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QM/MM modelling of human cytochrome P450 isoforms

Final Activity Report Summary - MODELLING CYPs (QM/MM modelling of human cytochrome P450 isoforms)

The cytochrome P450s consists of proteins that accelerate important chemical reactions in biological cells, i.e. enzymes. Enzymes of this type can be found in almost all living organisms, playing several roles in biochemical transformations. With respect to our work, their most important role was the degradation, or metabolism, of pharmaceutical drug molecules. By adding oxygen to these drugs, i.e. through an oxidation reaction, they made drug molecules easier to remove from the body, e.g. through urine, and hence prevented accumulation.

In mankind, these enzymes are responsible for 90 % of drug metabolism. The speed of metabolism for a given drug, i.e. the reactivity, influences the availability of the compound and therefore its therapeutic effect. In addition, the nature of the products formed upon metabolism, which depends on the part of the molecule to which oxygen gets added, termed as regioselectivity, is important as these species can in some cases be toxic. The factors influencing the reactivity and regioselectivity were not well understood, especially as there were several different P450 enzymes, or isoforms, that contributed to drug metabolism.

In our study, we used theoretical methods to try to understand these factors. We concentrated on one particular isoform, called P450 2D6, which played a critical role in human drug metabolism. We also selected one typical drug, called dextromethorphan, which was commonly used for relief of coughing, hence an antitussive drug. The key calculations described the energy of the joint enzyme and drug molecule system during the reaction, which led to different oxidised products. We considered both a reaction leading to addition of oxygen to a ‘methoxy’ (O-CH3) group and to a benzene ring. The method used to describe the system involved a ‘ball and spring’, or molecular mechanics (MM), model for most of the enzyme and a method based on quantum mechanics (QM) to describe the important atoms in which chemical bonds were formed and broken.

These QM and MM calculations showed that methoxy oxidation was preferred over benzene ring oxidation, as found experimentally. This was despite the facts that both groups could approach the oxidation centre in the enzyme and that they were both intrinsically able to undergo oxidation with similar ease. Our main discovery was that the preference for methoxy oxidation was because of a previously unappreciated factor, whereby the protein environment did not allow the drug molecule to move with respect to the oxidation centre in the way needed to allow benzene ring oxidation. This new insight could help scientists study P450 oxidation as it was likely to be a fairly general effect. Finally, in auxiliary calculations, we examined other aspects of the reactivity of cytochrome P450 enzymes and model systems.