Mechanism-based Enzyme Inactivation Research Articles

Human cytochrome P450 3A-mediated two-step oxidation metabolism of dimethomorph: Implications in the mechanism-based enzyme inactivation

Dimethomorph (DMM), an effective and broad-spectrum fungicide applied in agriculture, is toxic to environments and living organisms due to the hazardous nature of its toxic residues. This study aims to investigate the human cytochrome P450 enzyme (CYP)-mediated oxidative metabolism of DMM by combining experimental and computational approaches. Dimethomorph was metabolized predominantly through a two-step oxidation process mediated by CYPs, and CYP3A was identified as the major contributor to DMM sequential oxidative metabolism. Meanwhile, DMM elicited the mechanism-based inactivation (MBI) of CYP3A in a suicide manner, and the iminium ion and epoxide reactive intermediates generated in DMM metabolism were identified as the culprits of MBI. Furthermore, three common pesticides, prochloraz (PCZ), difenoconazole (DFZ) and chlorothalonil (CTL), could significantly inhibit CYP3A-mediated DMM metabolism, and consequently trigger elevated exposure to DMM in vivo. Computational studies elucidated that the differentiation effects in charge distribution and the interaction pattern played crucial roles in DMM-induced MBI of CYP3A4 during sequential oxidative metabolism. Collectively, this study provided a global view of the two-step metabolic activation process of DMM mediated by CYP3A, which was beneficial for elucidating the environmental fate and toxicological mechanism of DMM in humans from a new perspective.

Theoretical and Mechanistic Validation of Global Kinetic Parameters of the Inactivation of GABA Aminotransferase by OV329 and CPP-115

((S)-3-Amino-(difluoromethylenyl)cyclopent-1-ene-1-carboxylic acid (OV329) is a recently discovered inactivator of γ-aminobutyric acid aminotransferase (GABA-AT), which has 10 times better inactivation efficiency than its predecessor, CPP-115, despite the only structural difference being an endocyclic double bond in OV329. Both compounds are mechanism-based enzyme inactivators (MBEIs), which inactivate GABA-AT by a similar mechanism. Here, a combination of a variety of computational chemistry tools and experimental methods, including quantum mechanical (QM) calculations, molecular dynamic simulations, progress curve analysis, and deuterium kinetic isotope effect (KIE) experiments, are utilized to comprehensively study the mechanism of inactivation of GABA-AT by CPP-115 and OV329 and account for their experimentally obtained global kinetic parameters kinact and KI. Our first key finding is that the rate-limiting step of the inactivation mechanism is the deprotonation step, and according to QM calculations and the KIE experiments, kinact accurately represents the enhancement of the rate-limiting step for the given mechanism. Second, the present study shows that the widely used simple QM models do not accurately represent the geometric criteria that are present in the enzyme for the deprotonation step. In contrast, QM cluster models successfully represent both the ground state destabilization and the transition state stabilization, as revealed by natural bond orbital analysis. Furthermore, the globally derived KI values for both of the inactivators represent the inhibitor constants for the initial binding complexes (Kd) and indicate the inactivator competition with the substrate according to progress curve analysis and the observed binding isotope effect. The configurational entropy loss accounts for the difference in KI values between the inactivators. The approach we describe in this work can be employed to determine the validity of globally derived parameters in the process of MBEI optimization for given inactivation mechanisms.

Human Cytochrome P450 3a-Mediated Two-Step Oxidation Metabolism of Dimethomorph: Implicated in Mechanism-Based Enzyme Inactivation

Human Cytochrome P450 3a-Mediated Two-Step Oxidation Metabolism of Dimethomorph: Implicated in Mechanism-Based Enzyme Inactivation

Identification of Ketene-Reactive Intermediate of Erlotinib Possibly Responsible for Inactivation of P450 Enzymes.

Erlotinib (ELT), a tyrosine kinase inhibitor, is widely used for the treatment of nonsmall cell lung cancer in clinic. Unfortunately, severe drug-induced liver injury and other adverse effects occurred during the treatment. Meanwhile, ELT has been reported to be a mechanism-based inactivator of cytochrome P450(CYPs) 3A4 and 3A5. The objectives of this study were to identify ketene intermediate of ELT and investigate the association of the acetylenic bioactivation with the enzyme inactivation caused by ELT. A ketene intermediate was detected in human microsomal incubations of ELT, using 4-bromobenzylamine as a trapping agent. CYPs 3A4 and 3A5 mainly contributed to the bioactivation of ELT. Microsomal incubation study showed that the ketene intermediate covalently modified the enzyme protein at lysine residues and destroyed the structure of heme. The vinyl and ethyl analogs of ELT showed minor enzyme inhibitory effect (less than 20%), whereas ELT inactivated more than 60% of the enzyme. The present study provided a novel bioactivation pathway of ELT and facilitated the understanding of the mechanisms of ELT-induced mechanism-based enzyme inactivation and liver injury.

A mechanism-based inactivator of glycoside hydrolases involving formation of a transient non-classical carbocation.

The design of mechanism-based enzyme inactivators to generate chemical probes for biological research is an important challenge in carbohydrate chemistry. Here we describe the synthesis and biological evaluation of a novel carbocyclic mechanism-based inactivator of galactosidases (glycoside hydrolase families 27 and 36). Upon catalysis of this unnatural substrate, a transient non-classical carbocation forms within the enzyme active site. We show that the inactivation event, which proceeds via a bicyclobutonium ion intermediate, leads to a single alkylation event that occurs on the enzymatic nucleophile, an aspartic acid residue in this case. We also show that the catalytic proficiencies for enzymatic hydrolysis of substrates and inactivation by our bicyclo[4.1.0]heptyl analogue of galactose differ by only a factor of 20. This inactivator has the potential for further development as a useful biological research tool for both basic research and biotechnological applications.

β-Glucosidase 2 (GBA2) Activity and Imino Sugar Pharmacology

β-Glucosidase 2 (GBA2) is an enzyme that cleaves the membrane lipid glucosylceramide into glucose and ceramide. The GBA2 gene is mutated in genetic neurological diseases (hereditary spastic paraplegia and cerebellar ataxia). Pharmacologically, GBA2 is reversibly inhibited by alkylated imino sugars that are in clinical use or are being developed for this purpose. We have addressed the ambiguity surrounding one of the defining characteristics of GBA2, which is its sensitivity to inhibition by conduritol B epoxide (CBE). We found that CBE inhibited GBA2, in vitro and in live cells, in a time-dependent fashion, which is typical for mechanism-based enzyme inactivators. Compared with the well characterized impact of CBE on the lysosomal glucosylceramide-degrading enzyme (glucocerebrosidase, GBA), CBE inactivated GBA2 less efficiently, due to a lower affinity for this enzyme (higher KI) and a lower rate of enzyme inactivation (k(inact)). In contrast to CBE, N-butyldeoxygalactonojirimycin exclusively inhibited GBA2. Accordingly, we propose to redefine GBA2 activity as the β-glucosidase that is sensitive to inhibition by N-butyldeoxygalactonojirimycin. Revised as such, GBA2 activity 1) was optimal at pH 5.5-6.0; 2) accounted for a much higher proportion of detergent-independent membrane-associated β-glucosidase activity; 3) was more variable among mouse tissues and neuroblastoma and monocyte cell lines; and 4) was more sensitive to inhibition by N-butyldeoxynojirimycin (miglustat, Zavesca®), in comparison with earlier studies. Our evaluation of GBA2 makes it possible to assess its activity more accurately, which will be helpful in analyzing its physiological roles and involvement in disease and in the pharmacological profiling of monosaccharide mimetics.

Covalent and Noncovalent Intermediates of an NAD Utilizing Enzyme, Human CD38

Enzymatic utilization of nicotinamide adenine dinucleotide (NAD) has increasingly been shown to have fundamental roles in gene regulation, signal transduction, and protein modification. Many of the processes require the cleavage of the nicotinamide moiety from the substrate and the formation of a reactive intermediate. Using X-ray crystallography, we show that human CD38, an NAD-utilizing enzyme, is capable of catalyzing the cleavage reactions through both covalent and noncovalent intermediates, depending on the substrate used. The covalent intermediate is resistant to further attack by nucleophiles, resulting in mechanism-based enzyme inactivation. The noncovalent intermediate is stabilized mainly through H-bond interactions, but appears to remain reactive. Our structural results favor the proposal of a noncovalent intermediate during normal enzymatic utilization of NAD by human CD38 and provide structural insights into the design of covalent and noncovalent inhibitors targeting NAD-utilization pathways.

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.

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.

Integrating In Vitro Kinetic Data from Compounds Exhibiting Induction, Reversible Inhibition and Mechanism-Based Inactivation: In Vitro Study Design

Drug:drug interactions continue to be an obstacle for the pharmaceutical industry in the development of potential drug candidates. Considering the number of compounds that have been withdrawn from the market due to drug:drug interactions (e.g. cisapride, terfenadine and mibefradil), more pressure is placed on the pharmaceutical industry to investigate potential interactions prior to regulatory submission. In particular, induction and inhibition of drug metabolizing enzymes can profoundly alter the pharmacological and toxicological effects observed during monotherapy. However, due to differences in the expression and regulation of both metabolic enzymes and nuclear receptors responsible for induction, in vivo studies with pre-clinical species are not predictive of the human clinical situation. Although in vitro kinetic data also have limitations when extrapolating in vivo, in vitro testing has become more commonplace due to reduced cost and higher throughput. However, in the in vitro setting, complex enzyme kinetics can alter the estimation of kinetic parameters. Time-dependent or non-Michaelis-Menten kinetics can alter parameter estimates if experimental conditions are not optimal, and can therefore confound clinical predictions. Furthermore, mechanism-based inactivation (MBI) will reduce the active enzyme pool, both in vitro and in vivo, and thus complicate any parameter estimates. To further complicate matters, some compounds (e.g., ritonavir) inhibit, induce, as well as cause mechanism-based enzyme inactivation. For compounds such as ritonavir, the accurate estimation of kinetic parameters requires optimal experimental design at a minimum. This review will highlight the challenges in estimating enzyme kinetic parameters when both inhibition and induction are present, and will offer experimental viewpoints for the optimization of the experimental conditions.

Selective covalent labeling with radiolabeled suicide substrates for isolating P450s

This chapter describes the use of covalent tagging technique to isolate a target P450 protein, the obtainment of specific peptide sequences, and the subsequent cloning of the corresponding complementary deoxyribonucleic acid (cDNA). Mechanism-based enzyme inactivators are irreversible inactivators of specific target enzymes that catalyze their own destruction by unmasking a latent functional group during the catalytic cycle of the enzyme. The reactive intermediate thus formed may either evolve to a normal reaction product, which is then released from the enzyme, or become covalently attached. It is the ratio between these two competing reactions that decides primarily the rate of enzyme inactivation. A promising route is offered by introducing a substrate-specific step into the separation procedure. This may be achieved by using so-called “suicide substrates” really mechanism-based inhibitors) to introduce a covalent tag into the target enzyme and to allow tracking it during separation. As an example of the power of this approach and its shortcomings, this chapter describes the isolation of the first plant fatty acid ω-hydroxylase and its subsequent cloning.

Ticlopidine as a selective mechanism-based inhibitor of human cytochrome P450 2C19.

Experiments using recombinant yeast-expressed human liver cytochromes P450 confirmed previous literature data indicating that ticlopidine is an inhibitor of CYP 2C19. The present studies demonstrated that ticlopidine is selective for CYP 2C19 within the CYP 2C subfamily. UV-visible studies on the interaction of a series of ticlopidine derivatives with CYP 2C19 showed that ticlopidine binds to the CYP 2C19 active site with a K(s) value of 2.8 +/- 1 microM. Derivatives that do not involve either the o-chlorophenyl substituent, the free tertiary amine function, or the thiophene ring of ticlopidine did not lead to such spectral interactions and failed to inhibit CYP 2C19. Ticlopidine is oxidized by CYP 2C19 with formation of two major metabolites, the keto tautomer of 2-hydroxyticlopidine (1) and the dimers of ticlopidine S-oxide (TSOD) (V(max) = 13 +/- 2 and 0.4 +/- 0.1 min(-1)). During this oxidation, CYP 2C19 was inactivated; the rate of its inactivation was time and ticlopidine concentration dependent. This process meets the chemical and kinetic criteria generally accepted for mechanism-based enzyme inactivation. It occurs in parralel with CYP 2C19-catalyzed oxidation of ticlopidine, is inhibited by an alternative well-known substrate of CYP 2C19, omeprazole, and correlates with the covalent binding of ticlopidine metabolite(s) to proteins. Moreover, CYP 2C19 inactivation is not inhibited by the presence of 5 mM glutathione, suggesting that it is due to an alkylation occurring inside the CYP 2C19 active site. The effects of ticlopidine on CYP 2C19 are very analogous with those previously described for the inactivation of CYP 2C9 by tienilic acid. This suggests that a similar electrophilic intermediate, possibly a thiophene S-oxide, is involved in the inactivation of CYP 2C19 and CYP 2C9 by ticlopidine and tienilic acid, respectively. The kinetic parameters calculated for ticlopidine-dependent inactivation of CYP 2C19, i.e., t(1/2max) = 3.4 min, k(inact) = 3.2 10(-3) s(-1), K(I) = 87 microM, k(inact)/K(I) = 37 L.mol(-1).s(-1), and r (partition ratio) = 26 (in relation with formation of 1 + TSOD), classify ticlopidine as an efficient mechanism-based inhibitor although somewhat less efficient than tienilic acid for CYP 2C9. Importantly, ticlopidine is the first selective mechanism-based inhibitor of human liver CYP 2C19 and should be a new interesting tool for studying the topology of the active site of CYP 2C19.

Impact of Mechanism‐Based Enzyme Inactivation on Inhibitor Potency: Implications for Rational Drug Discovery

Mechanism-based enzyme inactivators (MBEIs) have unique kinetic actions that make predictions of potency, selectivity, and potential for metabolic drug interactions more complex than for competitive antagonists. We have derived a mathematical relationship that links the influence of substrate concentration and binding constant ([S] and K(m), respectively), inhibitor concentration and binding constant ([I] and K(I), respectively), and inactivation rate constant (k(inact)) to enzyme activity (v) and maximal activity (V(max)) at any time (t). The kinetic behavior of this relationship was validated in murine-macrophage cell cultures using MBEIs of nitric oxide synthase (NOS). This initial equation was also used in the derivation of a new relationship that directly links the kinetic parameters of mechanism-based inactivation to inhibitory potency at a particular time (IC((t))(50)). Using this direct relationship, we observed that the predicted rank inhibitory potency of a series of MBEIs was improved over that predicted by the K(I) parameter alone. These relationships offer a fundamental understanding of the kinetics of MBEI action and may be useful in the evaluation of these compounds during the discovery process.

Impact of Mechanism‐Based Enzyme Inactivation on Inhibitor Potency: Implications for Rational Drug Discovery

Mechanism‐based enzyme inactivators (MBEIs) have unique kinetic actions that make predictions of potency, selectivity, and potential for metabolic drug interactions more complex than for competitive antagonists. We have derived a mathematical relationship that links the influence of substrate concentration and binding constant ([S] and Km, respectively), inhibitor concentration and binding constant ([I] and KI, respectively), and inactivation rate constant (kinact) to enzyme activity (v) and maximal activity (Vmax) at any time (t). The kinetic behavior of this relationship was validated in murine‐macrophage cell cultures using MBEIs of nitric oxide synthase (NOS). This initial equation was also used in the derivation of a new relationship that directly links the kinetic parameters of mechanism‐based inactivation to inhibitory potency at a particular time (IC50(t)). Using this direct relationship, we observed that the predicted rank inhibitory potency of a series of MBEIs was improved over that predicted by the KI parameter alone. These relationships offer a fundamental understanding of the kinetics of MBEI action and may be useful in the evaluation of these compounds during the discovery process. © 2000 Wiley‐Liss, Inc. and the American Pharmaceutical Association J Pharm Sci 89: 1404–1414, 2000

Assignment of Sweet Almond β-Glucosidase as a Family 1 Glycosidase and Identification of Its Active Site Nucleophile

Sweet almond beta-glucosidase is a well studied glycosidase, having been subjected to numerous kinetic analyses and inhibition studies. However, it is not known to which glycosidase family it belongs, nor is the identity of the active site nucleophile known with certainty. It can be inactivated using the specific, mechanism-based enzyme inactivator 2-deoxy-2-fluoro-beta-D-glucopyranosyl fluoride, which functions by forming a stable 2-deoxy-2-fluoro-alpha-D-glucopyranosyl-enzyme intermediate. The glycosylated peptide present in a peptic digest of this trapped glycosyl-enzyme intermediate was identified by use of neutral loss scans on an electrospray ionization triple quadrupole mass spectrometer. Comparative liquid chromatographic/mass spectrometric analysis of peptic digests of labeled and unlabeled enzyme samples confirmed the unique presence of this peptide of m/z = 1041 in the labeled sample. The sequence of this peptide was determined to be Ile-Thr-Glu-Gln-Gly-Val-Asp-Glu by further tandem mass spectrometric analysis in the daughter ion scan mode in conjunction with Edman degradation of the purified peptide. The identity of the labeled side chain was determined by further tandem mass spectrometric analysis in the daughter ion scan mode of a partially purified sample of the labeled peptide subjected to methyl esterification, the fragmentation pattern being consistent only with the first Glu in the sequence being labeled. The sequence around this residue is identical to that surrounding the catalytic nucleophile in many members of glycosidase Family 1, confirming the assignment of this enzyme to that family. The residue labeled is, however, different from that (Asp) identified previously in the enzyme from bitter almonds by use of conduritol epoxide affinity labels, although apparently close in the primary sequence.

Potency and inactivation rates of analogues of an irreversible inhibitor of vertebrate oxidosqualene cyclase

Truncated, 22(23)-dihydro, and fluorinated analogues of (3 S)-29-methylidene-2,3-oxidosqualene (29-MOS) were prepared and inhibitory potencies and rates of inactivation of rat oxidosqualene cyclase were measured. Rapid mechanism-based enzyme inactivation was observed for both methylidene and difluoromethylidene analogues with complete pro-side chains, but not for truncated analogues.

Verification of the Mechanism of Oxidative Ring Expansion in the Biosynthesis of Stipitatic Acid by Talaromyces stipitatus

The pattern of incorporation of 13C from 13C-labeled acetate into stipitatic acid by Talaromyces stipitatus was studied by 13C NMR. The results obtained were consistent with the biosynthetic routes previously elucidated for similar fungal tropolones. These studies, which both required and enabled the first complete 13C NMR assignments of stipitatic acid, also demonstrated that the decarboxylation step in the biosynthesis of stipitatic acid occurs after the formation of the tropolone ring. The biosynthetic pathway to stipitatic acid includes an oxidative expansion of the benzene ring of 3-methylorsellinic acid to a seven-membered tropolone ring. As a prelude to mechanism-based enzyme inactivation studies, the mechanism of this step was reinvestigated by the biosynthetic incorporation of 18O into stipitatic acid from 18O 2. The 13C NMR spectrum of the resulting [ 18O]stipitatic acid showed an 18O-induced isotope shift for the tropolone-ring carbonyl resonance with no evidence of 18O enrichment at the C-6 hydroxyl group. This result provides conclusive evidence in support of the earlier report that the ring expansion involves oxidation by a monooxygenase to form a hydroxymethyl intermediate, which undergoes a pinacol rearrangement to form the tropolone ring.

Chapter 2 Radical thoughts about the life of MAO

Publisher Summary Monoamine oxidase (MAO)—a flavoenzyme that oxidatively deaminates a variety of biogenic and xenobiotic amines—plays an important role in the regulation of the intracellular concentrations of these monoamine neurotransmitters. Two different isozymes of MAO, known as MAO A and MAO B, have been identified; MAO A selectively oxidizes norepinephrine and serotonin and MAO B oxidizes phenylethylamine and benzylamine. Because of the importance of MAO in the treatment of neurological diseases, this chapter elucidates its catalytic mechanism so that this information can be used in the design of new classes of inactivators for this enzyme. Mechanism-based enzyme inactivators are unreactive compounds that bear a structural similarity to the substrate or product for a target enzyme. Once inside the active site, they are converted by the normal catalytic mechanism into species that inactivate the enzyme. These inactivators are important for the study of enzyme mechanisms because they are substrates for the target enzyme that are converted via the normal catalytic mechanism into products that inactivate the enzyme. From the inactivation mechanism, then, information about the catalytic mechanism can be gleaned. Much of the discussion in the chapter is based on this principle.

Identification of Glu340 as the active-site nucleophile in human glucocerebrosidase by use of electrospray tandem mass spectrometry

Gaucher disease is an inherited lysosomal storage disorder caused by a deficiency of human acid beta-glucosidase (glucocerebrosidase). This enzyme is inactivated by the specific, mechanism-based enzyme inactivator 2-deoxy-2-fluoro-beta-D-glucopyranosyl fluoride, which functions by forming a stable 2-deoxy-2-fluoro-alpha-D-gluco-pyranosyl-enzyme intermediate. The key nucleophilic amino acid residue involved in formation of this intermediate was conclusively identified by tandem mass spectrometry as Glu340, and not Asp443 as thought previously. This was confirmed by site-directed mutagenesis. Identification, and mass determination, of the labeled peptide in a proteolytic hydrolysate involved detection of a collision-induced fragmentation reaction specific to the sugar-peptide linkage. Confirmation of the identity of the labeled peptide was obtained both by tandem mass spectrometric sequencing and by chemical degradation of the purified peptide. This method allowed the rapid, sensitive, and non-isotopic determination of an essential amino acid residue in a clinically important enzyme.

Mechanism-based enzyme inactivation via a diactivated cyclopropane intermediate

Mechanism-based enzyme inactivation via a diactivated cyclopropane intermediate