N- and S-Oxidation Model of the Flavin-containing Monooxygenases
Peter J. Walton1, Mario Oeren1, Peter A. Hunt1, Matthew D. Segall1
1Optibrium Ltd.
An important aspect of the drug design process is understanding the detoxification and excretion pathways of endo- and xenobiotics. While the Cytochrome P450 superfamily is considered to be the most important enzyme group involved in the phase I metabolism of drugs, the importance of the flavin-containing monooxygenase (FMO) class of enzymes is increasingly recognised. Of 860 drugs surveyed, FMOs contribute to the metabolism of at least 5%. Their wide range of possible reactions (e.g. oxidation, hydroxylation, demethylation) means that modelling of these enzymes’ behaviour, particularly N- and S-oxidation, is warranted in order to obtain a greater understanding of how a potential drug compound may be metabolised.
The aim of our work is to develop an in silico model that is able to identify potential FMO substrates and their sites of metabolism. The reaction mechanism of N- and S-oxidation is not clear, and it is debated whether it is a free-radical or an SN2 process. In this presentation we will propose a substantiated reaction mechanism for N- and S-oxidation of FMOs based on density functional theory (DFT) calculations. The reactant, transition state and product geometries and energies suggest that SN2 is the most feasible reaction type, and this was subsequently confirmed with further DFT tests and electronic wave function analysis. It is anticipated that the confirmation of this reaction mechanism can be applied in the future for the development of an in silico model.
All initial molecular structures (ground and transition states) were built using the molecular editor Avogadro and pre-optimized using the semi-empirical method AM1 (MOPAC 7). Further geometry-optimisations were conducted with DFT using the B3LYP functional along with the def2-SVP basis set. The DFT calculations were performed using the NWChem ab initio computational chemistry software package. Besides geometry optimisation, vibrational frequency calculations were performed to ensure that all found geometries were at stationary points. Electronic wave function analysis was conducted using the program MultiWFN, with the required .wfn file generated using NWChem. Avogadro, MultiWFN, and Jmol were used to visualise structures, electron density maps and frontier orbitals.
