a knowledge-rich approach to drug discovery
TRANSCRIPT
© 2009 Ariadne. All Rights Reserved.
A knowledge-rich approach to drug discoveryFinding of potential drug against glioblastoma
© 2009 Ariadne. All Rights Reserved.
Ekaterina Kotelnikova PhD | 07.23.2009
© 2009 Ariadne. All Rights Reserved.
Ariadne Pathway Studio
Knowledge Databases
ChemEffect:Compound protein
targets, and molecular, cellular and physiological
effects
MedScan®
LibraryLibrary
Knowledge databases:
- ResNet® Mammalian - ChemEffect®
Pathway Building
Gene expression analysis
© 2009 Ariadne. All Rights Reserved.
ChemEffect
Relation Description CountSmall molecule -> Conditions/CellProcess effects (+/-)
Physiological effects, generally indirect. Toxicities, including positive and negative effects
~340,000
Small molecule– protein binding Protein – small molecule bindings 17,186
Small molecule –> Protein inhibitor/activator
Direct drug effects on protein targets 46,748
Small molecule -> protein expression Regulation of protein expression by drugs 63,296
Small molecule -> Protein effects (+/-) Indirect effects of small molecules on proteins ~150,000
Small molecule metabolization Proteins/Enzymes metabolizing drug 6,541
Small molecule transport Proteins/Enzymes involved in drug transport 1,757
Toxicities
Cell processes
Expression, Binding, Regulation
Conditions
Regulation
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Entities in ChemEffect
Proteins: 9,058Small molecules: 20,718Diseases/Toxicities: 4,479Cellular processes: 1,866Protein classes/Enzymes: 2,339
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Workflow
Disease: Glioblastoma
Canonical pathway
Expression profile
Significant regulators(Cyr61 and NOV)
Intersection:Fulvestrant
Compounds known to affect proteins in the
pathway
Compounds known to inhibit Cyr61/NOV
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Glioblastoma quick facts
AstrocytomaSurvival: 5-10yrsLoci: p53, PDGF/RPathobiology: moderate proliferation, invasion
Anaplastic astrocytomaSurvival: 2-3yrsLoci: CDK4/6, Rb, 19q/11q lossPathobiology: proliferation, invasion, angiogenesis
GlioblastomaSurvival: 9-12mosLoci: PTEN, 10q loss, EGFR, Cyclin D, mdm2, Bcl2L12Pathobiology: proliferation, invasion, angiogenesis,necrosis
Furnari, et al; Genes Dev. 2007 21: 2683-2710
• Most vascularized cancer• relentless malignant progression• Apoptosis - resistant
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Glioblastoma pathway
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• Pathway was built from few latest reviews
• Main signaling pathways (PKC, NFkB, MAPK, mTOR, beta-Catenin) and other key proteins were identified
• These signaling pathways and proteins were found in the PathwayStudio® database
• They have been combined into one pathway
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Glioblastoma Treatment
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• No effective treatment yet• Current treatment: radiotherapy
& traditional chemotherapy• Inhibitors of glioblastoma
pathway are in various stages of clinical trials with mixed outcome
Wong, et al; J Clin. Neurosci. 2007 21: 301-308Tuettenberg, et al; Crit. Rev. in Onc. Hemat. 2006 59: 181-193
Becavizumab
Cetuximab
ImatinibZD6474PazopanibGefitinibErlotinibLapatinib
EnzastaurinTamoxifen
TipifarnibLonafarnib
Sorafenib
Bortezomib
SirolimusEverolimusTemsirolimus
Current opinion: targeting multiple proteins may be more efficient
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ChemEffect drugs against Glioblastoma pathway, targeting multiple proteins
• 750+ compounds in ChemEffect down-regulating pathway
• Top 40 targeting multiple proteins
• Many of them haven’t been tried against glioblastoma?
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Fulvestrant: effective against Glioblastoma?
• Estrogen receptor antagonist
• Used in treatment of hormone receptor-positive metastatic breast cancer
• Tamoxifen, another ER antagonist and PKC inhibitor is partially effective against glioblastoma
Couldwell, et al; Clin. Cancer Res.. 1996; 2: 619-622
© 2009 Ariadne. All Rights Reserved.
Workflow
Disease: Glioblastoma
Canonical pathway
Expression profile
Significant regulators(Cyr61 and NOV)
Intersection:Fulvestrant
Compounds known to affect proteins in the
pathway
Compounds known to inhibit Cyr61/NOV
© 2009 Ariadne. All Rights Reserved.
Glioblastoma Gene Expression Analysis Workflow
GE: Glioblastoma vs. Normal
Differential expressionprofile
Sub-Network Enrichment Analysis
High-scoring components
• PathwayStudio 6 Sub-Network Enrichment Analysis Tool
• Statistical test, similar to Broad Institute Gene Set Enrichment Analysis (GSEA)
• Sub-networks are built dynamically around all proteins and represent their expression targets in the database
• Identify key regulators of differentially expressed genes
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Result: Cyr61 and NOV: Novel therapeutic targets ?
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Regulated by estrogen
Inhibit apoptosis
Act through integrins
Activate cancer pathways: AKT, FAK and beta-Catenin
Matricellular proteins, interact with matrix proteins, growth factors and their receptors
Regulate angiogenesis and cell migration
Regulate ECM remodeling
Regulated by HIF1A, a main regulator of angiogenesis
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Cyr 61 and NOV: ChemEffect activators and inhibitors
Inhibitors: potential drugs?
Activators: steroids
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Fulvestrant: effective against Glioblastoma?
• Estrogen receptor antagonist
• Used in treatment of hormone receptor-positive metastatic breast cancer
• Tamoxifen, another ER antagonist and PKC inhibitor is partially effective against glioblastoma
Couldwell, et al; Clin. Cancer Res.. 1996; 2: 619-622
© 2009 Ariadne. All Rights Reserved.
Summary
• Identify compounds affecting target proteins or pathways
• Identify targets affected by similar compounds
• Survey side-effects associated with compounds
• Use experimental data to build drug action hypothesis and identify potential drug targets
• Identify potential alternative drug indications
Disease: Glioblastoma
Canonical pathway
Expression profile
Significant regulators(Cyr61 and NOV)
Intersection:Fulvestrant
Compounds known to affect proteins in
the pathway
Compounds known to inhibit
Cyr61/NOV
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Acknowledgements
• Nikolai Daraselia, PhD
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Left shiftLeft shift
Glioblastoma vs. Normal values distribution
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Look at potential side effects