title: PROXIMAL: a method for Prediction of Xenobiotic Metabolism.
abstract: BACKGROUND
  Contamination of the environment with bioactive chemicals has emerged as a potential public health risk. These substances that may cause distress or disease in humans can be found in air, water and food supplies. An open question is whether these chemicals transform into potentially more active or toxic derivatives via xenobiotic metabolizing enzymes expressed in the body. We present a new prediction tool, which we call PROXIMAL (Prediction of Xenobiotic Metabolism) for identifying possible transformation products of xenobiotic chemicals in the liver. Using reaction data from DrugBank and KEGG, PROXIMAL builds look-up tables that catalog the sites and types of structural modifications performed by Phase I and Phase II enzymes. Given a compound of interest, PROXIMAL searches for substructures that match the sites cataloged in the look-up tables, applies the corresponding modifications to generate a panel of possible transformation products, and ranks the products based on the activity and abundance of the enzymes involved.
  
  
  RESULTS
  PROXIMAL generates transformations that are specific for the chemical of interest by analyzing the chemical's substructures. We evaluate the accuracy of PROXIMAL's predictions through case studies on two environmental chemicals with suspected endocrine disrupting activity, bisphenol A (BPA) and 4-chlorobiphenyl (PCB3). Comparisons with published reports confirm 5 out of 7 and 17 out of 26 of the predicted derivatives for BPA and PCB3, respectively. We also compare biotransformation predictions generated by PROXIMAL with those generated by METEOR and Metaprint2D-react, two other prediction tools.
  
  
  CONCLUSIONS
  PROXIMAL can predict transformations of chemicals that contain substructures recognizable by human liver enzymes. It also has the ability to rank the predicted metabolites based on the activity and abundance of enzymes involved in xenobiotic transformation.
authors.affiliation: Department of Computer Science, Tufts University, 161 College Ave., Medford, MA, 02155, USA. Mona.Yousofshahi@tufts.edu.
authors.forename: Mona
authors.initials: M
authors.lastname: Yousofshahi
authors.affiliation: Department of Chemical and Biological Engineering, Tufts University, Medford, MA, USA. Sara.Manteiga@tufts.edu.
authors.forename: Sara
authors.initials: S
authors.lastname: Manteiga
authors.affiliation: Department of Chemical and Biological Engineering, Tufts University, Medford, MA, USA. Charwu08@gmail.com.
authors.forename: Charmian
authors.initials: C
authors.lastname: Wu
authors.affiliation: Department of Chemical and Biological Engineering, Tufts University, Medford, MA, USA. Kyongbum.Lee@tufts.edu.
authors.forename: Kyongbum
authors.initials: K
authors.lastname: Lee
authors.affiliation: Department of Computer Science, Tufts University, 161 College Ave., Medford, MA, 02155, USA. Soha@cs.tufts.edu.|Department of Chemical and Biological Engineering, Tufts University, Medford, MA, USA. Soha@cs.tufts.edu.
authors.forename: Soha
authors.initials: S
authors.lastname: Hassoun
mesh_terms: D001559:Benzhydryl Compounds / Q000378:metabolism; D001713:Biphenyl Compounds / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D004798:Enzymes / Q000378:metabolism; D006801:Humans; D050216:Metabolic Detoxication, Phase I; D050217:Metabolic Detoxication, Phase II; D010636:Phenols / Q000378:metabolism; D015262:Xenobiotics / Q000378:metabolism*; D000098826:Bisphenol A Compounds
chemical_list: D001559:Benzhydryl Compounds; D001713:Biphenyl Compounds; D004798:Enzymes; D010636:Phenols; D015262:Xenobiotics; C006780:bisphenol A; D000098826:Bisphenol A Compounds; C006983:4-chlorobiphenyl