Identification of structural features and associated mechanisms of action for carcinogens in rats

A set of chemicals tested for carcinogenicity in rats that have been analyzed in the Carcinogenic Potency Database (CPDB) was subjected to CASE/MULTICASE (a computer-automated structure evaluation system) structure-activity relationship (SAR) analyses. This SAR system identifies structural features of chemicals in a learning set that are associated with a predefined activity and produces an SAR model based on these characteristics. The rat CPDB used in this study consisted of 745 chemicals, 383 of which are carcinogens, 14 marginally active carcinogens (i.e., chemicals that require a relatively high dose to induce carcinogenesis) and 348 are non-carcinogens. In an internal prediction analysis where CASE/MULTICASE 'predicted' the activity of chemicals in the learning set, the system was able to achieve a concordance between experimental and predicted results of 95%. This indicates that the program is able to adequately assess the chemicals in the database. In a 10-fold cross-validation study where 10 disjoint sets of 10% of the chemicals were removed from the database and the remaining 90% of the chemicals were used as a learning set, CASE/MULTICASE was able to achieve a concordance between experimental and predicted results of 64%. Using a modified validation process designed to investigate the predictivity of a more focused SAR model, the system was able to achieve a concordance of 71% between experimental and predicted results. Among the major biophores identified by CASE/MULTICASE as associated with cancer causation in rats, several are derived from electrophilic or potentially electrophilic compounds (e.g., aromatic amines, nitrogen mustards, isocyanates, epoxides). Other biophores however are derived from chemicals seemingly devoid of actual or potential DNA-reactivity and as such may represent structural features of non-genotoxic carcinogens.