AN EVALUATION OF THE OECD QSAR TOOLBOX
PROFILERS FOR IDENTIFYING DNA REACTIVE AND
GENOTOXIC CHEMICALSTerry SchultzProfessor Emeritus, The University of Tennessee-Knoxville & Secretariat, OECD, Paris
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Outlook• The Toolbox• 1st Exercise: Goal, Methods & Results• 2nd Exercise: Goal, Methods & Results• 3rd Exercise: Goal, Methods & Results• Conclusions
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The OECD QSAR Toolbox The seminal feature of the Toolbox is its ability to quickly evaluate all members of a category for common toxicological behaviour or consistent trends within important regulatory endpoint data.
This is done by first profiling the chemical by type, class or defined hazard identifiers and then selecting a category or subcategory.
This feature often links the chemicals in the category to a single mechanism or mode of action.
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Advantages of the Profile/Category Approach
1) it shifted emphasis to intrinsic chemical activity,
2) it allows for entire categories of chemicals to be assessed when only a few members are tested,
3) it allows for filling data gaps using read-across and trend analysis, and not just (Q)SAR models, and
4) it enables defensible hazard assessment through mechanistic comparisons without testing.
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1st McKim Workshop on Reducing Data Redundancy in Cancer Assessment
The participants agreed that chemical which are QSAR predicted to be DNA reactive (+) and are also AMES test positive (+) would be chemicals of “very high concern” for the Rodent Cancer Assay.
But you can have direct or indirect DNA-reactivity and AMES positive w/o S9 and w/ S9.
So the first exercise was to look for members of the direct DNA-reactivity and AMES positive w/o S9 category.
Inventory
Direct DNA
reactive
Indirect DNA
reactive
Ames Positive with S9
Ames Positive w/o S9
Bacterial Mutagen
Chrom Ab ?
MicroNucl ?
Protein OASIS
Generate metabolites
N
Y
Y
Receptor-Based Epigenetic
Screen
Low Carcinogenicity
Potential
Y
Chrom Ab ?
MicroNucl ?
Refine TIMES/Structural alerts
N
YY
N
Oxidative stress?
In vivo Mammal
Tests
Protein Reactive
Return for further screening
General Flow Diagram for Screening Large Inventories for Carcinogenicity
Focus Area of this Discussion
Inventory
Direct DNA
reactive
Indirect DNA
reactive
Ames Positive with S9
Ames Positive w/o S9
Bacterial Mutagen
Chrom Ab ?
MicroNucl ?
Protein OASIS
Generate metabolites
N
Y
Y
Receptor-Based Epigenetic
Screen
Low Carcinogenicity
Potential
Y
Chrom Ab ?
MicroNucl ?
Refine TIMES/Structural alerts
N
YY
N
Oxidative stress?
In vivo Mammal
Tests
Protein Reactive
Return for further screening
Chemicalinput Profiling
CategoryDefinition
Fillingdata gap Report
Endpoints
Toolbox Work Flow
OASIS databasefor AMES mutagenicity
QSAR Toolbox profiles for DNA binding by OASIS by OECD Direct
DNA Reactive & Ames Positive w/o S9
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Factors Which Effect Makeup of Chemical CategoryHow one defines the initial target chemical.For Example: Using CH4 as the initial target chemical and profiling for chemicals containing a C-atom one retrieves 8684 chemicals from the Toolbox.Whether one used DNA-binding OASIS or DNA-binding OECD.This impacts the number and definitions of the SAs which are fired.
Inventory
Direct DNA
reactive
Indirect DNA
reactive
Ames Positive with S9
Ames Positive w/o S9
Bacterial Mutagen
Chrom Ab ?
MicroNucl ?
Protein alerts?
Generate metabolites
N
Y
Y
Receptor-Based
Epigenetic Screen
Low Carcinogenit Potential
Y
2832
Chrom Ab ?
MicroNucl ?
N
YY
N
Oxidative stress?
In vivo Mammal
Tests
Protein Reactive
Return for further screening
Refine TIMES/Structural alerts
N
Y
Initial Database
Inventory
Direct DNA
reactive
Indirect DNA
reactive
Ames Positive with S9
Ames Positive w/o S9
Bacterial Mutagen
Chrom Ab ?
MicroNucl ?
Protein alerts?
Generate metabolites
N
Y
Y
Receptor-Based
Epigenetic Screen
Low Carcinogenit Potential
Y
2832
745
Chrom Ab ?
MicroNucl ?
N
YY
N
Oxidative stress?
In vivo Mammal
Tests
Protein Reactive
Return for further screening
Refine TIMES/Structural alerts
N
Y
OASIS Direct DNA Binder in Initial Database
Inventory
Direct DNA
reactive
Indirect DNA
reactive
Ames Positive with S9
Ames Positive w/o S9
Bacterial Mutagen
Chrom Ab ?
MicroNucl ?
Protein alerts?
Generate metabolites
N
Y
Y
Receptor-Based
Epigenetic Screen
Low Carcinogenit Potential
Y
2832
745
Chrom Ab ?
MicroNucl ?
N
YY
N
Oxidative stress?
In vivo Mammal
Tests
Protein Reactive
Return for further screening
Refine TIMES/Structural alerts
N
307
Y
OASIS Direct DNA Binders & Ames Positive w/o S9 in Initial Database
OASIS (+/+) category
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020406080
100120140
Distribution of 307 across classes
134
28 25 24 19 17 16 15 13 12 8 8 7 6
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DNA-binding OECD Eliminated:
Nitro Aromatic Compounds, Aromatic Amines, PAHs etc.Classes where it is unclear that a bacterial test would mimic the reactions well.
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2nd Exercise
Designed to look for which members of the +/+ category have been evaluated in a Rodent Cancer Assay (RCA) and to report what classes they represent.
Chemicalinput Profiling
CategoryDefinition
Fillingdata gap
Report
Endpoints
Toolbox Work Flow
CPDB Carcinogenic Potency Data Base and/or ISSCAN Carcinogenicity & mutagenicitydata base
Direct DNA Reactive &
Ames Positive w/o S9
Inventory
Direct DNA
reactive
Indirect DNA
reactive
Ames Positive with S9
Ames Positive w/o S9
Bacterial Mutagen
Chrom Ab ?MicroNucl
?
Protein alerts?
Generate metabolites
N
Y
Y
Receptor-Based
Epigenetic Screen
Low Carcinogenit Potential
Y
Chrom Ab ?
MicroNucl ?
N
YY
N
Oxidative stress?
In vivo Mammal
Tests
Protein Reactive
Return for further screening
Refine TIMES/Structural alerts
N
307
243No data
53Positive
11Negative
Carcinogenicity Data
Y
RCA for +/+ Category
Carcinogenicity of 307 +/+ chemicals
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020406080
100120140160
17 3 5 4 2 1 3 1 4 3 3 1 1 3 1 1 1 0 1 2 0 0 1 0 0 3 0 0 0
Distribution of 53 compounds across carcinogenicity classes
CounterPositive carcinog
134
28 25 24 19 17 16 15 13 12 8 8 7 6
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3RD EXERCISE
Designed to look at which DNA-reactions are represented by the (+/+) chemicals that are also positive in the RCA.
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Major Classes
Aliphatic Halides [CX]; 17 CRA positive; 2 CRA negative (1-chlorobutane; 2-chloroethanol)Stressed Hetero-Ring Systems(e.g. C1CO1); 13 CRA positive
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Minor Classes
SN2 addition at an sp3 carbon atom sulfates and sulfonates; 4 CRA positivePhosphorates; 2 CRA positiveHydazines; 1 CRA positive
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SummaryIn this discussion we used a hypothesis testing scheme with the QSAR Toolbox; the DNA-binding profiler generate the initial hypothesis and an in vitro test (AMES testing w/o S9) tested the hypotheses.
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Summary
We maintain that chemicals that pass this hypothesis testing are “chemicals of high concern” for cancer.
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SummaryWe then asked which of these chemicals of high concern have been tested in the RCA?What are the DNA reactions covered by this suite of RCA-tested chemical?
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ConclusionThere is experimental evidence that there are opportunities to reduce the use of RCA, especially for chemicals with an aliphatic halide or stressed hetero-ring sub-structure.
