a knowledge-rich approach to drug discovery

© 2009 Ariadne. All Rights Reserved.

A knowledge-rich approach to drug discoveryFinding of potential drug against glioblastoma


Ekaterina Kotelnikova PhD | 07.23.2009


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


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

http://images.google.com/imgres?imgurl=http://www.cbs.dtu.dk/courses/27617.struc/protein_blue_brown.gif&imgrefurl=http://www.cbs.dtu.dk/courses/27617.struc/&h=250&w=275&sz=32&hl=en&start=25&sig2=YE5gjpp2yAWktZ-qIOgYjg&um=1&tbnid=Bhmes6OqOS8BLM:&tbnh=104&tbnw=114&ei=suvlRr6PFJaCepGozZIK&prev=/images%3Fq%3Dprotein%2Bstructure%26start%3D21%26ndsp%3D21%26svnum%3D100%26um%3D1%26hl%3Den%26sa%3DN

http://images.google.com/imgres?imgurl=http://www.pharm-marketing.com/image/olmesartan_medoxomil.gif&imgrefurl=http://www.pharm-marketing.com/bulk_drug_hp_eng.htm&h=434&w=480&sz=27&hl=en&start=31&sig2=ZKZMSZG4O1HgtaNoC0yyjg&um=1&tbnid=zlpcihhf_EJ1zM:&tbnh=117&tbnw=129&ei=D-zlRvWSLqeSeIbupZQK&prev=/images%3Fq%3Dchemical%2Bformula%26start%3D21%26ndsp%3D21%26svnum%3D100%26um%3D1%26hl%3Den%26sa%3DN


Entities in ChemEffect

Proteins: 9,058Small molecules: 20,718Diseases/Toxicities: 4,479Cellular processes: 1,866Protein classes/Enzymes: 2,339


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


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

http://www.olympusfluoview.com/gallery/cells/u118/u118large.html

http://images.google.com/imgres?imgurl=http://www.stronghealth.com/pr/uploadedimages/cancer%2520stem%2520cellUCLA3.jpg&imgrefurl=http://avemar.world-cancer.net/archives/category/stem-cells&usg=__lJ6jryCw8gMTwHVHEX-2HgI5MZw=&h=270&w=360&sz=47&hl=en&start=169&um=1&tbnid=f6C2349jOa5-sM:&tbnh=91&tbnw=121&prev=/images%3Fq%3Dastrocytoma%2Bcells%26start%3D160%26ndsp%3D20%26um%3D1%26hl%3Den%26sa%3DN

http://images.google.com/imgres?imgurl=http://www.abcam.com/cms/displayImage.cfm%3FintImageID%3D4479&imgrefurl=http://www.abcam.com/index.html%3Fpageconfig%3Dresource%26rid%3D172%26pid%3D7&usg=__VyWhA19RIV0gvJy6UQF8MtKJ8Ps=&h=516&w=647&sz=44&hl=en&start=6&um=1&tbnid=vXqJqfSFtvF3pM:&tbnh=109&tbnw=137&prev=/images%3Fq%3Dglioblastoma%2Bcells%26um%3D1%26hl%3Den


Glioblastoma pathway


• 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


Glioblastoma Treatment


• 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


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?


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


Workflow


Canonical pathway

Expression profile



Compounds known to affect proteins in the

pathway

Compounds known to inhibit Cyr61/NOV


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


Result: Cyr61 and NOV: Novel therapeutic targets ?


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


Cyr 61 and NOV: ChemEffect activators and inhibitors

Inhibitors: potential drugs?

Activators: steroids


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


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


Canonical pathway

Expression profile



Compounds known to affect proteins in

the pathway

Compounds known to inhibit

Cyr61/NOV


Acknowledgements

• Nikolai Daraselia, PhD


Left shiftLeft shift

Glioblastoma vs. Normal values distribution


Look at potential side effects

a knowledge-rich approach to drug discovery

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