Office of Research and Development National Center for Computational Toxicology Carcinogenicity and Mutagenicity Data: New Initiatives to Improve Access & Utility for Modeling http://www.epa.gov/ncct/toxcast April 2-4, 2008 SCARLET Workshop, Milan, Italy
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Office of Research and DevelopmentNational Center for Computational Toxicology
Carcinogenicity and Mutagenicity Data: New Initiatives to Improve Access & Utility for Modeling
http://www.epa.gov/ncct/toxcast
April 2-4, 2008SCARLET Workshop, Milan, Italy
Part IPart IData & Data LinkagesData & Data Linkages
Mutagenicity_SAL_CPDBTD50_Rat_mgTD50_Rat_mmolTD50_Rat_NoteTargetSites_Rat_Male, Female, Both SexesTD50_Mouse_mgTD50_Mouse_mmolTD50_Mouse_NoteTargetSites_Mouse_Male, Female, Both SexesTD50_Hamster_mgTD50_Hamster_mmolTD50_Hamster_NoteTargetSites_Hamster_Male, Female, Both SexesTD50_Dog_mgTargetSites_DogTD50_Rhesus_mgTargetSites_RhesusTD50_Cynomolgus_mgTargetSites_CynomolgusTD50_Dog_Rhesus_Cynomolgus_NoteActivityCategory_SingleCellCallActivityCategory_MultiCellCallActivityCategory_MultiCellCall_DetailsToxicityNoteNTP_TechnicalReportWebsite_URL
Office of Research and DevelopmentNational Center for Computational Toxicology 29
Prioritize List of ~840 Pesticide Actives
Data availability
Toxicological interest
Environmental relevance
Pesticide Registration RecordsPesticide Registration Records
DSSTox File IncidenceDSSTox File Incidence
Office of Research and DevelopmentNational Center for Computational Toxicology 30
Meet minimal HTS phys-chem requirementsSoluble in DMSO / waterNot highly volatileMolecular Weight in approx range [100-1,000]Available in ~pure or standard form with structure
Span diverse structural space
Include clusters of similar chemicals
Prioritize Chemicals for ToxCast Phase I: Chemical Characteristics
Office of Research and DevelopmentNational Center for Computational Toxicology 31
Office of Research and DevelopmentNational Center for Computational Toxicology
Minimum Dose at which specific effects observed(mg/kg/day)
Chemicals
Effects
Office of Research and DevelopmentNational Center for Computational Toxicology
ToxCast HTS Assay Contractors and Collaborators
40
The Home of TFomics TM
attageneattageneattageneattagene
Compound Focus, Inc.a subsidiary of
Nine contracts, one IAG and an MOU provide chemical procurement; hundreds of
biochemical, cellular, tissue and genomic assays; model organisms; and the capacity to
screen up to 10,000 chemicals
41
Multiple concentration (5) data underwayHamner InstitutesPrecision-cutTissue slices
Rat liver, lung, kidney11Tissue Slice
Culture
Multiple concentration (11) data from 2 of 10 assays delivered
NIH Chemical Genomics Center
Nuclear receptor reporter gene assays
Human and rodent10+10+uHTS
22,433265TOTAL
Multiple concentration (3) data underway for 20 chemicalsPhylonixTeratogenesisDanio rerio111Zebrafish
Multiple concentration (10) data deliveredCellumenImaging cytotoxicityHepG2 cells (human liver)111HCS
Multiple concentration (4) data deliveredBioseekCell signaling pathways
Primary human cells878Complex Cell
Culture
Multiple concentration (8) data underwayIVALCytotoxicity, shared metabolism
Human liver, lung, kidney
cells61Cell Co-
Culture
Multiple concentration (8) data deliveredACEA BiosciencesReal time electrical impedance
A549 cells (human lung)Kinetic1Kinetic Cell
Growth
Multiple concentration (5) in rat system underway
IVAL and Expression
AnalysisPCR, microarrays
Hepatocyte-Kupffer co-
culture22,0001Genomics
Single concentration data delivered; multiple concentration to followAttageneNuclear receptor,
transcription factorHepG2 cells
(human liver)672Reporter Gene Assays
Single concentration data delivered; multiple concentration to followNovaScreenEnzyme inhibition,
receptor bindingHuman, rat,
other240240HTS
ToxCast_320 Status 04dec2007SourceCommentAssay Source# Endpoints# AssaysAssay Type
Multiple concentration (5) data underwayHamner InstitutesPrecision-cutTissue slices
Rat liver, lung, kidney11Tissue Slice
Culture
Multiple concentration (11) data from 2 of 10 assays delivered
NIH Chemical Genomics Center
Nuclear receptor reporter gene assays
Human and rodent10+10+uHTS
22,433265TOTAL
Multiple concentration (3) data underway for 20 chemicalsPhylonixTeratogenesisDanio rerio111Zebrafish
Multiple concentration (10) data deliveredCellumenImaging cytotoxicityHepG2 cells (human liver)111HCS
Multiple concentration (4) data deliveredBioseekCell signaling pathways
Primary human cells878Complex Cell
Culture
Multiple concentration (8) data underwayIVALCytotoxicity, shared metabolism
Human liver, lung, kidney
cells61Cell Co-
Culture
Multiple concentration (8) data deliveredACEA BiosciencesReal time electrical impedance
A549 cells (human lung)Kinetic1Kinetic Cell
Growth
Multiple concentration (5) in rat system underway
IVAL and Expression
AnalysisPCR, microarrays
Hepatocyte-Kupffer co-
culture22,0001Genomics
Single concentration data delivered; multiple concentration to followAttageneNuclear receptor,
transcription factorHepG2 cells
(human liver)672Reporter Gene Assays
Single concentration data delivered; multiple concentration to followNovaScreenEnzyme inhibition,
receptor bindingHuman, rat,
other240240HTS
ToxCast_320 Status 04dec2007SourceCommentAssay Source# Endpoints# AssaysAssay Type
Office of Research and DevelopmentNational Center for Computational Toxicology 42
AttageneHeatmap
67 Assays
320
Che
mic
als
Part IIIPart IIIIncorporating SAR Concepts Incorporating SAR Concepts
into ToxCastinto ToxCast
Bioassay DataBioassay Data
ToxRef DB, NTP, IRIS, etc
ToxCast: Multidimensional Data
Biochemical, Cell-based, …HTS Data HTS Data
Chemical StructuresChemical StructuresN
NNH
O
O
NH
O
CH3
CH3
O
N
O
SCl
ClCl
Cl
Cl
O
O
OHP
NHO
S OO
CH3
CH3
CH3
Bioassay DataBioassay Data
Global modeling
SummaryActivity
+/-
Large chemical coverage
Uses no prior chemical knowledge
Calculated descriptors, properties, fragments
Chemical StructuresChemical Structures
Structure-Activity Approaches to Toxicity Prediction
O
N
O
SCl
ClCl
N
NNH
O
O
NH
O
CH3
CH3
Cl
Cl
O
O
OHP
NHO
S OO
CH3
CH3
CH3
Bioassay DataBioassay Data
Chemical Class-Based Modeling
SummaryActivity
+/-
Limited chemical coverage
Heavy reliance on perceived “chemical similarity”
Assumes chemical class equates to MOA
Calculated descriptors, properties, fragments
N
NNH
O
O
NH
O
CH3
CH3
Cl
Cl
O
O
OHP
NHO
S OO
CH3
CH3
CH3
Structure-Activity Approaches to Toxicity Prediction
O
N
O
SCl
ClCl
Oncologic Carcinogenicity Estimation Expert System:Chemical Class – Based Prediction Modules
Acyl and Benzoyl Halide Type Compounds Acrylate Reactive Functional GroupsAcrylamide Reactive Functional GroupsAflatoxin Type CompoundsAldehyde Type CompoundsAliphatic Azo and Azoxy Type CompoundsAlkanesulfonoxy Ester Type CompoundsAlkyl Sulfate and Alkyl Alkanesulfonate Type CompoundsAromatic Amine Type CompoundsAnhydride Type CompoundsArylazo Type CompoundsAryldiazonium SaltsC-Nitroso and Oxime Type CompoundsCarbamate Type CompoundsCarbamyl Halide Type CompoundsCoumarin and Furocoumarin Type Compounds Dicarbonyl Type CompoundsEpoxide Reactive Functional GroupsEthyleneimine Reactive Functional GroupsHaloalkylamine Reactive Functional GroupsHaloether Reactive Functional GroupsHalogenated Aromatic Hydrocarbon Type Compounds Halogenated Cycloalkane Type Compounds
ortho-Halogenated Heterocyclic Type CompoundsHalogenated Nitroaromatic Type CompoundHalogenated Linear Aliphatic Type CompoundsHalothioether Reactive Functional GroupsHydrazo Type CompoundsReactive Ketone Reactive Functional GroupsLactone Type Reactive Functional GroupsNitrosamide Type CompoundsNitrosamine Type CompoundsNitroalkane and Nitroalkene Type CompoundsNitrogen Mustard Reactive Functional GroupsOrganophosphorus Type CompoundPeroxide Type CompoundsPhenol Type CompoundsPhosgene Type CompoundsPolycyclic Aromatic Hydrocarbons -HeterocyclicPolycyclic Aromatic Hydrocarbons -Homocyclic Siloxane Type CompoundsReactive Sulfone Reactive Functional GroupsSulfur Mustard Reactive Functional GroupsSultone Reactive Functional GroupsThiocarbamate Type CompoundsThiocarbonyl Type CompoundsTriazene Type CompoundsUrea Type Compounds
Organophosphorus Type Compound
P R3R1
R2
X
P
R3R1
R2
PN
R1
R2
CH2CH2Cl
phosphate-type phosphine-type
cyclophosphamide-type
R1/R2/R3 = alkyl groups or aryl groups
P X-alkyl or X-aryl where X is oxygen, sulfur or in some cases nitrogen, linking the phosphorus to the alkyl/aryl group
Combining SAR and Biofunctional Information in Oncologic: Predicting Carcinogenicity of Organophosphates
-
+
-
LM+
L
High acute toxicity?
Increase serumalkaline phosphatase?
Mar+
-M
LM
-HM
+
Woo et al. (1996) Environ. Carc. & Ecotox. Revs., C14:1-42
In vitro genotoxicity?
In vivogenotoxicity?
Organophosphate
Oncologic Carcinogenicity Estimation Expert System:Chemical Class – Based Prediction Modules
Acyl and Benzoyl Halide Type Compounds Acrylate Reactive Functional GroupsAcrylamide Reactive Functional GroupsAflatoxin Type CompoundsAldehyde Type CompoundsAliphatic Azo and Azoxy Type CompoundsAlkanesulfonoxy Ester Type CompoundsAlkyl Sulfate and Alkyl Alkanesulfonate Type CompoundsAromatic Amine Type CompoundsAnhydride Type CompoundsArylazo Type CompoundsAryldiazonium SaltsC-Nitroso and Oxime Type CompoundsCarbamate Type CompoundsCarbamyl Halide Type CompoundsCoumarin and Furocoumarin Type Compounds Dicarbonyl Type CompoundsEpoxide Reactive Functional GroupsEthyleneimine Reactive Functional GroupsHaloalkylamine Reactive Functional GroupsHaloether Reactive Functional GroupsHalogenated Aromatic Hydrocarbon Type Compounds Halogenated Cycloalkane Type Compounds
ortho-Halogenated Heterocyclic Type CompoundsHalogenated Nitroaromatic Type CompoundHalogenated Linear Aliphatic Type CompoundsHalothioether Reactive Functional GroupsHydrazo Type CompoundsReactive Ketone Reactive Functional GroupsLactone Type Reactive Functional GroupsNitrosamide Type CompoundsNitrosamine Type CompoundsNitroalkane and Nitroalkene Type CompoundsNitrogen Mustard Reactive Functional GroupsOrganophosphorus Type CompoundPeroxide Type CompoundsPhenol Type CompoundsPhosgene Type CompoundsPolycyclic Aromatic Hydrocarbons -HeterocyclicPolycyclic Aromatic Hydrocarbons -Homocyclic Siloxane Type CompoundsReactive Sulfone Reactive Functional GroupsSulfur Mustard Reactive Functional GroupsSultone Reactive Functional GroupsThiocarbamate Type CompoundsThiocarbonyl Type CompoundsTriazene Type CompoundsUrea Type Compounds
ToxRef DB provides detailed hierarchical toxicity data model
Linkage to chemical structures enables flexible SAR and data mining
Bioassay DataBioassay Data
Use of Bioassay Activity Categories in SAR
SAR modeling
SummaryActivity
+/-
In vivoActivityClusters SAR
Chemical StructuresChemical StructuresN
NNH
O
O
NH
O
CH3
CH3
Cl
Cl
O
O
OHP
NHO
S OO
CH3
CH3
CH3
O
N
O
SCl
ClCl
ToxRefDB Profiling of Liver Effects for Pesticides
Activity Profile is refined “Endpoint” for
SAR modeling
Bioassay DataBioassay Data
Biochemical, Cell-based, …HTS Data HTS Data
ToxRef DB, NTP, IRIS, etc
Structure-Analog Approaches
SARSAR
Chemical StructuresChemical StructuresN
NNH
O
O
NH
O
CH3
CH3
O
N
O
SCl
ClCl
Cl
Cl
O
O
OHP
NHO
S OO
CH3
CH3
CH3
ToxCast: Data Publication & Exploration
Summarized endpoint data for use in SAR modeling
HTS data
Register ToxCast Substances in PubChem
ToxCast_320
Bioactivity Analysis:
Retrieve all bioassay data in PubChem for ToxCast_320
482 Bioassays45 Compounds
Selected bioassays
Show details for 7 Bioassays
Structure-ActivityBioactivity Analysis:
7 bioassays, 45 Actives
View Bioassay Profile by Structure Similarity Cluster
View bioassay profile of structure similarity cluster
Similar Bioassay Profile across structure space
Office of Research and DevelopmentNational Center for Computational Toxicology
HTS data offers:activity-based clustering of chemicalsbiofunctional information for refining class-based SARnew “biological” descriptors for global SAR
In vivo bioassay profiles expanding “endpoints” for SAR
Structure-analog approaches coupled with HTS and ToxRefin vivo data offer powerful data mining tools
Public tools for structure-based exploration of data becoming available
Incorporating SAR Concepts into ToxCast: Conclusions
Acknowledgements:EPA DSSTox Team:
Maritja Wolf (DSSTox) and Tom Transue (Structure-browser) – Lockheed Martin, Contractors to the US EPA