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SYSTEMS BIOLOGY
A P P L I C A T I O N S 101
Systems Biology at a conceptual level refers to an integrated view of a biological system for
which the individual components are well understood through research and related ap-
proaches. The term “Systems Biology” is quite often used interchangeably with terms like
Systems biology ideally “in-silico design” and “computational modeling and simulation” though they may in all cases
seeks to understand not indicate the same intent or context. While the definition of Systems Biology is well un-
complex biological derstood; the end application or usage context varies as it is confused with all aspects of
systems in their entirety computational modeling deployed in drug discovery. The key distinction between bio-
by integrating all levels of
informatics techniques and Systems Biology approach is that the former is targeted to repre-
functional information
into a cohesive model. sent existing or known data in an efficient structured way for further statistical and other
That stands in contrast to analysis. The Systems Biology approach is targeted towards predictive hypothesis genera-
the reductionist tion and that is the key differentiator compared to other bioinformatics approaches.
approaches that became
standard in the twentieth Systems Biology or computational modeling or the in-silico approach can and is deployed in
century, with biologists different flavors. At the structural level – it enables screening of library of compounds
teasing out functional against biological targets to analyze and study drug docking and binding properties. Here
information on organisms the objective is to screen or identify compounds which bind to the specified biological target
one gene or one protein at and falls in the domain of chemistry. At the clinical level which is at the animal or human
a time.
testing level – pharmacokinetic based modeling studies enable understanding of Absorp-
“Systems Biology! tion, Distribution, Metabolism and Excretion (ADME) properties of the drug in the context of
Incorporated” by Karl Thiel,
Portland, Oregon - Nature efficacy and associated toxicity. Different patient sub-types based studies or analysis can be
Biotechnology, Volume 24, done to understand ADME variations impact for the drug. This approach enables determin-
Number 9, September 2006 ing the optimum concentration of drug for maximum efficacy with tolerable side-effects. At
the human clinical trial stage modeling is used for optimization of clinical trial programs with
the objective of reducing the complexity and size of the trial protocol.
At the molecular functional level – the Systems Biology flavor or abstraction level involves
identifying relevant cellular processes associated with disease of interest and then captur-
Another contributing factor ing all functionality of protein level interactions. The functional relationships between these
is that many companies proteins are represented through mathematics which is the key to convert this system from
tend to pursue the same
a static map or atlas to a Global Positioning System. The functional relationship representa-
targets, owing to the lack
of good drugable and tion is what makes the system dynamic and really meaningful. This approach enables true
validated targets, with the “target aware” drug discovery by allowing research teams access to a “intra” and “inter”
result that if the target cellular processes integrated physiology aligned system for control and disease conditions.
fails the collective loss of This system can be assayed for significant nodes, understand and identify bio-markers, un-
resources across the derstand disease and drug mechanisms and the like. Also various “what-if” analyses can be
industry is substantial.
performed to guide and support in “in vitro” and “in vivo” experimentation. This “what-if”
With the physiology-based
approach, this risk is analysis makes the system really predictive and allows new hypothesis to be generated and
probably lower because qualified. For example when doing “what-if” knockout and/or knock-in (over-expression)
companies have different studies in traditional in vitro and in vivo systems; it is not practically feasible to do varied %
starting points in the knock-out or knock-in studies. Another in vitro and in vivo system limitation is that all nodes
chemical structures used, are not assayable and neither can be studied the integration of two cell-types in the context
and even if the of a disease.
compounds are screened
in the same complex The “omics” (genomic and proteomics) approaches are a high-throughput technique which
models to obtain the same enables identification of key molecular endpoints which are associated with disease patho-
physiological effects the genesis and progression. These molecular endpoints translate into biological drug targets
drug programs in different and bio-markers for toxicity, drug efficacy and monitoring during clinical trials. The omics
companies will develop in approach enables a major productivity improvement in the “target discovery and research”
different directions. phase of drug discovery. But knowing the potential constituent molecular components does
Frank Sams-Dodd, DDT • not enable direct mapping to disease and drug mechanism of action which is needed to
Volume 10, Number 2 • predict relevant bio-markers. The Systems Biology approach leverages the information gene-
January 2005 rated through the omics approach in identifying the key players involved and along with the
SYSTEMS BIOLOGY APPLICATIONS 101 2
mechanistic protein level interaction data; ties this information into an integrated transparent view. This approach of Sys-
tems Biology is a dynamic in-silico view of the integrated metabolic and bio-chemical pathways showing the interaction of
the different biological components like proteins/enzymes/receptors/adaptors/transcription factors etc. in the system.
The relationship between the biological components also includes all the cross-talk and known feedback paths in the sys-
tem and the relationship is represented using mathematics. This system is analogous to a “virtual experimental system”
which can be used in parallel to “in-vitro” and “in-vivo” studies but with the added capability of transparency and visibility
into every node in the system.
APPLICATIONS OVERVIEW
Physiology aligned Systems Biology or “in-silico” platforms can be deployed for a wide variety of applications across the
drug discovery process. This is analogous to having “virtual cell lines” customizable for specific/relevant diseases which
can be used as a virtual experimental system (VES).
Traditional experimental systems have limited transparency due to practical limitations. Activation of important nodes is
caused by various levels of the trigger. Such activation raises the levels of the node, but due to experimental limitations
these are undetectable. Using virtual experimental system the key sensitive nodes to be assayed through “in-vitro” means
can be pruned down from the big maze. Having a predictive system aligned to human physiology greatly helps to qualify
and streamline hypothesis, which will lead to much reduced experimentation for target qualification. This also enables to
get a much better insight into the biology related toxicity landscape at the initial stages of discovery before much more $
are spent in advancing the molecule.
Listed below are the key applications of these “in-silico” platforms in context of the different discovery process stages.
Based on discovery project type – New Molecular Entity (NME), NCE (New Chemical Entity) or New Drug Formulation (NDF)
the discovery stages will vary.
Target ID & Analysis: This involves identifying the biological target/receptor which upon manipulation shows the desired
response at the biological end-point with minimum biological toxicity effect. The VES can also be used to analyze a cou-
ple of different target options which cause the same effect at the physiological endpoint but through different mecha-
nisms and corresponding implications can be understood.
Biology Based Toxicity Analysis: Toxicity understanding of a given molecule is a very important consideration factor for its
approval and adoption. At a broad level toxicity is due to two main reasons – Biology and Chemistry. The chemistry toxic-
ity is related to non-specific drug binding to other than desired receptors and causing some undesired effect. It is also
caused due to process of drug pharmacokinetic properties related to absorption; distribution etc. Systems Biology based
platforms enables analysis of toxicity related to biology. Since a complete integrated transparent view of the system is
available, one can look at the impact of manipulation of a particular receptor on other nodes and endpoints in the sys-
tem and understand possible toxicity effects.
Cumulative toxicity studies would be a combination of understanding the biology and chemistry impact in the system.
Drug Mechanism Understanding: VES can be used for understanding the mechanism and pathways through which the
drug impacts the relevant clinical endpoint.
Virtual Cell-Line: Similar to how cell-lines are used for experimental “in-vitro” work, the virtual cell-lines are “in-silico”
models of cell types which may be customized for specific disease types and used as a “virtual experimental system” in
conjunction with the traditional in-vitro experiments.
Bio-markers Identification and Cell Assays: The VES can be configured for disease state and control state and analyzed
for with and without drug under various states of disease. Also different types of disease triggers can be implemented in
the platform. Based on these different configurations detailed sensitivity analysis can be performed to understand key
bio-markers for different conditions.
ADME Interface: Through ADME studies one can determine the concentration of the drug at the plasma level and ap-
proximately at the receptor level. This information can be back-annotated in the disease platform to show dose-drug re-
sponse analysis at the receptor level.
Adaptive Clinical Program Design: Current clinical protocol designs do not support built-in adaptation when unpredicted
side-effects and efficacy data are discovered. This causes the clinical design changes in the middle of trials. Using these
platforms, one can design clinical programs which can pre-emptively plan based on bio-markers what can go wrong and
correspondingly build in a decision tree in the protocol design.
Drug Re-Purposing Opportunities Identification: With an integrated transparent physiologically aligned VES – one can
identify other potential opportunities for a given drug action across diseases. Many block-buster drugs in the market
were originally created for a different application than the one for which it got finally approved and deployed for. Also on
similar lines combination drug therapy can be planned out to maximize efficacy and reduce side-effects for a given drug
candidate.
CELLWORKS SOLUTIONS
We, at FDA, envision
progress in medical
Cellworks provides a comprehensive range of disease focused drug discovery and research ap- product development as
plications and solutions to empower every aspect of your research. These solutions enable having new predictive
“Predictive” and “What-If” Analysis to identify early those product candidates of greatest efficacy
tools to identify early
against molecular and biological processes.
those product
Using this approach you gain the visibility to pinpoint inefficiencies in selected target and com-
pound – and the capabilities to transform them into competitive advantage. The foresight to candidates of greatest
identify new opportunities; the agility to change directions and the functionality to optimize your efficacy against
discovery flow. molecular and
Cellworks current disease focus area includes – Oncology, Inflammation (Rheumatoid Arthritis biological processes
and Inflammatory Bowel Disease), Diabetes Type 2, Skin pigmentation, Uterine-Endocrine envi-
and new evaluative
ronment (Pre-Term Labor) and Parkinson’s Disease.
tools to improve the
performance of clinical
trials and treatment
choices.
- FDA Critical Path
Report 2006
SYSTEMS BIOLOGY APPLICATIONS 101 4
For example – Which cytokine levels would get affected by manipulation of a specific pathway? Which key nodes are sig-
nificantly changing under different conditions? This would be analogous to a genomic or proteomics dataset but a more
relevant subset since only the pathways and proteins involved in the specific disease process under investigation are in-
cluded in the system. This eliminates a lot of the noise one generally encounters in the high throughput data analysis.
PREDICTION OF CHANGES IN CYTOKINES (EG., WOULD TARGETING TNF REDUCE
LEVELS OF INFLAMMATORY MARKERS, SUCH AS CRP/ESR, IL6, ETC. –
Such questions and hypothesis can be tested in the virtual experimental system.
UNDERSTANDING OF ASSOCIATED CROSSTALK TO UNDERSTAND TOXICITY AND
POSSIBLE REASONS FOR DISEASE RELAPSE
CASE STUDY - A20 plays a critical role in regulating inflammation. Rapid expression of A20 is absolutely essential for down-
regulating the inflammatory response and averting the damage unrestrained inflammation can cause in different tissues.
Using Cellworks virtual experimental system the study of Drug A which inhibits NF-kB, shows the level of A20 reduced in
the system, thereby affecting the negative regulation of TNF-alpha, TLRs and IL1. This shows that in the presence of Drug
A, normal regulatory molecule gets affected.
INDIVIDUAL CONTRIBUTION OF VARIOUS FACTORS TOWARDS THE LEVELS OF AN
END-POINT
CASE STUDY - IL-4 produced in T cell alone is taken as the end-point. IL-4 is transcribed by NFATC2, NFKB and AP-1 and its
production is inhibited by STAT5. The virtual experimental system under diseased state can be simulated under the follow-
ing conditions and the concentration of IL-4 and results collated:
i. NFATC2 alone transcribing IL-4
ii. NFKB alone transcribing IL-4
iii. AP-1 alone transcribing IL-4
iv. All the three transcription factors NFATC2, NFKB and AP-1 together transcribing IL-4
v. All the three transcription factors NFATC2, NFKB and AP-1 together transcribing IL-4 and STAT inhibiting the transcrip-
tion
NF-kB+NFAT+AP1
FACTORS NFATC2 NF-kB AP-1 NF-kB+NFAT+AP1
+ STAT5
CONCENTRATION OF
0.034 0.003 0.00325 0.04 0.0325
IL-4 (uM)
and TIMPs is essential for normal cellular function. Over expression studies with these molecules using Cellworks virtual
experimental system, have demonstrated that proper control of MMP activity is required. It is well known that there is very
tight stoichiometric control between TIMP2, MT1-MMP, ProMMP2 in 1:1:1 ratio. TIMPs together with MT-MMPs also facili-
tate the activation of some MMPs like MMP9. Therefore, any quantitative difference in TIMPs can drastically impact a sys-
tem thereby pushing it from a normal physiological condition to a full blown diseased condition of metastasis & abnormal
phenotypes. Ratios of nodes can be assayed in the system.
KNOCKOUT STUDIES
In about 60% of malignant gliomas, PTEN (Phosphatase and Tensin homologue) is mutated with a loss of function. Using
the virtual experimental system one can evaluate the tonic activation of Akt with various levels of PTEN knockouts. AKT
tonic activation is directly responsible for mTOR mediated HIF-1 activation and results in increased transcription of genes
leading to altered glycolysis and enhanced substrate and product transport in transformed cells. Graded knockout analysis
helps examine the role of key nodes in cancer initiation and progression.
COMBINATORIAL DRUG/COMPOUND ANALYSIS
A multi-drug regimen can be designed and implemented for disease remission or for circumvention of drug associated tox-
icities. Using the virtual experimental system, such scenarios can be studied and analyzed.
For example, inhibitors targeting two different pathways affecting the same endpoint can be used at lower concentrations
and combination is more synergistic and effective than a single inhibitor targeting only one pathway. Another example case
study could be combination drugs such as an anti-proliferative drug targeting cell cycle regulation in combination with anti-
metastatic or anti-inflammatory agents.
Using one drug to restore the programmed cell death mechanism or eliminate the proliferation mechanism and a second
drug to trigger the process might reduce or eliminate chemotherapy-resistance and be an effective strategy for treating
cancer. In another case, enhanced reliance on non-oxidative glycolysis by cancer cells having PTEN mutations has been
modeled. The simulations predict that cancer cells having PTEN mutations would have enhanced sensitivities to agents
that activate AMPK. AMPK, when activated, inhibits mTOR and ERK and blunt transcriptional activation by HIF to counter-
act the tonic activation of AKT produced by the PTEN mutation. Furthermore, the simulations predict that reduced glycoly-
sis can lead to AMPK activation with increased resistance to small molecule inhibitors of EGFR.
The underlying informational storage structure of the Cellworks platform permits optimization of inhibition of multiple sig-
naling pathways such that a multi-drug regimen can be proposed for pre-clinical testing that employ multiple existing phar-
macological agents in a unique way.
Cellworks System Biology Initiative (CSBI) mission is to be the hub for R&D and deployment of Systems Biology based
applications in the domain of drug discovery. The mission reach is global through collaborations and partnerships. The
eco-system consists of pharmaceutical and biotechnology companies, leading international academic institutions, govern-
ment representatives and regulatory bodies, Venture Capitalists and Investment Funds and country specific industry bod-
ies.
SYSTEMS BIOLOGY APPLICATIONS 101 8
The core component of this initiative is hands-on training programs and disease aligned virtual experimental system kits
which are made available to the initiative members. SBE-101 is one of the entry level training modules with focus on
usage and applications of this approach to disease physiology understanding and drug discovery.
The research and development leverages a combination of published literature on node level data and alignment
of system with drug data and clinical endpoints. This technology provides an integrated transparent view of the
physiological system with many applications to address drug discovery challenges.
C E L LWORKS G ROU P I NC .