Mechanism-based inactivation of cytochrome P450: isolation and characterization of N-alkyl heme adducts

Improved methods for the detection of heme and protoporphyrin IX adducts and quantification of heme B from cytochrome P450 containing systems

Heme B is a critical prosthetic group for the function of numerous proteins including the cytochrome P450 (CYP) family of enzymes. CYP enzymes are involved in the metabolism of endogenous and xenobiotic molecules that are of central interest in drug development. Formation of reactive metabolites by CYPs can lead to heme modification and destruction of the enzyme. The structure of the adducted heme can provide key information on the mechanism of inactivation, which is of great interest during preclinical drug discovery. Historically, techniques to extract the modified heme or protoporphyrin IX species involved harsh extraction conditions and esterification of propionate groups to aid chromatography. We have developed a simplified extraction method and LC/MS chromatography system that does not require derivatization to quantify heme B and identify modified heme B species from multiple CYP-containing matrices. The method uses mass defect filter triggered data dependent MS2 scans to rapidly identify heme and protoporphyrin IX adducts. These methods may also be useful for the analysis of other heme variants and hemoproteins.

Ortho-Methylarylamines as Time-Dependent Inhibitors of Cytochrome P450 1A1 Enzyme

BACKGROUND

Members of the cytochrome P450 1A family metabolize many procarcinogens such as polycyclicaromatic hydrocarbons and heterocyclic amines. Inactivation of these enzymes is a prerequisite for cancer prevention and treatment in certain cases. Mechanism-based inhibition (time and co-factor dependent) is an effective method for the inactivation of these enzymes. Our recent study on emodin analogs revealed an anthraquinone with ortho-methylarylamine moiety that exhibited timedependent inhibition of P450 enzymes 1A1 and 1A2.

METHODS

To determine whether the amino group or the methyl group or both were responsible for the time-dependent inhibition of these enzymes, a set of eleven compounds containing the orthomethylarylamine moiety were identified through a database search, and studied for the inhibition of the P450 enzymes 1A1, 1A2, 2A6 and 2B1. Our earlier studies on carbazole derivatives provided us with highly selective P450 1A2 inhibitors. Glycine scanning studies were performed on the docked proteinligand complexes of compounds 1-20 in order to understand the contribution of different protein residues towards the ligand binding.

RESULTS

Four compounds were found to cause selective time-dependent inhibition of P450 1A1 with KI values ranging from 0.24 to 8.25 mM. These compounds exhibited only direct inhibition of P450 1A2. Molecular modeling studies of these molecules indicated that the shapes of the molecules, their binding modes, and the methyl substituent in close proximity (4.5-5.7 Å) to the heme-Fe all contributed to their selective time-dependent inhibition activity on P450 1A1. Glycine scanning studies for P450 1A1 indicated that ligand interaction with Phe123 was the strongest binding contributor and similar studies for P450 1A2 indicated that ligand interactions with the phenylalanine residues 226 and 260 were the largest binding contributors.

CONCLUSION

Four compounds have been identified that exhibit selective time-dependent inhibition of P450 1A1. Modeling studies have indicated that the proximity of the aromatic methyl group to the heme-Fe could be the main contributor for time-dependent inhibition. Future studies will focus on the confirmation of the involvement of the aromatic methyl group in enzyme inactivation.

Cytochrome P450 family 1 inhibitors and structure-activity relationships

With the widespread use of O-alkoxyresorufin dealkylation assays since the 1990s, thousands of inhibitors of cytochrome P450 family 1 enzymes (P450s 1A1, 1A2, and 1B1) have been identified and studied. Generally, planar polycyclic molecules such as polycyclic aromatic hydrocarbons, stilbenoids, and flavonoids are considered to potentially be effective inhibitors of these enzymes, however, the details of the structure-activity relationships and selectivity of these inhibitors are still ambiguous. In this review, we thoroughly discuss the selectivity of many representative P450 family 1 inhibitors reported in the past 20 years through a meta-analysis.

Transduction of physical force by the vascular wall Role of phospholipase C and cytochrome P450 metabolites of arachidonic acid

The blood vessel wall responds actively to an elevation in transmural pressure. This pressure-induced myogenic response is thought to set the basal level of vascular tone upon which metabolic and neural influences operate in concert to regulate organ blood flow. The cellular mechanisms that mediate the vascular muscle response to mechanical deformation via a changing transmural pressure include membrane depolarization, activation of phospholipase C, and a rise in intracellular [Ca(2+)](i), which appear to be nonadapting-remaining active as long as the pressure stimulus is applied. This brief review addresses some of the cellular events mediating transduction of transmural pressure by the vessel wall. Two possible mechanisms that are responsible for the nonadapting nature of pressure-induced myogenic tone are also explored, namely, formation of a P450 metabolite of arachidonic acid, which acts to buffer activation of K(+) channels as intracellular Ca(2+) rises, and direct activation of Ca(2+) channels by diacylglycerol. Evidence is provided suggesting that activation of phospholipase C is responsible for both the release of the arachidonic acid substrate for P450 enzymes and for the formation of diacylglycerol via its action on membrane-bound phospholipids.

In silico studies of polyaromatic hydrocarbon inhibitors of cytochrome P450 enzymes 1A1, 1A2, 2A6, and 2B1

A computational study was undertaken to understand the nature of binding and the structural features that play a significant role in the binding of arylacetylene molecules to cytochrome P450 enzymes 1A1, 1A2, 2A6, and 2B1. Nine polycyclic arylacetylenes determined to be mechanism-based P450 enzyme inhibitors were studied. The lack of polar substituents in these compounds causes them to be incapable of hydrogen bonding to the polar protein residues. The four P450 enzymes of interest all have phenylalanine residues in the binding pocket for potential pi-pi interactions with the aromatic rings of the inhibitors. The inhibition potency of these arylacetylenes toward P450s 1A1 and 2B1 showed a dependence on the proximity of the inhibitor's triple bond to the prosthetic heme Fe of the enzyme. In P450 enzyme 1A2, the inhibitor's potency showed more dependence on the pi-pi interactions of the inhibitor's ring systems with the phenylalanine residues of the protein, with the proximity of the inhibitor triple bond to the heme Fe weighing in as the second most important factor. The results suggest that maximizing the pi-pi interactions with phenylalanine residues in the binding pocket and optimum proximity of the acetylene moiety to the heme Fe will provide for a substantial increase in the potency of the polyaromatic hydrocarbon mechanism-based inhibitors. A fine balance of these two aspects of binding coupled with attention to supplementing hydrophobic interactions could address potency and selectivity issues for these inhibitors.

MECHANISM-BASED INACTIVATION AND REVERSIBILITY: IS THERE A NEW TREND IN THE INACTIVATION OF CYTOCHROME P450 ENZYMES?

Recent studies with cytochrome P450 (P450) enzymes from the 2E and 2B subfamilies have shed light on what may be a new trend in the mechanism-based inactivation of P450s: reversibility. The reversible inactivation of P450-type enzymes was first reported in the mid-1990s by Dexter and Hager [Dexter AF and Hager LP (1995) J Am Chem Soc 117:817-818], who studied the transient heme N-alkylation of chloroperoxidase by allylbenzene and 1-hexyne. While characterizing small tert-butyl acetylenes as mechanism-based inactivators of P450s 2E1 and 2B4, Hollenberg and coworkers observed the reversible inactivation of an acetylene-inactivated T303A mutant of P450 2E1. The mechanism of reversibility was a combined product of the structure of the inactivator and the positioning of conserved amino acid residues, threonine 303 (alanine in the mutant) and glutamate 302, in the enzyme active site. Reversibility was also observed with both wild-type P450 2B4 and the T302A mutant of 2B4, although this inactivation and reversibility did not seem to depend on the T302 residue. Subsequent studies have attempted to elucidate the chemical/structural requirements of the inactivator in determining reversibility and have shown that both the size and the chemical nature of functional groups play an important role. At this time, reversibility has only been observed with P450 2E and 2B enzymes during their mechanism-based inactivation by terminal alkynes. Future studies with P450s from other subfamilies and structurally distinct inactivators will greatly aid our understanding of the molecular and chemical determinants of reversibility.

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.

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

N-(3,5-Dichloro-4-pyridyl)-3-(cyclopentyloxy)-4-methoxybenzamide (DCMB) is a known marker substrate for cytochrome p450 2B6. Based on the chemical template of DCMB, a novel terminal acetylene compound, N-(3,5-dichloro-4-pyridyl)-4-methoxy-3-(prop-2-ynyloxy)benzamide (TA) was synthesized and evaluated as a mechanism-based inactivator of p450 2B6. The pseudo first-order inactivation of expressed p450 2B6 by TA was both substrate and time-dependent. The kinetics of inhibition resulted in a maximal rate constant (k(inactivation)) of 0.09 min(-1) and an apparent K(I) of 5.1 microM. Incubation of expressed p450 2B6 with TA and NADPH resulted in a 68% loss in enzyme activity and a concurrent 62% loss in the formation of a reduced carbon monoxide complex, suggesting that heme destruction is the primary mode of enzyme inactivation. Enzyme inactivation of p450 2B6 was not reduced by the presence of 10 mM glutathione and was protected by incubation of excess DCMB with TA. The production of the carboxylic acid metabolite, N-(3,5-Dichloro-4-pyridyl)-3-(2-carboxyethoxy)-4-methoxybenzamide (TA-COOH), during the incubation of TA with 2B6 suggests that inactivation proceeds through a ketene intermediate. For 2B6 inactivation, the partition ratio was approximately 1.5 nmol TA-COOH formed/nmol P450 inactivated. Finally, TA was evaluated for mechanism-based inactivation of p450 3A4, 2C9, 2C19, 2D6, and 2E1 using human liver microsomes. In addition to 2B6, p450 2C forms were also found to be sensitive to TA-mediated inactivation, suggesting that subtle changes in the O-alkyl chain of the parent may be critical for the selectivity of enzyme inactivation.

Mechanism-based inactivation of cytochrome P450 3A4 by 17 alpha-ethynylestradiol: evidence for heme destruction and covalent binding to protein

17 alpha-Ethynylestradiol (EE), a major constituent of many oral contraceptives, inactivated the testosterone 6 beta-hydroxylation activity of purified P450 3A4 reconstituted with phospholipid and NADPH-cytochrome P450 reductase in a mechanism-based manner. The inactivation of P450 3A4 followed pseudo first order kinetics and was dependent on NADPH. The values for the K(I) and k(inact) were 18 microM and 0.04 min(-1), respectively, and the t(1/2) was 16 min. Incubation of 50 microM EE with P450 3A4 at 37 degrees C for 30 min resulted in a 67% loss of testosterone 6 beta-hydroxylation activity accompanied by a 35% loss of the spectral absorbance of the native protein at 415 nm and a 70% loss of the spectrally detectable P450-CO complex. The inactivation of P450 3A4 by EE was irreversible. Testosterone, an alternate substrate, was able to protect P450 3A4 from EE-dependent inactivation. The partition ratio was approximately 50. The stoichiometry of binding was approximately 1.3 nmol of an EE metabolite bound per nmol of P450 3A4 inactivated. SDS-polyacrylamide gel electrophoresis analysis demonstrated that [(3)H]EE was irreversibly bound to the P450 3A4 apoprotein. After extensive dialysis of the [(3)H]EE inactivated samples, high-pressure liquid chromatography (HPLC) analysis demonstrated that the inactivation resulting from EE metabolism led to the destruction of approximately half the heme with the concomitant generation of modified heme and EE-labeled heme fragments and produced covalently radiolabeled P450 3A4 apoprotein. Electrospray mass spectrometry demonstrated that the fraction corresponding to the major radiolabeled product of EE metabolism has a mass (M - H)(-) of 479 Da. HPLC and gas chromatography-mass spectometry analyses revealed that EE metabolism by P450 3A4 generated one major metabolite, 2-hydroxyethynylestradiol, and at least three additional metabolites. In conclusion, our results demonstrate that EE is an effective mechanism-based inactivator of P450 3A4 and that the mechanism of inactivation involves not only heme destruction, but also the irreversible modification of the apoprotein at the active site.

Pharmacological modulation of nitric oxide synthesis by mechanism-based inactivators and related inhibitors

Nitric oxide synthase (NOS) (EC 1.14.13.39) is a homodimeric cytochrome P450 monooxygenase analog that generates nitric oxide (NO) from the amino acid L-arginine. Enzymatically produced NO acts as an intracellular messenger in neuronal networks, blood pressure regulatory mechanisms, and immune responses. Isoform-selective pharmacological modulation of NO synthesis has emerged as a new therapeutic strategy for the treatment of diverse clinical conditions associated with NO overproduction. Mechanism-based inactivators (MBIs) represent a class of NOS mechanistic inhibitors that require catalytic turnover to produce irreversible inactivation of the ability of NOS to generate NO. Diverse isoform-selective NOS MBIs have been characterized with respect to their kinetic parameters and chemical mechanisms of inactivation. In studies with isolated and purified NOS isoforms, MBIs produce irreversible inactivation of NOS enzymatic activities. The inactivation process is associated with covalent modification of the NOS active site and proceeds either through heme destruction, its structural alteration, or covalent modification of the NOS protein chain. The behavior of NOS MBIs in intact cells is different from their behavior observed with the isolated NOS isoforms. In cytokine-induced RAW 264.7 macrophages, treatment with MBIs produces a complete loss of cellular NOS synthetic competence and inducible NOS activity. However, following drug removal, cells can recover at least partially in the absence of protein synthesis. In GH3 cells containing the neuronal NOS isoform, calcium transients are too low and abbreviated to allow significant NOS inactivation; hence, the cellular effects of MBIs on the neuronal isoform are almost completely and immediately reversible.

Mechanism-based inactivation of cytochromes P450 2E1 and 2B1 by 5-phenyl-1-pentyne

A series of acetylenic compounds whose structures were based on "P450 2E1-like" substrates was investigated for their ability to cause inactivation of P450 2E1-dependent p-nitrophenol hydroxylation. The most effective compound with liver microsomes from pyridine-treated rats or with rabbit P450 2E1 in a reconstituted system was 5-phenyl-1-pentyne. The inactivation of purified 2B1, 2E1, a truncated 2E1 lacking amino acids 3-29, 2E1(Delta3-29), or a truncated 2E1 in which threonine 303 was replaced with alanine, 2E1(Delta3-29, T303A), in a reconstituted system by 5-phenyl-1-pentyne was NADPH- and time-dependent and followed pseudo-first-order kinetics. The maximal rate constants for inactivation, the concentrations that gave half-maximal inactivation (KI), and the partition ratios (the number of 5-phenylvaleric acid molecules formed/inactivation event) were determined with each P450. The KI values for 2B1 and 2E1(Delta3-29, T303A) were twice those for 2E1 and 2E1(Delta3-29), and the partition ratios for 2B1 and 2E1(Delta3-29, T303A) were 5-10 times greater than those of 2E1 or 2E1(Delta3-29). During the incubation of P450 2E1 with 5-phenyl-1-pentyne, the loss of P450 as determined by the reduced-CO difference spectra was equal to the loss of catalytic activity. The formation of a heme adduct was demonstrated by HPLC analysis of reaction mixtures containing 5-[3H]phenyl-1-pentyne. HPLC analysis with diode-array detection showed that the Soret region of the proposed heme adduct was different from that of the unmodified heme. The HPLC peak containing the proposed heme adduct was further analyzed by matrix-assisted laser desorption ionization mass spectrometry, and the resulting peaks could result from the addition of a 2-oxo-5-phenylpentyl group to the heme.