Abstract
The Ames mutagenicity assay is a long established in vitro test to measure the mutagenicity potential of a new chemical used in regulatory testing globally. One of the key computational approaches to modeling of the Ames assay relies on the formation of chemical categories based on the different electrophilic compounds that are able to react directly with DNA and form a covalent bond. Such approaches sometimes predict false positives, as not all Michael acceptors are found to be Ames-positive. The formation of such covalent bonds can be explored computationally using density functional theory transition state modeling. We have applied this approach to mutagenicity, allowing us to calculate the activation energy required for α,β-unsaturated carbonyls to react with a model system for the guanine nucleobase of DNA. These calculations have allowed us to identify that chemical compounds with activation energies greater than or equal to 25.7 kcal/mol are not able to bind directly to DNA. This allows us to reduce the false positive rate for computationally predicted mutagenicity assays. This methodology can be used to investigate other covalent-bond-forming reactions that can lead to toxicological outcomes and learn more about experimental results.
Highlights
Cancer is a toxicological end point of much concern in the development of new chemical compounds
Activation energy barriers have been calculated for the reaction between a model nitrogen nucleophile, representing a DNA base, and electrophilic Michael acceptors
This methodology can be used to predict the Ames test results for new α,β-unsaturated carbonyls, with those having activation energies greater than 25.7 kcal/ mol expected to be unable to directly bind to DNA and to be Ames-negative. α,β-Unsaturated carbonyls with activation energies less than 22.0 kcal/mol would be expected to bind directly to DNA and to be Ames-positive
Summary
Cancer is a toxicological end point of much concern in the development of new chemical compounds. Cancer can be caused by mutagenic chemicals, those that have the ability to directly alter the DNA of an exposed organism.[1−3] The ability of a compound to be mutagenic is typically assessed in vitro using methods including the Ames mutagenicity assay.[1−4] This assay reports chemicals as mutagens if they produce a dosedependent increase in the number of revertant Salmonella colonies. In order to test this, a Salmonella strain lacking the ability to generate histidine required for growth is incubated in a medium containing minimal histidine both in the presence of the possible mutagen and without it as a control. In the presence of a mutagenic substance, the Salmonella are able to revert to a state in which they are able to synthesize the required histidine, resulting in an increased growth rate. The Ames test is widely used as an early screen in compound development
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