Mammary carcinogen-protein binding potentials: novel and biologically relevant structure–activity relationship model descriptors

Abstract

Previously, SAR models for carcinogenesis used descriptors that are essentially chemical descriptors. Herein we report the development of models with the cat-SAR expert system using biological descriptors (i.e., ligand–receptor interactions) rat mammary carcinogens. These new descriptors are derived from the virtual screening for ligand–receptor interactions of carcinogens, non-carcinogens, and mammary carcinogens to a set of 5494 target proteins. Leave-one-out validations of the ligand mammary carcinogen–non-carcinogen model had a concordance between experimental and predicted results of 71%, and the mammary carcinogen–non-mammary carcinogen model was 72% concordant. The development of a hybrid fragment–ligand model improved the concordances to 85 and 83%, respectively. In a separate external validation exercise, hybrid fragment–ligand models had concordances of 81 and 76%. Analyses of example rat mammary carcinogens including the food mutagen and oestrogenic compound PhIP, the herbicide atrazine, and the drug indomethacin; the ligand model identified a number of proteins associated with each compound that had previously been referenced in Medline in conjunction with the test chemical and separately with association to breast cancer. This new modelling approach can enhance model predictivity and help bridge the gap between chemical structure and carcinogenic activity by descriptors that are related to biological targets.

Keywords:

• breast cancer
• structure–activity relationship studies
• environmental carcinogenesis toxicology
• virtual screening
• predictive toxicology

Acknowledgments

This research was supported by the National Institutes of Health (P20 RR018733) and the James Graham Brown Cancer Center, University of Louisville, USA.