Mechanism-based inactivation of cytochrome P450 2B6 by a novel terminal acetylene inhibitor

Acetylene containing cyclo(L-Tyr-L-Tyr)-analogs as mechanism-based inhibitors of CYP121A1 from Mycobacterium tuberculosis

Tuberculosis (TB) is a globally significant infective disease that is caused by a single infectious agent, Mycobacterium tuberculosis (Mtb). Because of the rise in the number of multidrug-resistant (MDR) TB strains, identification of alternative drug targets for the development of drugs with different mechanism of actions is desired. CYP121A1, one of the twenty cytochrome P450 enzymes encoded in the Mtb genome, was previously shown to be essential for bacterial growth. This enzyme catalyzes the intramolecular C-C crosslinking reaction of the cyclopeptide cyclo(L-tyr-L-tyr) (cYY) yielding the metabolite mycocyclosin. In the present study, acetylene-substituted cYY-analogs were synthesized and evaluated as potential mechanism-based inhibitors of CYP121A1. The acetylene-substituted cYY-analogs were capable of binding to CYP121A1 with affinities comparable with cYY, and exhibited a Type I binding mode, indicative of a substrate-like binding, mandatory for metabolism. Only the cYY-analogs which contain an acetylene-substitution at one (2a) or both (3) para-positions of cYY showed mechanism-based inhibition of CYP121A1 activity. The values of K_I and k_inact were 236 µM and 0.045 min^-1, respectively, for compound 2a, and 145 µM and 0.015 min^-1, repectively, for compound 3 The inactivation could neither be reversed by dialysis nor be prevented by including glutathione. LC-MS analysis demonstrated that the inactivation results from covalent binding to the apoprotein, whereas the heme was unmodified. Interestingly, the mass increment of the CYP121A1 apoprotein was significantly smaller than was expected from the ketene formed by oxidation of the acetylene-group, indicative for a secondary cleavage reaction in the active site of CYP121A1. Although the two acetylene-containing cYY-analogs showed significant mechanism-based inhibition, growth inhibition of the Mtb strains was only observed at millimolar concentrations. This low efficacy may be due to insufficient irreversible inactivation of CYP121A1 and/or insufficient cellular uptake. Although the identified mechanism-based inhibitors have no perspective for Mtb-treatment, this study is the first proof-of-principle that mechanism-based inhibition of CYP121A1 is feasible and may provide the basis for new strategies in the design and development of compounds against this promising therapeutic target.

Acetylenes: cytochrome P450 oxidation and mechanism-based enzyme inactivation

The oxidation of carbon-carbon triple bonds by cytochrome P450 produces ketene metabolites that are hydrolyzed to acetic acid derivatives or are trapped by nucleophiles. In the special case of 17α-ethynyl sterols, D-ring expansion and de-ethynylation have been observed as competing pathways. The oxidation of acetylenic groups is also associated with mechanism-based inactivation of cytochrome P450 enzymes. One mechanism for this inactivation is reaction of the ketene metabolite with cytochrome P450 residues essential for substrate binding or catalysis. However, in the case of monosubstituted acetylenes, inactivation can also occur by addition of the oxidized acetylenic function to a nitrogen of the heme prosthetic group. This addition reaction is not mediated by the ketene metabolite, but rather occurs during oxygen transfer to the triple bond. In some instances, a detectable intermediate is formed that is most consistent with a ketocarbene-iron heme complex. This complex can progress to the N-alkylated heme or revert back to the unmodified enzyme. The ketocarbene complex may intervene in the formation of all the N-alkyl heme adducts, but is normally too unstable to be detected.

The Alkyne Moiety as a Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K

Irreversible covalent inhibitors can have a beneficial pharmacokinetic/pharmacodynamics profile but are still often avoided due to the risk of indiscriminate covalent reactivity and the resulting adverse effects. To overcome this potential liability, we introduced an alkyne moiety as a latent electrophile into small molecule inhibitors of cathepsin K (CatK). Alkyne-based inhibitors do not show indiscriminate thiol reactivity but potently inhibit CatK protease activity by formation of an irreversible covalent bond with the catalytic cysteine residue, confirmed by crystal structure analysis. The rate of covalent bond formation ( kinact) does not correlate with electrophilicity of the alkyne moiety, indicative of a proximity-driven reactivity. Inhibition of CatK-mediated bone resorption is validated in human osteoclasts. Together, this work illustrates the potential of alkynes as latent electrophiles in small molecule inhibitors, enabling the development of irreversible covalent inhibitors with an improved safety profile.

Targeting of the highly conserved threonine 302 residue of cytochromes P450 2B family during mechanism-based inactivation by aryl acetylenes

Cytochromes P450 (CYPs or P450s) contain a highly conserved threonine residue in the active site, which is referred to as Thr302 in the amino acid sequence of CYP2B4. Extensive biochemical and crystallographic studies have established that this Thr302 plays a critical role in activating molecular oxygen to generate Compound I, a putative iron(IV)-oxo porphyrin cation radical, that carries out the preliminary oxygenation of CYP substrates. Because of its proximity to the center of the P450 active site, this Thr302 is susceptible to mechanism-based inactivation under certain conditions. In this article, we review recent studies on the mechanism-based inactivation of three mammalian P450s in the 2B family, CYP2B1 (rat), 2B4 (rabbit) and 2B6 (human) by tert-butylphenylacetylene (tBPA). These studies showed that tBPA is a potent mechanism-based inactivator of CYP2B1, 2B4 and 2B6 with high k(inact)/K(I) ratios (0.23-2.3min(-1)μM(-1)) and low partition ratios (0-5). Furthermore, mechanistic studies revealed that tBPA inactivates these three CYP2B enzymes through the formation of a single ester adduct with the Thr302 in the active site. These inhibitory properties of tBPA allowed the preparation of a modified CYP2B4 where the Thr302 was covalently and stoichiometrically labeled by a reactive intermediate of tBPA in quantities large enough to permit spectroscopic and crystallographic studies of the consequences of covalent modification of Thr302. Molecular modeling studies revealed a unique binding mode of tBPA in the active site that may shed light on the potency of this inhibition. The results from these studies may serve as a basis for designing more specific and potent inhibitors for P450s by targeting this highly conserved threonine residue which is present in the active sites of most mammalian P450s.

Mechanism-based inhibition of cytochrome P450 enzymes: an evaluation of early decision making in vitro approaches and drug-drug interaction prediction methods

The ability to use in vitro human cytochrome P450 (CYP) time-dependent inhibition (TDI) data for in vivo drug-drug interaction (DDI) predictions should be viewed as a prerequisite to generating the data. Important terms in making such predictions are k(inact) and K(I) but first-line screening assays typically involve characterisation of an IC(50) value or a time dependent shift in IC(50). In the work presented here, two key screening methods from the scientific literature were appraised both in terms of practicality and quality of k(inact)/K(I) estimation. The utility of TDI screening data in DDI predictions was investigated and particular reference given to a simple DDI simulation model based on a spreadsheet that calculates the systemic exposure of unbound inhibitor drug following the input of human pharmacokinetic parameters. Using several clinical mechanism-based CYP DDI examples, the effectiveness of the approach was assessed and compared to other widely available approaches (a simple algorithm that employs a single in vivo unbound inhibitor concentration, a seven-compartment physiologically based pharmacokinetic (PBPK) model that defines the extent of interaction as a result of hepatic inhibitor concentrations and the commercially available software SimCYP). All the methods gave predictions that compared favourably with the observed DDIs, but various advantages and disadvantages of each were also given full consideration. The new model facilitates rapid sensitivity analysis (parameters can be easily input and altered to give a visual representation of the impact on the active enzyme concentration) and it was therefore used to derive "rules of thumb" demonstrating the relationship between extent of DDI, time-dependent IC(50) and dose for typical acidic and basic drugs. Additionally, a TDI decision tree linking into reactive metabolite investigations is proposed for use in a Drug Discovery setting.

Mechanism-based inactivation of human cytochromes p450s: experimental characterization, reactive intermediates, and clinical implications

The P450 type cytochromes are responsible for the metabolism of a wide variety of xenobiotics and endogenous compounds. Although P450-catalyzed reactions are generally thought to lead to detoxication of xenobiotics, the reactions can also produce reactive intermediates that can react with cellular macromolecules leading to toxicity or that can react with the P450s that form them leading to irreversible (i.e., mechanism-based) inactivation. This perspective describes the fundamentals of mechanism-based inactivation as it pertains to P450 enzymes. The experimental approaches used to characterize mechanism-based inactivators are discussed, and the criteria required for a compound to be classified as a mechanism-based inactivator are outlined. The kinetic scheme for mechanism-based inactivation and the calculation of the relevant kinetic constants that describe a particular inactivation event are presented. The structural aspects and important functional groups of several classes of molecules that have been found to impart mechanism-based inactivation upon metabolism by P450s such as acetylenes, thiol-containing compounds that include isothiocyanates, thiazolidinediones, and thiophenes, arylamines, quinones, furanocoumarins, and cyclic tertiary amines are described. Emphasis throughout this perspective is placed on more recent findings with human P450s where the site of modification, whether it be the apoprotein or the heme moiety, and, at least in part, the identity of the reactive intermediate responsible for the loss in P450 activity are known or inferred. Recent advances in trapping procedures as well as new methods for identification of reactive intermediates are presented. A variety of clinically important drugs that act as mechanism-based inactivators of P450s are discussed. The irreversible inactivation of human P450s by these drugs has the potential for causing serious drug-drug interactions that may have severe toxicological effects. The clinical significance of inactivating human P450s for improving drug efficacy as well as drug safety is discussed along with the potential for exploiting mechanism-based inactivators of P450s for therapeutic benefits.

Theoretical assessment of a new experimental protocol for determining kinetic values describing mechanism (time)-based enzyme inhibition

We have shown previously that the conventional experimental protocol (CEP) used to characterise mechanism-based enzyme inhibition (MBI) of drug metabolism in vitro may introduce substantial bias in estimates of the relevant kinetic parameters. The aim of this study was to develop and assess, by computer simulation, an alternative, mechanistically-based experimental protocol (MEP). This protocol comprises three parts viz. assessment of the metabolism of the mechanism-based enzyme inactivator (MBEI), of its ability to participate in competitive inhibition and its ability to cause time-dependent inhibition. Thus, values of the maximum inactivation rate constant (k(inact)), the inactivator concentration associated with half-maximal rate of inactivation (K(I)), the partition ration (r), and the reversible inhibition constant (K(i)) of the MBEI are determined by nonlinear optimization of the experimental data using a model that allows for metabolism of both probe substrate and MBEI, the time-course of inactivation of the enzyme, and reversible inhibition of the metabolism of both probe substrate and MBEI. Sensitivity analysis is used to estimate the degree of confidence in the final parameter values. Virtual experiments using the MEP and the CEP were simulated, applying starting kinetic parameters reported for 16 known MBEIs. In the presence of simulated experimental error (5% CV), the MEP recovered accurate estimates of the kinetic values for all compounds, while estimates using the CEP were less accurate and less precise. The MEP promises to improve consistency in the determination of in vitro measures of MBI and, thereby, the quantitative assessment of its in vivo consequences.

The biochemistry of drug metabolism--an introduction: Part 2. Redox reactions and their enzymes

This review continues a general presentation of the metabolism of drugs and other xenobiotics started in a recent issue of Chemistry & Biodiversity. This Part 2 presents the numerous oxidoreductases involved, their nomenclature, relevant biochemical properties, catalytic mechanisms, and the very diverse reactions they catalyze. Many medicinally, environmentally, and toxicologically relevant examples are presented and discussed. Cytochromes P450 occupy a majority of the pages of Part 2, but a large number of relevant oxidoreductases are also considered, e.g., flavin-containing monooxygenases, amine oxidases, molybdenum hydroxylases, peroxidases, and the innumerable dehydrogenases/reductases.

Kinetic values for mechanism-based enzyme inhibition: Assessing the bias introduced by the conventional experimental protocol

The in vitro characterisation of a mechanism-based enzyme inactivator (MBEI) includes determination of the maximum inactivation rate constant (k(inact)), the inactivator concentration that produces half-maximal rate of inactivation (K(I)), and the partition ratio (r). Conventional experimental protocols (CEPs) assume insignificant metabolism of the MBEI during the "pre-incubation" stage and negligible inactivation of enzyme during the "incubation" stage. The aim of this study was to evaluate the bias in the estimation of kinetic values as a consequence of these assumptions. Ranges of values of k(inact), K(I), and r for reported MBEIs were collated and data for 27 virtual compounds were generated by combining the median, high and low values of each parameter. The kinetics of the virtual compounds and of four reported MBEIs were simulated under CEP, but taking account of enzyme inactivation, metabolism of the MBEI and the probe substrate, and their interaction at relevant stages. The differences between the estimated and starting kinetic values reflect the bias introduced by the CEP in the absence of experimental error. Despite simulating a stringent experimental procedure, 19% of the estimated kinetic values of the 27 virtual MBEIs had greater than 100% bias. Simulations relating to two of the actual MBEIs indicated no bias in k(inact) and 8-33% bias in K(I). However, the bias in K(I) values of the two other compounds exceeded 98% and corresponding bias in k(inact) was greater than 300%. Thus, CEP may introduce substantial bias in estimated kinetic values for mechanism-based inhibition, and the validity of some of the reported kinetic parameters may be questionable.

Automated assessment of time-dependent inhibition of human cytochrome P450 enzymes using liquid chromatography-tandem mass spectrometry analysis

Increasing reports of time-dependent inhibition of cytochrome P450 (P450) suggest further emphasis on interpreting the consequences, either from a pharmacokinetic or toxicological perspective. Two automated, time-dependent inhibition assays with a liquid chromatography-tandem mass spectrometric endpoint are presented. The initial assay utilizes human liver microsomes, a single concentration of inhibitor, and a single preincubation time of 30 min. Phenacetin, diclofenac, S-mephenytoin, bufuralol, and midazolam are used as substrates for CYP1A2, 2C9, 2C19, 2D6, and 3A4, and the assay differentiates between reversible and irreversible inhibition. The second assay uses individual recombinant human P450s, six inhibitor concentrations, and three time points to accurately define kinact and KI. A good correlation is demonstrated between kinact/KI and partition ratio, indicating that both terms are related in describing the efficiency of enzyme inactivation. Despite the single preincubation time point of 30 min used in the initial assay, a good relationship has been found to exist between the unbound IC50 estimated from this initial screen and the kinact/KI ratio derived from the more extensive subsequent single P450 assay. The higher throughput human liver microsomal assay can therefore generate IC50 values that can be used to predict the pharmacokinetic impact on cotherapies from the estimated kinact/KI ratio, predicted human dose, and pharmacokinetics.

Inhibitory effects of memantine on human cytochrome P450 activities: prediction of in vivo drug interactions

OBJECTIVE

The aim of the present study was to predict the drug interaction potential of memantine by elucidation of its inhibitory effects on cytochrome P450 enzymes using pooled human liver microsomes (HLM) and recombinant P450s.

METHODS

The inhibitory potency of memantine on CYP1A2, CYP2A6, CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP2E1, and CYP3A4 activities was examined with specific probe drugs in HLM and recombinant P450s. The in vivo drug interactions of memantine were predicted in vitro using the [ I]/([ I] + KI) values.

RESULTS

In HLM, memantine inhibited CYP2B6 and CYP2D6 activities, with KI (IC50) values of 76.7 (279.7) and 94.9 (368.7) microM, respectively. Both inhibitions were competitive. In addition, cDNA-expressed P450s were used to confirm these results. Memantine strongly inhibited recombinant CYP2B6 activity with IC50 ( KI) value of 1.12 (0.51) microM and activity of recombinant CYP2D6 with IC50 (KI) value of 242.4 (84.4) microM. With concentrations up to 1,000 microM, memantine showed no appreciable effect on CYP1A2, CYP2E1, CYP2C9, or CYP3A4 activities and a slight decrease of CYP2A6 and CYP2C19 activities. Based on [ I]/([ I] + KI) values calculated using peak total plasma concentration (or enzyme-available concentration in the liver) of memantine and the KI obtained in HLM, 1.3 (13.5), and 1.0% (11.2%), inhibition of the clearance of CYP2B6 and CYP2D6 substrates could be expected, respectively. Nevertheless, when considering KI values obtained from cDNA-expressed CYP2B6, as generally recommended, even 66.2% (95.9%) decrease in metabolism of coadministered CYP2B6 substrates could be anticipated.

CONCLUSION

Memantine exerts selective inhibition of CYP2B6 activity at clinically relevant concentrations, suggesting the potential for clinically significant drug interactions. Inhibition of other CYPs during memantine therapy is unlikely. Moreover, memantine represents a new, potent, selective inhibitor of recombinant CYP2B6, which may prove useful for screening purposes during early phases of in vitro drug metabolism studies with new chemical entities.

The mechanism-based inactivation of p450 2B4 by tert-butyl 1-methyl-2-propynyl ether: structural determination of the adducts to the p450 heme

tert-Butyl 1-methyl-2-propynyl ether (tBMP) was analyzed for its ability to act as a mechanism-based inactivator of p450 2B4. tBMP inactivated p450 2B4 in a time-, concentration-, and NADPH-dependent manner. Losses in activity occurred with concurrent losses in the reduced CO spectrum and native p450 heme; however, there was a greater loss in activity than could be accounted for by reduced CO spectra or native heme loss. LC/MS analysis demonstrated that the losses in native heme were accompanied by the appearance of two modified hemes with m/z values of 705Da, consistent with tBMP adducted hemes. Both adducts had identical fragmentation patterns when analyzed by LC/MS/MS. The spectra were consistent with a tBMP molecule and an oxygen atom attached to iron-depleted heme. Proton NMR studies suggest that the two modified hemes in p450 2B1 are N-alkylated on pyrrole rings A and D.

Developmental expression of human hepatic CYP2C9 and CYP2C19

The CYP2C subfamily is responsible for metabolizing many important drugs and accounts for about 20% of the cytochrome p450 in adult liver. To determine developmental expression patterns, liver microsomal CYP2C9 and -2C19 were measured (n = 237; ages, 8 weeks gestation-18 years) by Western blotting and with diclofenac or mephenytoin, respectively, as probe substrates. CYP2C9-specific content and catalytic activity were consistent with expression at 1 to 2% of mature values (i.e., specific content, 18.3 pmol/mg protein and n = 79; specific activity, 549.5 pmol/mg/min and n = 72) during the first trimester, with progressive increases during the second and third trimesters to levels approximately 30% of mature values. From birth to 5 months, CYP2C9 protein values varied 35-fold and were significantly higher than those observed during the late fetal period, with 51% of samples exhibiting values commensurate with mature levels. Less variable CYP2C9 protein and activity values were observed between 5 months and 18 years. CYP2C19 protein and catalytic activities that were 12 to 15% of mature values (i.e., specific content, 14.6 pmol/mg and n = 20; specific activity, 18.5 pmol/mg/min and n = 19) were observed as early as 8 weeks of gestation and were similar throughout the prenatal period. CYP2C19 expression did not change at birth, increased linearly over the first 5 postnatal months, and varied 21-fold from 5 months to 10 years. Adult CYP2C19 protein and activity values were observed in samples older than 10 years. The ontogeny of CYP2C9 and -2C19 were dissimilar among both fetal and 0- to 5-months postnatal samples, implying different developmental regulatory mechanisms.