosca R, Farres J, Aloy P. Unveiling the role ofnetwork and systems biology in drug discovery.Trends Pharmacol Sci. 2010;31(3):115-23
25. Hopkins AL. Network pharmacology: the nextparadigm in drug discovery. Nat Chem Biol.2008;4(11):682-90
26. Murphy RF. An active role for machine learning in drugdevelopment. Nat Chem Biol. 2011;7(6):327-30
27. Faeden J, Blinov M, Hlavacek W. Rule-based modelingof biochemical systems with BioNetGen. In: Maly I,editor. Methods in Molecular Biology: SystemsBiology. Totowa, NJ: Humana Press; 2009
28. Bernards R. A missing link in genotype-directed cancertherapy. Cell. 2012;151(3):465-8.
29. Molina G, Vogt A, Bakan A, Dai W, Queiroz de Oliveira P,Znosko W, et al. Zebrafish chemical screening revealsan inhibitor of Dusp6 that expands cardiac celllineages. Nat Chem Biol. 2009;5(9):680-7. PMCID:2771339
30. Liu Z, Fang H, Reagan K, Xu X, Mendrick DL, Slikker W,Jr., et al. In silico drug repositioning – what we need toknow. Drug Discov Today. 2012;00(00):13-6
31. Keiser MJ, Setola V, Irwin JJ, Laggner C, Abbas AI,Hufeisen SJ, et al. Predicting new molecular targets forknown drugs. Nature. 2009;462(7270):175-81. PMCID:2784146
32. Link W, Oyarzabal J, Serelde BG, Albarran MI, Rabal O,Cebria A, et al. Chemical interrogation of FOXO3anuclear translocation identifies potent and selectiveinhibitors of phosphoinositide 3-kinases. J Biol Chem.2009;284(41):28392-400. PMCID: 2788888
33. Zanella F, Rosado A, Garcia B, Carnero A, Link W.Chemical genetic analysis of FOXO nuclear-cytoplasmic shuttling by using image-based cellscreening. Chembiochem. 2008;9(14):2229-37
34. Mestres J, Gregori-Puigjane E, Valverde S, Sole RV. Thetopology of drug-target interaction networks: implicitdependence on drug properties and target families.Mol Biosyst. 2009;5(9):1051-7
35. Mullard A. Drug repurposing programmes get lift off.Nature Reviews Drug Discovery. 2012;11(7):505-6
36. Cong F, Cheung AK, Huang SM. Chemical genetics-based target identification in drug discovery. AnnuRev Pharmacol Toxicol. 2012;52:57-78
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38. Vernetti L, Irwin W, Giuliano K, Gough A, Johnston K,Taylor D. Cellular Systems Biology Applied to Pre-Clinical Safety Testing: A Case Study of CellCiphr™Cytotoxicity Profiling. In: Xu J, Ekins S, editor. DrugEfficacy, Safety, and Biologics Discovery: EmergingTechnologies and Tools. New Jersey: John Wiley andSons; 2008. p. 53-73
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