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Predicting Indirect DNA Damage by Simulating Metabolic Activation of Chemicals

Predicting Indirect DNA Damage by Simulating Metabolic Activation of Chemicals. Ovanes Mekenyan, Milen Todorov, Ksenia Gerova. Laboratory of Mathematical Chemistry, Bulgaria. 2 nd McKim Workshop on Reducing Data Redundancy in Cancer Assessment Baltimore, 8-10 May 2012. Outlook Goal Methods

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Predicting Indirect DNA Damage by Simulating Metabolic Activation of Chemicals

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  1. Predicting Indirect DNA Damage by Simulating Metabolic Activation of Chemicals Ovanes Mekenyan, Milen Todorov, Ksenia Gerova Laboratory of Mathematical Chemistry, Bulgaria 2nd McKim Workshop on Reducing Data Redundancy in Cancer Assessment Baltimore, 8-10 May 2012

  2. Outlook • Goal • Methods • Data • Predicting: • AMES mutagenicity without metabolic activation • AMES metabolic activation chemicals negative as parents • Illustrating metabolic activation • False positives after metabolic activation • False negatives after metabolic activation • Conclusions

  3. Outlook • Goal • Methods • Data • Predicting: • AMES mutagenicity without metabolic activation • AMES metabolic activation chemicals negative as parents • Illustrating metabolic activation • False positives after metabolic activation • False negatives after metabolic activation • Conclusions

  4. Goal • Predicting indirect DNA damage in the General Workflow Diagram for screening large chemicals inventories for carcinogenicity

  5. General Flow Diagram for Screening Large Inventories for carcinogenicity Inventory Classify as Genotoxic Bacterial Mutagen High Carcinogenicity Potential? High Priority for Tumor Promotion Assays No-Threshold Risk Assessment Y Direct DNA Reactive Chemicals Ames Positive w/o S9 Y Y N Generate metabolites Y Y DNA reactive Metabolites Ames Positive with S9 Intermediate Priority for Tumor Promotion Assays Threshold Effect Risk Assessment Protein Reactive Chemicals CTA Assays for Nongenotoxic/ Epigenetic Chemicals Receptor-Based Screening Low Carcinogenit Potential

  6. General Flow Diagram for Screening Large Inventories for carcinogenicity Inventory Protein OASIS Y ChromAb ? MicroNucl ? N Direct DNA reactive Ames Positive w/o S9 Y Bacterial Mutagen In vivo Mammal Tests Y N Generate metabolites Y Y Indirect DNA reactive Ames Positive with S9 Refine TIMES/ Structural alerts ChromAb ? MicroNucl ? N Return for further screening Protein Reactive Oxidative stress? Receptor-Based Epigenetic Screen Low Carcinogenit Potential

  7. Outlook • Goal • Methods • Data • Predicting: • AMES mutagenicity without metabolic activation • AMES metabolic activation chemicals negative as parents • Illustrating metabolic activation • False positives after metabolic activation • False negatives after metabolic activation • Conclusions

  8. Methods: • QSAR Toolbox profiles for DNA binding • DNA binding profile by OASIS • DNA binding profile by OECD

  9. Illustration of the DNA binding profile of the QSAR Toolbox

  10. Known DNA (covalent) binding mechanisms

  11. Known DNA (covalent) binding mechanisms

  12. Structural boundaries of the category

  13. Structural boundaries of the category

  14. Methods: • QSAR Toolbox profiles for DNA binding • DNA binding profile by OASIS • DNA binding profile by OECD • TIMES Metabolic simulator for rat liver S9

  15. OASIS Metabolic Simulator • Prioritized list of non-enzymatic (abiotic) and enzymatic molecular transformations; • Molecular transformations are characterized by: • Source and product fragments; • Inhibiting “masks” preventing the application of metabolic reactions if necessary; • Substructure-matching software engine applies the simulated biochemical • Reproduces the documented metabolic pathways and toxicity endpoint resulting from metabolic activation of chemicals 26

  16. Illustration the OASIS Metabolic Simulators (extract from the Rat in vivo metabolism simulator)

  17. Substrate Principle transformations Metabolites Simulator of metabolism Epoxidation Aliphatic C-oxidation Aliphatic C-oxidation Epoxide Hydration Aliphatic C-oxidation O-Glucuronidation

  18. Substrate Principle transformations Metabolites Simulator of metabolism Epoxidation Aliphatic C-oxidation P= 0.97 Aliphatic C-oxidation Epoxide Hydration P= 0.96 P= 0.95 P= 0.94 Aliphatic C-oxidation P= 0.93 O-Glucuronidation P= 0.90

  19. Substrate Principle transformations Metabolites - Isopropenylbenzene Epoxidation Aliphatic C-oxidation P= 0.97 Aliphatic C-oxidation Epoxide Hydration P= 0.96 P= 0.95 P= 0.94 Aliphatic C-oxidation P= 0.93 O-Glucuronidation P= 0.90

  20. Substrate Principle transformations Metabolites - Isopropenylbenzene Epoxidation Aliphatic C-oxidation P= 0.97 Aliphatic C-oxidation Match? - No! Epoxide Hydration P= 0.96 P= 0.95 P= 0.94 Aliphatic C-oxidation P= 0.93 O-Glucuronidation P= 0.90

  21. Substrate Principle transformations Metabolites - Isopropenylbenzene Epoxidation Aliphatic C-oxidation P= 0.97 Aliphatic C-oxidation Epoxide Hydration P= 0.96 P= 0.95 P= 0.94 Aliphatic C-oxidation P= 0.93 O-Glucuronidation P= 0.90

  22. Substrate Principle transformations Metabolites - Isopropenylbenzene Epoxidation Aliphatic C-oxidation P= 0.97 Aliphatic C-oxidation Epoxide Hydration P= 0.96 Match? - No! P= 0.95 P= 0.94 Aliphatic C-oxidation P= 0.93 O-Glucuronidation P= 0.90

  23. Substrate Principle transformations Metabolites - Isopropenylbenzene Generated map Aliphatic C-oxidation P= 0.97 Aliphatic C-oxidation Epoxidation 1.1 Epoxide Hydration P= 0.96 Epoxidation RESULT P= 0.95 Match? - Yes! P= 0.94 Aliphatic C-oxidation P= 0.93 O-Glucuronidation P= 0.90

  24. Substrate Principle transformations Metabolites - Isopropenylbenzene Epoxidation Generated map Aliphatic C-oxidation P= 0.97 C-oxidation Epoxidation 1.2 1.1 Epoxide Hydration P= 0.96 P= 0.95 Aliphatic C-oxidation RESULT P= 0.94 Match? - Yes! Aliphatic C-oxidation P= 0.93 O-Glucuronidation P= 0.90

  25. Substrate Principle transformations Metabolites - Isopropenylbenzene Generated map Aliphatic C-oxidation P= 0.97 C-oxidation Epoxidation 1.1 1.2 Epoxide Hydration P= 0.96 Epoxidation P= 0.95 Aliphatic C-oxidation P= 0.94 Aliphatic C-oxidation Match? - No! P= 0.93 O-Glucuronidation P= 0.90

  26. Substrate Principle transformations Metabolites - Isopropenylbenzene Generated map Aliphatic C-oxidation P= 0.97 C-oxidation Epoxidation 1.1 1.2 Epoxide Hydration P= 0.96 Epoxidation P= 0.95 Aliphatic C-oxidation P= 0.94 Aliphatic C-oxidation P= 0.93 O-Glucuronidation P= 0.90 Match? - No!

  27. Substrate Principle transformations Metabolites - Metabolite 1.1 Generated map Aliphatic C-oxidation Match? - No! P= 0.97 C-oxidation Epoxidation 1.1 1.2 Epoxide Hydration P= 0.96 Epoxidation P= 0.95 Aliphatic C-oxidation P= 0.94 Aliphatic C-oxidation P= 0.93 O-Glucuronidation P= 0.90

  28. Substrate Principle transformations Metabolites - Metabolite 1.1 Hydration Generated map 2.1 Aliphatic C-oxidation P= 0.97 Epoxidation C-oxidation 1.1 1.2 Epoxide Hydration RESULT P= 0.96 Match? - Yes! Epoxidation P= 0.95 Aliphatic C-oxidation P= 0.94 Aliphatic C-oxidation P= 0.93 O-Glucuronidation P= 0.90

  29. Substrate Principle transformations Metabolites - Metabolite 2.1 Generated map Aliphatic C-oxidation RESULT C-oxidation P= 0.97 Match? - Yes! Epoxidation C-oxidation 3.1 1.1 1.2 1.1 1.2 Epoxide Hydration P= 0.96 Hydration 2.1 Epoxidation P= 0.95 Aliphatic C-oxidation P= 0.94 Aliphatic C-oxidation P= 0.93 O-Glucuronidation P= 0.90

  30. Substrate Principle transformations Metabolites - Metabolite 1.2. Generated map Aliphatic C-oxidation RESULT C-oxidation P= 0.97 Match? - Yes! Epoxidation C-oxidation 3.1 1.1 1.2 1.1 1.2 Epoxide Hydration P= 0.96 Hydration C-oxidation 2.2 2.1 Epoxidation P= 0.95 Aliphatic C-oxidation P= 0.94 Aliphatic C-oxidation P= 0.93 O-Glucuronidation P= 0.90

  31. Substrate Principle transformations Metabolites - Metabolite 2.2. Generated map Aliphatic C-oxidation C-oxidation P= 0.97 Match? - No! Epoxidation C-oxidation 3.1 1.1 1.2 1.1 1.2 Epoxide Hydration P= 0.96 Hydration C-oxidation 2.2 2.1 Epoxidation P= 0.95 Aliphatic C-oxidation P= 0.94 Aliphatic C-oxidation P= 0.93 O-Glucuronidation P= 0.90

  32. Substrate Principle transformations Metabolites - Metabolite 2.2. Generated map Aliphatic C-oxidation C-oxidation P= 0.97 Epoxidation C-oxidation 3.1 1.1 1.2 1.1 1.2 Epoxide Hydration P= 0.96 Match? - No! Hydration C-oxidation 2.2 2.1 Epoxidation P= 0.95 Aliphatic C-oxidation P= 0.94 Aliphatic C-oxidation P= 0.93 O-Glucuronidation P= 0.90

  33. Substrate Principle transformations Metabolites - Metabolite 2.2. Generated map Aliphatic C-oxidation C-oxidation P= 0.97 Epoxidation C-oxidation 3.1 1.1 1.2 1.1 1.2 Epoxide Hydration P= 0.96 Hydration C-oxidation 2.2 2.1 Epoxidation Match? - Yes! (Conjugated aldehyde group prevents epoxidation) Aliphatic C-oxidation P= 0.94 Aliphatic C-oxidation P= 0.93 O-Glucuronidation P= 0.90

  34. Substrate Principle transformations Metabolites - Metabolite 2.2. Generated map Aliphatic C-oxidation C-oxidation P= 0.97 Epoxidation C-oxidation 3.1 1.1 1.2 1.1 1.2 Epoxide Hydration P= 0.96 Hydration C-oxidation 2.2 2.1 Epoxidation P= 0.95 Aliphatic C-oxidation P= 0.94 Match? - No! Aliphatic C-oxidation P= 0.93 O-Glucuronidation P= 0.90

  35. Substrate Principle transformations Metabolites - Metabolite 2.2. Generated map Aliphatic C-oxidation C-oxidation P= 0.97 Epoxidation C-oxidation 3.1 1.1 1.2 1.1 1.2 Epoxide Hydration P= 0.96 Hydration C-oxidation 2.2 2.1 Epoxidation P= 0.95 Aliphatic C-oxidation C-oxidation 3.2 P= 0.94 Aliphatic C-oxidation RESULT Match? - Yes! P= 0.93 O-Glucuronidation P= 0.90

  36. Metabolic Simulators Bridging the “Parent Gap” Library of Biotransformations & Abiotic Reactions Parent Chemicals Algorithm for optimizing Transformation Probabilities (Rate constants) Metabolic Simulators Documented Partial Maps Metabolic Maps and Reactivity Profiles Virtual metabolism uses a heuristic substructure search engine applied to a hierarchy of possible molecular transformations

  37. Simulated Metabolic Activation of 2-Acetylaminofluorene (AMES mutagenicity in Rat liverS9) Documented

  38. The OASIS Simulators of Mammalian Metabolism • Liver S9 metabolism • Different level of biological organisms (US EPA) • Rat liver subcellular (microsomal) • Rat liver cellular (in vitro) • Organism (in vivo) • In vivo metabolism – rat liver (in vivo MNT) • In vivo detoxification logic • In vivo bioactivation • Skin metabolism

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