title: Precursors for cytochrome P450 profiling breath tests from an in silico screening approach.
abstract: The family of cytochrome P450 enzymes (CYPs) is a major player in the metabolism of drugs and xenobiotics. Genetic polymorphisms and transcriptional regulation give a complex patient-individual CYP activity profile for each human being. Therefore, personalized medicine demands easy and non-invasive measurement of the CYP phenotype. Breath tests detect volatile organic compounds (VOCs) in the patients' exhaled air after administration of a precursor molecule. CYP breath tests established for individual CYP isoforms are based on the detection of (13)CO2 or (14)CO2 originating from CYP-catalyzed oxidative degradation reactions of isotopically labeled precursors.We present an in silico work-flow aiming at the identification of novel precursor molecules, likely to result in VOCs other than CO2 upon oxidative degradation as we aim at label-free precursor molecules. The ligand-based work-flow comprises five parts: (1) CYP profiling was encoded as a decision tree based on 2D molecular descriptors derived from established models in the literature and validated against publicly available data extracted from the DrugBank. (2) Likely sites of metabolism were identified by reactivity and accessibility estimation for abstractable hydrogen radical. (3) Oxidative degradation reactions (O- and N-dealkylations) were found to be most promising in the release of VOCs. Thus, the CYP-catalyzed oxidative degradation reaction was encoded as SMIRKS (a programming language style to implement reactions based on the SMARTS description) to enumerate possible reaction products. (4) A quantitative structure property relation (QSPR) model aiming to predict the Henry constant H was derived from data for 488 organic compounds and identifies potentially VOCs amongst CYP reaction products. (5) A blacklist of naturally occurring breath components was implemented to identify marker molecules allowing straightforward detection within the exhaled air.Evident oxidative degradation reactions served as test case for the screening approach. Comparisons to metabolism data from literature support the results' plausibility. Thus, a large scale screening for potential novel breath test precursor using the presented five stage work-flow is promising.
authors.affiliation: Department of Theoretical Chemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria.
authors.forename: Susanne
authors.initials: S
authors.lastname: von Grafenstein
authors.forename: Julian E
authors.initials: JE
authors.lastname: Fuchs
authors.forename: Markus M
authors.initials: MM
authors.lastname: Huber
authors.forename: Andrea
authors.initials: A
authors.lastname: Bassi
authors.forename: Alessandra
authors.initials: A
authors.lastname: Lacetera
authors.forename: Veronika
authors.initials: V
authors.lastname: Ruzsanyi
authors.forename: Jakob
authors.initials: J
authors.lastname: Troppmair
authors.forename: Anton
authors.initials: A
authors.lastname: Amann
authors.forename: Klaus R
authors.initials: KR
authors.lastname: Liedl
mesh_terms: D001944:Breath Tests / Q000379:methods*; D003198:Computer Simulation; D003577:Cytochrome P-450 Enzyme System / Q000378:metabolism*; D003663:Decision Trees; D045853:Exhalation; D006801:Humans; D007527:Isoenzymes / Q000378:metabolism; D010084:Oxidation-Reduction; D055549:Volatile Organic Compounds / Q000032:analysis*; D014835:Volatilization
chemical_list: D007527:Isoenzymes; D055549:Volatile Organic Compounds; D003577:Cytochrome P-450 Enzyme System