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Goracci L.,University of Perugia | Buratta S.,University of Perugia | Urbanelli L.,University of Perugia | Ferrara G.,University of Perugia | And 3 more authors.
European Journal of Medicinal Chemistry

Phospholipidosis (PLD) is an undesirable potential side-effect of drugs, and cationic amphiphilic drugs (CADs) represent the main class of PLD inducers. A CADs toxicophore has been recently proposed, although the CADs definition is far from being trivial. In this work we derive a three-dimensional CADs toxicophore (here named PLD-phore) using a molecular interaction field approach, and test its suitability to discriminate between PLD inducers and non-inducers in a virtual screening approach. Ten commercially available compounds predicted to be PLD inducers and non-inducers based on their similarity to the PLD-phore were experimentally tested for PLD induction using two cell-based in vitro assays (fluorescent lipid uptake, activity of secreted lysosomal 2-hexosaminidase). When a positive effect was observed, the PLD induction was also confirmed by transmission electron microscopy. Two exceptions to the general statement about CADs and PLD induction were detected and discussed, and for one compound the cell-based in-vitro assays lead to different outcomes. © 2014 Elsevier Masson SAS. Source

Cruciani G.,University of Perugia | Valeri A.,University of Perugia | Goracci L.,University of Perugia | Pellegrino R.M.,University of Perugia | And 2 more authors.
Journal of Medicinal Chemistry

FMO enzymes (FMOs) play a key role in the processes of detoxification and/or bioactivation of specific pharmaceuticals and xenobiotics bearing nucleophilic centers. The N-oxide and S-oxide metabolites produced by FMOs are often active metabolites. The FMOs are more active than cytochromes in the brain and work in tandem with CYP3A4 in the liver. FMOs might reduce the risk of phospholipidosis of CAD-like drugs, although some FMOs metabolites seem to be neurotoxic and hepatotoxic. However, in silico methods for FMO metabolism prediction are not yet available. This paper reports, for the first time, a substrate-specificity and catalytic-activity model for FMO3, the most relevant isoform of the FMOs in humans. The application of this model to a series of compounds with unknown FMO metabolism is also reported. The model has also been very useful to design compounds with optimal clearance and in finding erroneous literature data, particularly cases in which substances have been reported to be FMO3 substrates when, in reality, the experimentally validated in silico model correctly predicts that they are not. © 2014 American Chemical Society. Source

Zelesky V.,Pfizer | Schneider R.,Pfizer | Janiszewski J.,Pfizer | Zamora I.,Molecular Discovery | And 2 more authors.

Background: The ability to supplement high-throughput metabolic clearance data with structural information defining the site of metabolism should allow design teams to streamline their synthetic decisions. However, broad application of metabolite identification in early drug discovery has been limited, largely due to the time required for data review and structural assignment. The advent of mass defect filtering and its application toward metabolite scouting paved the way for the development of software automation tools capable of rapidly identifying drug-related material in complex biological matrices. Two semi-automated commercial software applications, MetabolitePilot™ and Mass-MetaSite™, were evaluated to assess the relative speed and accuracy of structural assignments using data generated on a high-resolution MS platform. Results/Conclusion: Review of these applications has demonstrated their utility in providing accurate results in a time-efficient manner, leading to acceleration of metabolite identification initiatives while highlighting the continued need for biotransformation expertise in the interpretation of more complex metabolic reactions. © 2013 Future Science Ltd. Source

Cece-Esencan E.N.,University Pompeu Fabra | Fontaine F.,Molecular Discovery | Plasencia G.,Molecular Discovery | Plasencia G.,S.L. San Cugat del Valles | And 4 more authors.
Rapid Communications in Mass Spectrometry

Rationale Cytochrome P450 (CYP450) reaction phenotyping (CRP) and kinetic studies are essential in early drug discovery to determine which metabolic enzymes react with new drug entities. A new semi-automated computer-assisted workflow for CRP is introduced in this work. This workflow provides not only information regarding parent disappearance, but also metabolite identification and relative metabolite formation rates for kinetic analysis. Methods Time-course experiments based on incubating six probe substrates (dextromethorphan, imipramine, buspirone, midazolam, ethoxyresorufin and diclofenac) with recombinant human enzymes (CYP1A2, CYP2C9, CYP2C19, CYP2D6 and CYP3A4) and human liver microsomes (HLM) were performed. Liquid chromatography/high-resolution mass spectrometry (LC/HRMS) analysis was conducted with an internal standard to obtain high-resolution full-scan and MS/MS data. Data were analyzed using Mass-MetaSite software. A server application (WebMetabase) was used for data visualization and review. Results CRP experiments were performed, and the data were analyzed using a software-aided approach. This automated-evaluation approach led to (1) the detection of the CYP450 enzymes responsible for both substrate depletion and metabolite formation, (2) the identification of specific biotransformations, (3) the elucidation of metabolite structures based on MS/MS fragment analysis, and (4) the determination of the initial relative formation rates of major metabolites by CYP450 enzymes. Conclusions This largely automated workflow enabled the efficient analysis of HRMS data, allowing rapid evaluation of the involvement of the main CYP450 enzymes in the metabolism of new molecules during drug discovery. © 2015 John Wiley & Sons, Ltd. Source

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