Sites of metabolic substitution: investigating metabolite structures utilising ion mobility and molecular modelling

Abstract

Drug metabolism is an integral part of the drug development and drug discovery process. It is required to validate the toxicity of metabolites in support of safety testing and in particular provide information on the potential to form pharmacologically active or toxic metabolites. The current methodologies of choice for metabolite structural elucidation are liquid chromatography/tandem mass spectrometry (LC/MS/MS) and nuclear magnetic resonance (NMR) spectroscopy. There are, in certain cases, examples of metabolites whose sites of metabolism cannot be unequivocally identified by MS/MS alone. Utilising commercially available molecular dynamics packages and known quantum chemistry basis sets, an ensemble of lowest energy structures were generated for a group of aromatic hydroxylated metabolites of the model compound ondansetron. Theoretical collision cross-sections were calculated for each structure. Travelling-wave ion mobility (IMS) measurements were also performed on the compounds, thus enabling experimentally derived collision cross-sections to be calculated. A comparison of the theoretical and experimentally derived collision cross-sections were utilised for the accurate assignment of isomeric drug metabolites. The UPLC/IMS-MS method, described herein, demonstrates the ability to measure reproducibly by ion mobility, metabolite structural isomers, which differ in collision cross-section, both theoretical and experimentally derived, by less than 1 Å(2). This application has the potential to supplement and/or complement current methods of metabolite structural characterisation.

A Novel Method for the Determination of the Site of Glucuronidation by Ion Mobility Spectrometry-Mass Spectrometry

“…Theoretical values of CCS were calculated using the method suggested by Dear et al (2010). In brief, the conformation for each molecule was energy-minimized with the MMFF94 force field followed by the extraction of 3D coordinate sets of each atom.…”

“…The MOBCAL output is based on three different models/algorithms including Projection Approximation, Exact Hard Sphere Scattering, and the Trajectory Method (TM). Among three outputs, the MOBCAL TM has been demonstrated to provide most accurate projections of CCS values with percentage differences of Ͻ4.5% for isomeric organoruthenium anticancer complexes (Williams et al, 2009b) and of Ͻ1% for ondansetron and its hydroxylated metabolites (Dear et al, 2010). Therefore, the outputs of MOBCAL TM were used for the projections in this study.…”

“…There are many examples of structure analysis using IMS-mass spectrometry (MS), in most cases for the macromolecules such as protein complexes or three-dimensional (3D) structure of polypeptide (for review, see Jarrold, 2000Jarrold, , 2007. In contrast, there have been only a few examples of structure analyses of metabolites of small molecule drugs: the structure analysis of hydroxylated metabolite of ondansetron (Dear et al, 2010) and the analysis for ortho-, meta-, and para-terphenyl complexes of organoruthenium anticancer drug (Williams et al, 2009a).…”

“…Despite promising technical innovation of IMS-MS for the structure determination of isomeric metabolites (Dear et al, 2010), the application of technology at the early development stage of new drug candidates has been very limited so far: the calculated 3D structures under vacuum phase by the energy-minimizing modeling vary with the adopted 2D-3D conversion methods; the theoretical CCS value is significantly affected by error ratios in the modeling, especially for small molecule metabolites; and both prevent the application of this novel technology from the routine analysis without authentic standards at the early development stage.…”

Anomerization of Acrylated Glucose During Traveling Wave Ion Mobility Spectrometry

“…The collisional cross-section value for each structure was calculated using the standard sigma projection method by averaging over all relevant MD equilibrated configurations. In brief, CCSs were obtained according to the method suggested by Dear et al [24] and the open source software MOBCAL (http://www.indiana.edu/~nano/ software.html) [25], using the 3D coordinate data sets extracted from the MD trajectories. The 12-6 parameter set recently developed by Siu et al [26] for He, H, C, N, and O atoms were adopted.…”