The biotransformation of benzene derivatives : the influence of active site and substrate characteristics on the metabolic fate

J. Koerts

Research output: Thesisinternal PhD, WU


<br/>The amount of newly developed chemicals such as agrochemicals, drugs and food additives in our modem society is ever increasing. The industrial production, use and also the release in the environment of these chemicals expose organisms to these xenobiotics. Due to the often hydrophobic character of these xenobiotics they can be easily absorbed and accumulated in the body. However, organisms defend themselves against these agents by converting them enzymatically to more hydrophilic easily excretable products. Sometimes these biotransformation reactions can lead to reactive intermediates which cause cell damage, toxicity, malignancy and/or ultimately carcinogenicity. This indicates why a lot of toxicological screening and safety tests have to be performed during the development of these agents.<p>However, modern society still requires new compounds with better properties. As it is unfeasible to test the biological activity and toxic effects of all newly developed chemicals in experimental animals, many in vitro systems have been developed in which these chemicals can be quickly tested for various biological and/or toxicological effects. To diminish the use of experimental test systems the QSAR concept has been developed, describing so-called Quantitative StructureActivity Relationships. This QSAR approach should make it possible to predict the biological effect, the biotransformation pattern and/or the toxicity of a chemical based on its physical and chemical characteristics. In this respect the application of MO (Molecular Orbital) computer calculations to describe at least some of these chemical characteristics appears to become more and more useful.<p>The present thesis focuses on the use of these computer calculated MO parameters for the prediction of biotransformation characteristics of benzene derivatives. Benzene derivatives play an important role as precursors for the synthesis of many xenobiotics and industrially relevant chemicals. The cytochrome P450-catalysed biotransformation of various substituted benzenes was studied and the results were evaluated to determine whether (MO-based) computer calculated chemical parameters of benzenes could explain the results obtained. Where results could not be described well by the chemical reactivity of the substrate itself, additional experimental work was performed to investigate to which factors and/or interactions the observed deviations could be ascribed. This information can then be used to adopt and improve the predictive model.<p>Biotransformation of xenobiotics by higher organisms is an enzymatic process in which cytochromes P450 play a major role. This system is able to handle an enormous amount of very structurally different chemicals. The cytochrome P450 enzymes differ in their substrate specificity, metabolic activity and their extent of contribution to the production of toxic metabolites. As outlined in the introduction of this thesis <em>(Chapter 1</em> ), there are several factors which control the cytochrome P450-catalysed biotransformation. These factors include for example, electron donation to cytochrome P450, the accessibility of the active (FeO) <sup><font size="-1">3+</font></SUP>species in the active site of the enzyme, the interaction between the substrate and the active site and the chemical reactivity of the substrate itself. In cases where the latter factor controls the outcomes of the cytochrome P450-catalysed biotransformation, one could describe a QSARs for the reaction. Based on these QSARs the cytochrome P450-catalysed biotransformation of other chemicals might be predicted. Furthermore, these QSARs might give more insight in the mechanistic background of the biotransformation reaction for which it has been developed.<p>An example of this approach is described in <em>Chapter 2</em> of this thesis. In this chapter <em>in vivo</em> cytochrome P450-catalysed aromatic ring hydroxylation of various substituted benzene derivatives was determined using <sup><font size="-1">19</font></SUP>F NMR. Previous reported results on the regioselectivity of cytochrome P450-catalysed aromatic ring hydroxylation of a series (poly)fluorobenzenes demonstrated a clear QSAR (correlation 0.96) relating the site of hydroxylation of the site of the reactive HOMO π-electrons in the benzene substrate. Thus, in <em>Chapter 2</em> the same parameter was tested for its ability to predict the regioselectivity of aromatic hydroxylation of a series C4-substituted fluorobenzenes. It turned out that the MO-QSAR approach could well predict the regioselectivity of the series of 4-X-substituted fluorobenzenes when X was a H, F, Cl, and CN group. However, this approach of predicting the regioselectivity of aromatic hydroxylation ran into problems when the <em>para</em> substituent was a bromine or iodine. The extent to which the hydroxylation adjacent to a bromine and iodine substituent was reduced, correlated qualitatively with the size of the substituents as given by their Van der Waals radius, i.e. the larger the substituent the greater the deviation between the predicted and observed hydroxylation at the adjacent aromatic carbon centre. Additional experiments showed that the observed deviations could not be ascribed to a stereoselective orientation of these substrates in the active sites of cytochromes P450. These results led to the hypothesis that bromine and iodine substituents sterically hamper the electrophilic attack of the cytochrome P450 high-valent iron-oxo species on the carbon atoms adjacent to the substituted carbon centres. This hypothesis was supported by calculating the steric effects of bromine and iodine substituents, thus defining a steric correction factor for prediction of the aromatic ring hydroxylation at sites <em>ortho</em> with respect to a bromine or iodine substituent. In a second series of regioselectivity experiments using a series of tri- substituted benzenes containing fluorine, chlorine, bromine, iodine and cyano substituents, these steric correction factors were validated. Without using the steric correction factors for bromine and iodine substituents no correlation between the predicted and observed regioselectivity was obtained. However, upon application of the correction factors a correlation factor of 0.91 was obtained for prediction and actually observed regioselectivity of cytochrome P450-catalysed aromatic hydroxylation of the series tri- substituted benzenes. These results show that the QSAR which was initially developed for a series of (poly)fluorobenzenes was still valid for other substituted benzenes taking into account the steric hindrance by relatively large substituents such as bromine and iodine. Furthermore, from a mechanistic point of view these MO-QSARs suggest that the cytochrome P450-catalysed aromatic ring hydroxylation of at least the benzene derivatives tested proceeds by an initial attack of the iron-oxo species on the ring carbon atom, without the formation of arene oxide intermediates as a major route.<p>The question remains why going from a chlorine to a bromine substituent, steric hindrance is observed rather abrupt. A possible explanation might be found in the observation that when two molecules approach each other the potential energy goes through a minimum and thereafter increases rapidly with decreasing distance.<p>Surprisingly, it was found that steric hindrance by the cyano group was not observed although this group is definitely larger than a bromine. However, with respect to steric hindrance of the electrophilic attack of the (FeO) <sup><font size="-1">3+</font></SUP>species, only the atom closest to the aromatic ring might have to be taken into account. Steric hindrance of this atom, a carbon, is not expected since a carbon, has a size similar to that of a chlorine.<p>More complicated substituents than H, F, Cl, Br, I and CN were investigated in <em>Chapter 3</em> where the regioselectivity of aromatic ring hydroxylation of 3-fluoro(methyl)anilines was investigated. Little is known about the cytochrome P450- catalysed biotransformation of such methylanilines. Results from the <em>in vivo</em> and <em>in vitro</em> cytochrome P450-catalysed regioselectivity of aromatic hydroxylation showed that the frontier orbital density distribution in the aromatic ring could only qualitatively predict the observed regioselectivity. Again, as for the bromine and iodine substituents the observed regioselectivity of aromatic ring hydroxylation for the various amino and methyl substituted substrates showed systematic deviations from the predicted regioselectivity, i.e. hydroxylation at the ring carbon C4 <em>para</em> with respect to the amino moiety was always higher than predicted while hydroxylation at the carbon atoms <em>ortho</em> with respect to the amino group (C2 and C6) was lower than expected. Further research was performed to investigate why for this series of amino and/or methyl substituted benzene derivatives the intrinsic chemical reactivity did not predict the observed regioselectivity of aromatic hydroxylation quantitatively. Three different experimental approaches were used to investigate possible reasons underlying the systematic deviations between predicted and observed regioselectivity for the cytochrome P450-catalysed aromatic hydroxylation of amino-containing benzenes. These results are discussed in some more detail hereafter.<p>1. As a first approach, incubations of 3-fluoro-2-methylaniline with different microsomal preparations containing various cytochrome P450 enzyme patterns as well as with purified cytochrome P4502B1 were performed. The regioselectivity for aromatic hydroxylation of 3- fluoro-2-methylaniline observed in all these incubations were similar. This result indicates that cytochromes P450 with different active sites give similar regioselectivities and, thus, in case of 3-fluoro-2-methylaniline similar deviations for predicted values. This suggests that the observed discrepancy between predicted and observed aromatic hydroxylation patterns can not be ascribed to a stereoselective orientation of the 3-fluoro(methyl)anilines imposed by the active sites of the cytochromes P450 catalysing its conversion.<p>2. Further support for this conclusion was obtained from <sup><font size="-1">1</font></SUP>H NMR T <sub><font size="-1">1</font></sub> relaxation studies on fluoromethylanilines. These studies are described in <em>Chapter 4.</em> It appears that the orientation of the tested fluoromethylanilines in the active sites of cytochromes P4501AI and 2B1 is similar. Based on the observation that all aromatic protons are at about the same average distance from the catalytic Fe <sup><font size="-1">3+</font></SUP>centre, these results are most compatible with a time-averaged orientation of the substrates with the Fe <sup><font size="-1">3+</font></SUP>above the aromatic ring and the π-orbitals of the aromatic ring and those of the porphyrin rings in a parallel position. This latter aspect would provide possibilities for energetically favourable π-πinteractions. Possibilities for a flip-flop rotation around an axis in the plane of the aromatic ring of the substrate can be included in this picture, as such rotations would still result in a similar average distance of all aromatic protons to the Fe <sup><font size="-1">3+</font></SUP>centre. Altogether, the data strongly suggest that, independent of the cytochrome P450 enzyme these substrates can rotate freely in the active site and are not hindered and/or specifically orientated by interactions with specific amino acid residues of the active site.<p>3. Finally, the possible influence of the active site on the cytochrome P450-catalysed aromatic hydroxylation was tested by using microperoxidase-8 as a model system for cytochrome P450-catalysed aromatic ring hydroxylation. Microperoxidase-8 is a so-called mini-enzyme prepared by proteolytic digestion of horse-heart cytochrome c. MP-8 contains a heme covalently attached to a peptide chain of only eight amino acids and thus it lacks an active site. MP-8 is well known to perform peroxidase-like reactions. However, experimental evidence has been obtained described in <em>Chapter 5</em> of this thesis that the MP-8-catalysed aromatic ring hydroxylation of aniline and phenol derivatives in a H <sub><font size="-1">2</font></sub> O <sub><font size="-1">2</font></sub> -driven system proceeds by a cytochrome P450-like oxygen-transfer mechanism. This could be concluded from the fact that <sup><font size="-1">18</font></SUP>O incorporation from H<font size="-1"><sub>2</sub><sup>18</SUP></font>O <sub><font size="-1">2</font></sub> into the 4-aminophenol formed from aniline was 100%. Thus, the H <sub><font size="-1">2</font></sub> O <sub><font size="-1">2</font></sub> -driven MP-8 system was used as a model to study regioselectivity of oxygen-transfer in a heme-based catalyst without an active site.<p>The results of such experiments demonstrated that the MP-8-catalysed aromatic ring hydroxylation of 3-fluoro(methyl)anilines <em>(Chapter 3)</em> results in similar regioselectivities of aromatic ring hydroxylation as those observed for cytochrome P450- catalysis. As a specific substrate binding site in MP-8 can be excluded, these results, together with those obtained from different microsomal preparations <em>(Chapter 3)</em> and the <sup><font size="-1">1</font></SUP>H NMR T <sub><font size="-1">1</font></sub> relaxation measurements <em>(Chapter 4),</em> clearly eliminates the possibility that the regioselectivity of aromatic ring hydroxylation is predominantly dictated by a stereoselective orientation of the substrate in the active site of cytochromes P450. Thus for these relatively small and non-polar substrates specific interactions between molecular sides in the substrate and amino acid side chains present in the active site are not dictating a stereoselective orientation of these substrates.<p>Since the MP-8-catalysed reactions showed similar deviations between predicted and observed regioselectivity of aromatic hydroxylation of 3-fluoro(methyl)anilines, it was concluded that the deviations must result from an orientating interaction between the substrate and the high-valent iron-oxo species (FeO) <sup><font size="-1">3+</font></SUP>itself, resulting in a stereoselective orientation of the substrate towards the catalytically active species. This interaction can be expected to be quite similar for different cytochromes P450 and might also be comparable in the active MP-8 system. This implies that, in contrast to what was observed by <sup><font size="-1">1</font></SUP>H NMR for substrates bound to the Fe <sup><font size="-1">3+</font></SUP>resting state of the enzyme, the (FeO) <sup><font size="-1">3+</font></SUP>form of the protein would impose a preferential orientation of the amino-containing substrate in such a way that on the average C4 ( <em>para</em> to the amino) is closer to whereas <em>C2/6 (ortho</em> to the amino) are further away from the (FeO) <sup><font size="-1">3+</font></SUP>species. Support for a different substrate orientation in the Fe <sup><font size="-1">3+</font></SUP>resting state and the (FeO) <sup><font size="-1">3+</font></SUP>activated form respectively can be found in a study of Paulsen and Ornstein. They showed that the orientation of camphor in the presence and absence of the high-valent iron-oxo species (FeO) <sup><font size="-1">3+</font></SUP>was different and that orientation in the presence of the catalytically active form of the enzyme (FeO) <sup><font size="-1">3+</font></SUP>was in accordance with the observed regioselectivity of oxidation.<p>Altogether, results from all studies on the regioselectivity of aromatic hydroxylation of the various benzene derivatives show that the regioselectivity of the H, F, Cl, Br, I, CN, CH <sub><font size="-1">3</font></sub> and NH <sub><font size="-1">2</font></sub> substituted benzene derivatives investigated is predominantly determined by their chemical reactivity. However, especially for amino-containing benzene derivatives interactions between the substrate and the high-valent iron-oxo species, resulting in a stereoselective orientation of the substrate, might also play a role. This means that the QSAR for aromatic ring hydroxylation in the case of amino-containing benzenes predicts only qualitatively the regioselectivity of aromatic ring hydroxylation for these series of substrates.<p>An additional result obtained in all regioselectivity studies was the absence of formation of NIH shifted phenolic metabolites. The formation of such NIH shifted phenolic metabolites has been well documented especially for the biotransformation of chlorinated and brominated benzene derivatives. As the benzenes in our studies were mainly fluorinated, we decided to investigate whether there was a (chemical) reason for this discrepancy.<p><em>In Chapter 6</em> the possibility of a cytochrome P450-catalysed fluorine NIH shift in a series of polyfluorobenzenes was investigated and compared with the literature data of the chlorinated analogues. The <em>in vivo</em> biotransformation of a series polyfluorobenzenes showed that formation of NIH shifted metabolites was not a significant biotransformation route. As outlined above, this is in contrast to the results reported in the literature for the chlorinated analogues. However, in contrast to the <em>in vivo</em> data, in <em>in vitro</em> microsomal studies with 1,4-difluorobenzene formation of a significant amount of fluorine NIH shifted phenolic metabolite was observed. Unfortunately, the <em>in vitro</em> microsomal conversion of the other used polyfluorobenzenes could not be detected, possibly due to the fact that the HOMO energy of these substrates was too low for an efficient conversion by cytochromes P450 [5]. It is generally accepted that formation of NIH shifted metabolites proceeds via arene oxide intermediates and that these arene oxides, especially <em>in vivo,</em> but not <em>in vitro</em> in a microsomal system, might react in competing conjugation pathways such as GSH conjugation. Additional <em>in vivo</em> and <em>in vitro</em> experiments showed that indeed GSH conjugation was a competing pathway for the arene oxide intermediates, its presence or absence resulting in an influence on the amount of NIH shifted phenolic metabolites observed.<p>Nevertheless, the results thus obtained also clearly illustrated and confirmed the reduced capacity for formation of NIH shifted phenolic metabolites for fluoro- as compared to chlorobenzenes. This differences between the NIH shift for fluorine and chlorine containing benzenes was further investigated and could be explained by MO computer calculations on the proposed reaction intermediates in the two biotransformation pathways. Epoxide ring opening, supposed to be the rate-limiting step in the formation of NIH shifted metabolites, appeared easier for chlorinated benzenes compared to their fluorinated analogues. Furthermore, these MO calculations in combination with a MO-QSAR for the rate of GS-conjugation of electrophilic model compounds were indicative for higher rates of GSH conjugation for the fluorinated benzene arene oxides than the chlorinated analogues. The detoxifying pathway of GSH conjugation is very important for assessing the risks of these kind of substrates as arene oxides are known to react with protein and DNA provoking toxic and/or mutagenic /carcinogenic responses.<p>Altogether, the results from this study show that MO calculations can not only explain and thus predict the regiospecificity of biotransformation in a molecule but also explain the relative rates, i.e. chances, on different biotransformation routes.<p>Finally, in addition to all studies on model benzene derivatives, the last chapter of this thesis <em>(Chapter 7)</em> describes studies on the biotransformation of a halogenated benzene derived compound that is used as an insecticide, i.e. teflubenzuron. This may provide some insight in the possibilities to use outcomes from studies on model compounds to obtain insights also in the biotransformation of other compounds. Teflubenzuron, which is used for the protection of fruit and vegetables against larves, contains two aromatic benzene-derived rings connected via an urea bridge. These aromatic rings are differently substituted and are a suitable starting point to evaluate the influence of various substituents on the metabolic fate of the chemical. Basically, they are an aniline and a benzoate derived moiety. Results of this study on the biotransformation of teflubenzuron demonstrate that upon an oral dose of the insecticide to male Wistar rats the metabolic fate of the two aromatic rings is significantly different. Though about 90% of the dose was excreted unchanged in the faeces, the remainder of the dose was absorbed from the gastrointestinal tract and -in part- excreted in the urine mainly after hydrolysis of the urea bridge. Interestingly, the urinary recovery of the benzoate moiety was about 8 times higher than that of the aniline moiety of teflubenzuron. Dose-recovery studies on the scission products of teflubenzuron confirmed these results as the urinary recovery of the metabolites from the benzoate moiety were nearly 100% while the recovery of the aniline derivatives was only about 50%. The benzoate moiety is excreted unchanged or after a Phase IIreaction, while the aniline moiety has to undergo both a Phase I and II reaction before it can be excreted.The significant difference between the recovery of the benzoate and aniline moiety can be best explained by the formation of a cytochrome P450-catalysed reactive benzoquinoneimine from the C4 halogenated aniline derivatives. Swift binding of these reactive benzoquinoneimines to tissue macromolecules might cause the compound to be withheld in the body. This is also important from a toxicological point of view as binding of these reactive benzoquinoneimines might provoke toxic and/or mutagenic /carcinogenic effects in the body.<p>Altogether, the results described in this thesis show that QSARs are very useful in explaining the biotransformation pattern of relatively small and non-polar benzene derivatives. Their biotransformation pattern was demonstrated to be predominantly determined by the chemical reactivity of the benzenes and - although to a much lesser extent for bromine, iodine and amino containing derivatives- more than by steric: factors (Br,I) and/or electronic dipole-dipole interactions with the activated (FeO) <sup><font size="-1">3+</font></SUP>cofactor (NH <sub><font size="-1">2</font></sub> ). However, the further extension of the presently developed QSARs to more complicated and especially to larger molecules might require the incorporation of computer techniques that take into account preferential stereoselective substrate orientations imposed by the active sites. Although the molecular modelling computer techniques to do these type of additional orientation analyses are available, such studies also require the availability of the enzyme crystal structures. Since such 3-D structures for cytochromes P450 are at present restricted to some bacterial cytochromes P450 and not available for mammalian cytochromes P450 the studies may have to await the elucidation of the mammalian cytochrome P450 structures. Nevertheless, the concept as such might be developed using either molecular modelling combined with quantum chemical calculations for the bacterial cytochrome P450 system as done recently by Zakharieva et al. and Freutel et al., or by performing similar studies for other biotransformation enzymes, such as for example the glutathione S-transferases for which several 3-D structures have been described.<p>In general, QSARs can be used to predict the biological activity of non-tested chemicals but they can also give more insight in the mechanistic rules of biotransformation of molecules. This knowledge can be very helpful for example when the technical ability of cloning cytochromes P450, and thus producing these enzymes in large quantities, is increasing. Cytochromes P450 could then be used for the synthesis of chemical products (P450 biotechnology). Especially cytochromes P450 are suitable as they are able to convert many structural diverse substrates. The advantage of enzymatic synthesis compared to chemical synthesis is that it causes among others less waste problems.
Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Veeger, C., Promotor
  • Rietjens, Ivonne, Promotor
Award date18 Dec 1996
Place of PublicationS.l.
Print ISBNs9789054856214
Publication statusPublished - 1996


  • biotransformation
  • cytochrome p-450
  • benzene
  • derivatives

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