title: Prediction of overall in vitro microsomal stability of drug candidates based on molecular modeling and support vector machines. Case study of novel arylpiperazines derivatives.
abstract: Other than efficacy of interaction with the molecular target, metabolic stability is the primary factor responsible for the failure or success of a compound in the drug development pipeline. The ideal drug candidate should be stable enough to reach its therapeutic site of action. Despite many recent excellent achievements in the field of computational methods supporting drug metabolism studies, a well-recognized procedure to model and predict metabolic stability quantitatively is still lacking. This study proposes a workflow for developing quantitative metabolic stability-structure relationships, taking a set of 30 arylpiperazine derivatives as an example. The metabolic stability of the compounds was assessed in in vitro incubations in the presence of human liver microsomes and NADPH and subsequently quantified by liquid chromatography-mass spectrometry (LC-MS). Density functional theory (DFT) calculations were used to obtain 30 models of the molecules, and Dragon software served as a source of structure-based molecular descriptors. For modeling structure-metabolic stability relationships, Support Vector Machines (SVM), a non-linear machine learning technique, were found to be more effective than a regression technique, based on the validation parameters obtained. Moreover, for the first time, general sites of metabolism for arylpiperazines bearing the 4-aryl-2H-pyrido[1,2-c]pyrimidine-1,3-dione system were defined by analysis of Q-TOF-MS/MS spectra. The results indicated that the application of one of the most advanced chemometric techniques combined with a simple and quick in vitro procedure and LC-MS analysis provides a novel and valuable tool for predicting metabolic half-life values. Given the reduced time and simplicity of analysis, together with the accuracy of the predictions obtained, this is a valid approach for predicting metabolic stability using structural data. The approach presented provides a novel, comprehensive and reliable tool for investigating metabolic stability, factors that affect it, and the proposed structures of metabolites at the same time. The performance of the DFT-SVM-based approach provides an opportunity to implement it in a standard drug development pipeline.
authors.affiliation: Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk, Poland.
authors.forename: Szymon
authors.initials: S
authors.lastname: Ulenberg
authors.affiliation: Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk, Poland.
authors.forename: Mariusz
authors.initials: M
authors.lastname: Belka
authors.affiliation: Department of Drug Technology and Pharmaceutical Biotechnology, Medical University of Warsaw, Warsaw, Poland.
authors.forename: Marek
authors.initials: M
authors.lastname: Król
authors.affiliation: Department of Drug Technology and Pharmaceutical Biotechnology, Medical University of Warsaw, Warsaw, Poland.
authors.forename: Franciszek
authors.initials: F
authors.lastname: Herold
authors.affiliation: Department of Analytical Chemistry, Chemical Faculty, Gdańsk University of Technology, Poland.
authors.forename: Weronika
authors.initials: W
authors.lastname: Hewelt-Belka
authors.affiliation: Department of Analytical Chemistry, Chemical Faculty, Gdańsk University of Technology, Poland.
authors.forename: Agata
authors.initials: A
authors.lastname: Kot-Wasik
authors.affiliation: Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk, Poland.
authors.forename: Tomasz
authors.initials: T
authors.lastname: Bączek
mesh_terms: D002853:Chromatography, Liquid; D006207:Half-Life; D008861:Microsomes / Q000187:drug effects*; D008958:Models, Molecular; D010879:Piperazines / Q000737:chemistry / Q000493:pharmacokinetics / Q000494:pharmacology*; D021241:Spectrometry, Mass, Electrospray Ionization; D060388:Support Vector Machine; D053719:Tandem Mass Spectrometry
chemical_list: D010879:Piperazines
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