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DMD #58636 Short Communication Regioselective Hydroxylation of Omeprazole Enantiomers by Bacterial CYP102A1 Mutants Sang Hoon Ryu, Bo-Yeon Park, So-Young Kim, Sun-Ha Park, Hyun-Jin Jung, Min Park, Ki Deok Park, Taeho Ahn, Hyung-Sik Kang, and Chul-Ho Yun School of Biological Sciences and Technology, Chonnam National University, Gwangju 500- 757, Republic of Korea (S.H.R, B.-Y.P., S.-Y.K, S.-H.P., H.-J.J., M.P., H.-S.K., C.-H.Y.); Gwangju Center, Korea Basic Science Institute, Gwangju 500-757, Republic of Korea (K.D.P.); Department of Biochemistry, College of Veterinary Medicine, Chonnam National University, Gwangju 500-757, Republic of Korea (T.A.). DMD Fast Forward. Published on July 9, 2014 as doi:10.1124/dmd.114.058636 Copyright 2014 by the American Society for Pharmacology and Experimental Therapeutics. This article has not been copyedited and formatted. The final version may differ from this version. DMD Fast Forward. Published on July 9, 2014 as DOI: 10.1124/dmd.114.058636 at ASPET Journals on November 23, 2020 dmd.aspetjournals.org Downloaded from

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DMD #58636

1

Short Communication

Regioselective Hydroxylation of Omeprazole Enantiomers by Bacterial

CYP102A1 Mutants

Sang Hoon Ryu, Bo-Yeon Park, So-Young Kim, Sun-Ha Park, Hyun-Jin Jung, Min Park, Ki

Deok Park, Taeho Ahn, Hyung-Sik Kang, and Chul-Ho Yun

School of Biological Sciences and Technology, Chonnam National University, Gwangju 500-

757, Republic of Korea (S.H.R, B.-Y.P., S.-Y.K, S.-H.P., H.-J.J., M.P., H.-S.K., C.-H.Y.);

Gwangju Center, Korea Basic Science Institute, Gwangju 500-757, Republic of Korea

(K.D.P.); Department of Biochemistry, College of Veterinary Medicine, Chonnam National

University, Gwangju 500-757, Republic of Korea (T.A.).

DMD Fast Forward. Published on July 9, 2014 as doi:10.1124/dmd.114.058636

Copyright 2014 by the American Society for Pharmacology and Experimental Therapeutics.

This article has not been copyedited and formatted. The final version may differ from this version.DMD Fast Forward. Published on July 9, 2014 as DOI: 10.1124/dmd.114.058636

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Running title: Regioselective hydroxylation of omeprazole by CYP102A1

Corresponding author: Professor Chul-Ho Yun

School of Biological Sciences and Technology, Chonnam National University,

Gwangju 500-757, Republic of Korea.

Tel: +82-62-530-2194; Fax: +82-62-530-2199; E-mail: [email protected]

Number of Text pages: 14

Number of Tables: 0

Number of Figures: 3

Number of References: 25

Number of words in Abstract: 211 words

Number of words in Introduction: 611 words

Number of words in Results and Discussion: 1421 words

Supplemental Tables S1-S4 and Figures S1-S11

Abbreviations: CYP or P450, cytochrome P450; CPR, NADPH-cytochrome P450 reductase;

LC-MS, liquid chromatography-mass spectrometry; OMP, omeprazole; PPI, proton pump

inhibitor; TTN, total turnover number

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ABSTRACT: A large set of Bacillus megaterium CYP102A1 mutants are known to

metabolize various drugs to form human metabolites. Omeprazole (OMP), a proton pump

inhibitor, has been widely used as an acid inhibitory agent for the treatment of gastric acid

hypersecretion disorders. It is primarily metabolized by human CYP2C19 and CYP3A4 to 5’-

OH OMP and a sulfone product, respectively. Recently, it was reported that several

CYP102A1 mutants can oxidize racemic and S-OMP to 5’-OH OMP and that these mutants

can further oxidize 5’-OH racemic OMP to 5’-COOH OMP. Here, we report that the S- and

R-enantiomers of OMP are hydroxylated by 26 mutants of CYP102A1 to produce one major

metabolite (5’-OH OMP) regardless of the chirality of the parent substrates. Although the

binding of R-OMP to the CYP102A1 active site caused a more apparent change of heme

environment compared to binding of S-OMP, there was no correlation between the spectral

change upon substrate binding and catalytic activity of either enantiomer. The 5’-OH OMP

produced from racemic, S-, and R-OMP could be obtained with a high conversion rate and

high selectivity when the triple R47L/F87V/L188Q mutant was used. These results suggest

that bacterial CYP102A1 mutants can be used to produce the human metabolite 5’-OH OMP

from both the S- and R-enantiomers of OMP.

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Introduction

Omeprazole (OMP), a proton pump inhibitor (PPI), acts to regulate acid production in

the stomach by irreversible binding to the proton pump (H+-K+) ATPase in the gastric parietal

cell. It is used for the treatment of gastric acid hypersecretion disorders including dyspepsia,

peptic ulcer disease, gastroesophageal reflux disease, laryngopharyngeal reflux, and

Zollinger–Ellison syndrome. It is administered as a racemic mixture of the R- and S-

enantiomers. OMP is primarily metabolized by the hepatic enzymes CYP2C19 and CYP3A4.

Both CYP2C19 and CYP3A4 exhibit a stereoselective metabolism of OMP. CYP2C19 favors

5’-hydroxylation of R-OMP, whereas sulfoxidation mediated by CYP3A4 highly favors the S-

form (Li et al., 2005; Abelö et al., 2000; Yamazaki et al., 1997) (Figure 1). S-OMP

(esomeprazole; Nexium®) has been developed as a new drug with the goal of improving the

pharmacokinetic and pharmacodynamic profiles of racemic omeprazole (McKeage et al.,

2008). It is known that esomeprazole is significantly more active against Helicobacter pylori

than omeprazole. Esomeprazole was not associated with either gastric dysplasia or neoplasia

after long-term treatment in patients with healed reflux esophagitis.

CYP2C19 is a highly polymorphic enzyme, with variations in both mRNA and protein

expression as well as differences in the protein coding region, which give rise to differing

rates of catalysis (Goldstein, 2001). The proportion of the poor metabolizer phenotype varies

widely between populations, from ~2% for Caucasians to nearly ~20% in Asians. Several

pharmacogenomic studies have suggested that PPI treatment should be tailored according to

the patient’s CYP2C19 metabolism status (Furuta et al., 2005). A large set of CYP2C19

alleles from ethnically different populations has been reported

(http://www.cypalleles.ki.se/cyp2c19.htm). The PPI omeprazole and related ulcer drugs are

primarily oxidized by CYP2C19, and poor metabolizers show a better response to these drugs

(Kawabata et al., 2003).

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The importance of drug metabolites has been recognized in several International

Committees on Harmonization (ICH) and safety guidelines such as the ICH S7A, the ICH

S3A, and the ICH M3 (Atrakchi, 2009;

http://www.ich.org/products/guidelines/safety/article/safety-guidelines.html). Some drug

metabolites of concern can be prepared by chemical methods, but others are generally

prepared by several enzyme sources, including recombinant human P450 enzymes (Yun et al.,

2006). Some bacterial P450s are already known to be competitive biocatalysts for metabolite

production due to their high activities and stabilities (Julsing et al., 2008; Whitehouse et al.,

2012; Kang et al., 2014). Currently, a large set of CYP102A1 mutants are known to have

similar activities to human P450 as well as the ability to metabolize a number of marketed

drugs and steroids (Yun et al., 2007; Whitehouse et al., 2012; Kang et al., 2014). Therefore,

CYP102A1 is generally accepted as a prototype monooxygenase for the development of

versatile biocatalysts for use in drug discovery and synthesis (Urlacher and Girhard, 2012;

Kang et al., 2014). Recently, the 5’-hydroxylation activity of CYP102A1 mutants on racemic

OMP (Yun et al., 2013; Butler et al., 2013) and S-OMP (Butler et al., 2014) has been reported.

It was also shown that 5’-OH racemic OMP can be further oxidized to a carboxylated product

(Butler et al., 2013).

The aim of this study was to investigate the enzymatic properties of CYP102A1

mutants to generate the 5’-OH product from S- and R-OMP enantiomers. It was found that a

set of CYP102A1 mutants could catalyze the formation of 5’-OH OMP regardless of the

chirality of the substrate. Although human CYP2C19 and CYP3A4 form 5’-OH and sulfone

products, respectively, CYP102A1 mutants could produce 5’-OH OMP (but not other

products) as the major metabolite. Some of the CYP102A1 mutants tested here were able to

catalyze the oxidation of OMP to generate its primary metabolite, 5’-OH OMP, from S- and

R- enantiomers with a high conversion rate and high selectivity.

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Materials and Methods

Chemicals. OMP (racemic mixture), S-OMP and NADPH were purchased from

Sigma-Aldrich (St. Louis, MO). R-OMP was obtained from Santa Cruz Biotechnology

(Dallas, Texas, USA). Other chemicals were of the highest grade commercially available.

Construction of CYP102A1 mutants by site-directed mutagenesis and random

mutagenesis. Wild type and 26 different mutants of CYP102A1 used in this study were

prepared as previously described (Kim et al., 2008; Park et al., 2010). The mutants were

selected based on their activities toward a variety of human P450 substrates and drugs.

Mutants #1-17 have mutations in the substrate channel and active site (Kim et al., 2008), and

mutants #18-26 have mutations outside of the active site and substrate channel (Park et al.,

2010). Each mutant bears amino acid substitution(s) relative to wild type CYP102A1, as

summarized in Supplemental Table S1.

Expression and purification of wild type and mutant enzymes of CYP102A1. Wild

type and 26 mutants of CYP102A1 were expressed in the Escherichia coli strain DH5αF′-IQ

and purified as previously described (Kim et al., 2008; Park et al., 2010). The CYP102A1

concentrations were determined by CO difference spectra using ε = 91 mM-1cm-1. For all of

the wild type and mutated enzymes, a typical culture yielded 200 to 700 nM P450.

Hydroxylation of OMP. Typical steady-state reactions for the hydroxylation of each

OMP enantiomer included 50 pmol of CYP102A1 in 0.25 ml of 100 mM potassium

phosphate buffer (pH 7.4) containing a final concentration of 100 μM OMP (racemic mixture,

S-, or R-enantiomer). To determine the kinetic parameters of several CYP102A1 mutants, a

range of concentrations of OMP (2 to 1000 μM) was used. An aliquot of a NADPH-

generating system was used to initiate reactions (final concentrations: 10 mM glucose 6-

phosphate, 0.5 mM NADP+, and 1 IU/ml yeast glucose 6-phosphate dehydrogenase). A stock

solution of OMP (200 mM) was prepared in dimethyl sulfoxide and diluted into the enzyme

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reactions with a final organic solvent concentration of <1% (v/v). OMP is soluble at the

diluted solution of 2 mM concentration (1%, v/v). Reactions were incubated for 30 min at

37°C and terminated with 0.50 ml of ice-cold dichloromethane. After centrifugation of the

reaction mixture, organic phases were evaporated under nitrogen gas. The product was

analyzed by HPLC using a Gemini C18 column (4.6 × 150 mm, 5 μm; Phenomenex,

Torrance, CA) with an acetonitrile-water (30:70, v/v) mobile phase. Elutes were detected by

UV at 302 nm. Phenacetin was used as an internal standard as previously described

(Kobayashi et al., 1994). The kinetic parameters (kcat and Km) were determined using

nonlinear regression analysis based on the Michaelis-Menten kinetics model with GraphPad

Prism software (GraphPad, Software Inc., San Diego, CA).

To determine the total turnover numbers (TTNs) of each CYP102A1 mutant, 1.0 mM

OMP (racemic mixture, S-, or R-enantiomer) and 200 pmol of enzyme were used in 0.50 ml

of 100 mM potassium phosphate buffer (pH 7.4). The reaction was initiated by the addition of

the NADPH-generating system and incubated for 10 min to 4 h at 37°C. The formation rate

of the OMP metabolite was determined by HPLC as described above.

Isolation of 5’-OH OMP. To prepare the metabolites of racemic and S-OMP, we used

a scale of 20 ml reaction volume in 20 test tubes (each 1 ml, under air). Each reaction mixture

contained 400 pmol of CYP102A1 mutant #10, a NADPH-generating system, and 1 mM

racemic OMP or S-OMP in 1 ml of 100 mM potassium phosphate buffer (pH 7.4). Reaction

was initiated by the addition of the NADPH-generating system and was incubated for 2 h at

37°C. The reaction was terminated with two volume of ice-cold dichloromethane. After

centrifugation of the reaction mixture, organic phases from 20 test tubes were combined and

evaporated under nitrogen gas. The chromatographic separation was achieved using a semi-

preparative Gemini C18 column (10 x 250 mm, 10 μm particle size; Phenomenex) with

monitored at A302. The mobile phase was 30% acetonitrile and was delivered at a flow rate of

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3.0 ml/min. Retention times for 5’-OH metabolite and OMP were 8.75 and 21.01 min-1,

respectively. After collection of the 5’-OH metabolite fraction and drying under nitrogen gas,

the dried metabolite was obtained and used for NMR analysis. The 5’-OH OMP was also

used an authentic standard. For typical reaction, about 3.0 mg of the 5’-OH OMP was

obtained from the 20 ml reaction.

LC-MS analysis. To identify the metabolite of each OMP enantiomer produced by the

CYP102A1 mutants, LC-MS analysis was carried out. The oxidation reaction of OMP by

CYP102A1 mutants was performed as described above. For the activity assays of human

CYP2C19 and CYP3A4, a control experiment of 50 pmol P450, 100 pmol rat NADPH-P450

reductase, and 50 μM L-α-dilauroyl-sn-glycero-3-phosphocholine was performed in 0.25 ml

of 100 mM potassium phosphate buffer (pH 7.4). After extraction and centrifugation, organic

phases were evaporated under nitrogen gas. An aliquot (5 μl) of the reconstituted residue was

injected onto the LC column. LC-MS analysis was performed on a Shimadzu LCMS-2010

EV system (Shimadzu, Kyoto, Japan) including LC-MS solution software. The separation

was performed on a Shim-pack VP-ODS column (2.0 × 250 mm; Shimadzu) with a mobile

phase of CH3CN/H2O (70:30, v/v) at a flow rate of 0.10 ml/min. To identify the metabolites,

mass spectra were recorded by electrospray ionization in positive mode. The interface and

detector voltages were 4.4 and 1.5 kV, respectively. The nebulization gas flow was set at 1.5

l/min. The interface, curve desolvation line, and heat block temperatures were 250°C, 230°C,

and 200°C, respectively.

Identification of OMP metabolites by NMR spectroscopy. NMR experiments were

performed on a Varian VNMRS 600 MHz NMR spectrometer equipped with a carbon-

enhanced cryogenic probe (Korea Basic Science Institute, Gwangju, Korea). Acetone-d6 was

used as a solvent, and chemical shifts for the proton NMR spectrum were measured in parts

per million (ppm) relative to the TMS. All of the NMR experiments were performed with

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standard pulse sequences in VNMRJ (v. 2.3) library and processed with the same software.

There have been reports on proton and carbon chemical shifts of racemic omeprazole in

acetone-d6. Spectral assignments of racemic 5'-OH OMP were carried out mainly with one-

dimensional proton NMR spectrum of 5'-OH OMP by comparing with reported chemical

shift values of racemic omeprazole (Folli et al., 1995; Yang et al., 2003). Redondo et al.

(2010) showed that it is possible to differentiate chiral isomers of omeprazole in non-polar

NMR solvents by adding (S)-1,10-binaphthyl-2,20-diol as NMR chiral solvating agent.

Spectral binding titrations. Spectral binding titrations were used to determine the

dissociation constants (Ks) for substrates as previously described (Kim et al., 2008). The

binding affinities of the ligands to the CYP102A1 enzymes were determined at 23°C by

titrating 1.5 µM enzyme with the ligand in a total volume of 1.0 ml of 100 mM potassium

phosphate buffer (pH 7.4). The final dimethyl sulfoxide concentration was <2% (v/v). The

spectral dissociation constants (Ks) were estimated using GraphPad Prism software.

Results and Discussion

Hydroxylation of OMP enantiomers by wild type CYP102A1 and its mutants.

Initially, the catalytic activity of wild type and various CYP102A1 mutants toward S- and R-

OMP was investigated at a fixed substrate concentration of 100 μM (Fig. 2). The wild type

and mutant enzymes produced only one major metabolite (5’-OH OMP) for both enantiomers.

The 5’-OH product formation rates for the mutants for R-OMP were much higher than those

for S-OMP (Fig. 2). The turnover numbers from the 26 mutants for 5’-OH OMP formation

varied over a wide range. The wild type enzyme as well as mutants #2, #4, #5, #12, #14, and

#15 showed lower catalytic activity for both enantiomers (<1.0 min-1). Although 13 mutants

showed high catalytic activity (>10 min-1) for R-OMP, only 4 mutants exhibited catalytic

activity >10 min-1 for S-OMP. The turnover numbers for mutants #10, #17, and #21 were

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140~220-fold and 90~140-fold higher than those of the wild type enzyme for S-OMP (0.16

min-1) and R-OMP (0.37 min-1), respectively. The metabolites were identified by HPLC, LC-

MS and NMR. The retention time and fragmentation pattern of the major OMP metabolite

from both S- and R-OMP were matched to the 5’-OH OMP standard (Supplemental Figs. S1

and S2). Mutants #10, #13, #16, #21, and #22 were selected for additional kinetic analysis

and binding studies.

When we compared the S-OMP 5’-hydroxylation activity with R-OMP 5’-

hydroxylation activity in the 26 mutants, several statistically significant correlations (r = 0.97,

P < 0.0001) were observed (Supplemental Fig. S3). This result indicates that chirality of the

sulfur center is not critical for the hydroxylation reaction at the 5’-C position. Taken together,

this suggests that the CYP102A1 mutants can be used to prepare the 5’-OH OMP product

regardless of the chirality of the parent substrates.

Structural characterization of the major metabolite 5’-OH S-OMP generated by

CYP102A1. Mutant #10 was used to prepare the 5’-OH OMP from S-OMP for structural

analysis by NMR and LC-MS. Racemic 5'-OH OMP (Supplemental Fig. S4a), a metabolite

from racemic omeprazole (Supplemental Fig. S4b), was first identified by comparing with

reported chemical shift values of racemic omeprazole (Folli et al., 1995; Yang et al., 2003).

No structural change in benzoimidazole moiety is evident in 1H spectra of the racemic OMP

and racemic 5'-OH OMP, while chemical shift changes in the pyridine moiety with

conversion of 5'-CH3 (δ 2.245 ppm) in racemic OMP to 5'-CH2OH (δ 4.698 ppm) in racemic

5'-OH OMP can be seen in the 1H spectrum of racemic 5'-OH OMP (Supplemental Fig. S5).

1H chemical shift assignments of racemic 5'-OH OMP are shown (Supplemental Table S2).

The position of racemic 5'-hydroxymethyl group was further confirmed with 1-dimensional

selective ROE (Rotating Frame NOE) experiments. When already-assigned proton NMR

peaks from H-6' (δ 8.41 ppm) or 4'-OCH3 (δ 3.81 ppm) were selectively irradiated, proton

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NMR peak from 5'-CH2 (δ 4.70 ppm) appeared (Supplemental Fig. S6). The key ROE results

are shown in Supplemental Fig. S4c. Proton NMR spectrum of the metabolite from S-OMP,

was identical to that of the metabolite from racemic 5'-OH OMP as we expected

(Supplemental Fig. S7).

Kinetic parameters and total turnover numbers of OMP 5’-hydroxylation by

CYP102A1 mutants. Five mutants were selected to compare the kinetic parameters for the

5’-hydroxylation of S- and R-OMP (Supplemental Table S3 and Supplemental Fig. S8).

Although the kcat values of each mutant were similar among the racemate, S-, and R-OMP, the

Km values were in the wide range for all tested mutants. Mutants #10 (R47L/F87V/L188Q

mutant) and #22 (F162I/E228K) showed high kcat values (47-122 min-1) for the three OMP

substrates. The results indicate that the mutants did not show any preference toward a specific

enantiomer. The mutant #10 was used to measure the TTN (mol product/mol catalyst) for the

5’-hydroxylation reaction of S- and R-OMP (Supplemental Fig. S9). The overall values were

950 and 1,200 for 5’-OH product from S- and R-OMP, respectively, when 1 mM of substrate

was used.

Selective conversion of OMP to 5’-OH OMP. Of the 26 mutants of CYP102A1 that

reacted with 1 mM of OMP for 1 h, mutant #10 possessed the most ideal combination of 5’-

OH OMP formation activity and regioselectivity. Mutant #10 produced 5’-OH OMP at 93%,

98%, and 88% selectivity with the racemic, S-, and R-OMP, respectively (Fig. 2 and

Supplemental Table S4). It also converted up to 97%, 99%, and 100% of the racemic, S-, and

R-OMP into 5’-OH OMP, respectively. This result indicates that 5’-OH OMP can be obtained

with a high conversion rate and high selectivity from racemic, S-, and R-OMP.

Binding of OMP to CYP102A1 mutants. Ferric CYP102A1 exhibits a low-spin state,

and the addition of substrate (OMP) produced a conversion rate in the spin-state depending

on the different types of CYP102A1 mutant (Butler et al., 2013). Mutants #10, #13, #16, #22,

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and #23 (which were the same enzymes used to determine the kinetic parameters) were used

for the binding titration. Among the 18 samples tested here for spectral titration, only five

samples showed typical conversion (Type I) from the low-spin to high-spin state, with an

increase in absorbance at 390 nm and a decrease in absorbance at 420 nm (Supplemental Fig.

S10). The binding affinities of mutants #10 and #16 to racemic OMP were determined (Ks =

109 ± 5 μM and 209 ± 26 μM, respectively). The binding affinities of mutants #10, #13, and

#16 to R-OMP were also determined (Ks = 64 ± 5 μM, 10 ± 2 μM, and 48 ± 2 μM,

respectively). Six of the samples did not show apparent conversion. Although seven samples

showed a spectral change, the Ks value could be not obtained based on the spectral change.

Binding titration showed that there were no correlations between the spectral change

upon substrate binding and catalytic activity. In the cases of mutants showing typical spectral

conversion upon OMP binding, the binding affinities of the CYP102A1 mutants tested here

were much lower than that of the CYP102A1 F87A/A82F mutant (Ks = 0.212 μM) (Butler at

al., 2013).

Mutants #21 (F162I/K187E) and #22 (F162I/E228K) showed different spectral

changes from other mutants that had mutations in the substrate channel and active site. The

mutations (F162 and E228) outside of active site and substrate channel appear to have

different effects on the conformation of the active site upon binding to the substrates

(Supplemental Fig. S11).

It has been reported that 5’-OH OMP was a superior agent for gastric acid

hypersecretion disorders with fewer severe adverse effects, reduced potential for drug-drug

interactions, and a more predictable dosing regimen compared to OMP (Yelle and Handley,

2001). However, there are no reports to show that 5’-OH OMP is an active metabolite.

Although the racemate of 5’-OH OMP could be obtained by chemical synthesis, this

synthesis includes 21 steps (Renberg et al., 1989). The individual enantiomers from the

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racemate could be separated by additional oxidation and reduction steps (Yelle and Handley,

2001).

It is now possible to study the effects of 5’-OH OMP of each enantiomer on gastric

acid hypersecretion disorders in in vitro, in vivo, and animal model systems because scalable

production of the metabolite is possible. Specifically, the effects of the 5’-OH metabolites

from racemic, S-, and R-OMP on several diseases caused by gastric acid hypersecretion are of

particular interest. The effects of these metabolites on gastric acid hypersecretion disorders

may suggest that the metabolites could be used as ‘drug leads’ to avoid interindividual

variations in drug metabolizing enzymes and drug-drug interactions. Furthermore, the

metabolites can be used as leads and subjected to further structural modifications to obtain

improved clinical candidates during the lead optimization phase of the drug discovery process.

In summary, we report that the S- and R-enantiomers of OMP are hydroxylated by a set

of 26 CYP102A1 mutants to produce the major metabolite 5’-OH OMP regardless of the

chirality of the parent substrates. The 5’-OH product formation rates of the mutants for R-

OMP were much higher than those for S-OMP. There were no differences for regioselectivity

of the oxidation reaction for both enantiomers. Although the binding of R-OMP to the

CYP102A1 active site causes a more obvious change of the heme environment than that of S-

OMP, there were no correlations between the spectral change upon substrate binding and

catalytic activity. The 5’-OH OMP of racemic, S-, and R-OMP could be obtained with a high

conversion rate and high selectivity when the triple R47L/F87V/L188Q mutant was used.

These results show that the 5’-OH OMP of each enantiomer could be obtained using a one-

step reaction with the CYP102A1 mutants with a high yield.

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Authorship Contributions

Participated in research design: Kang, Ahn, and Yun.

Conducted experiments: Ryu, B.Y. Park, Kim, S.H. Park, Jung, M. Park, and K.D. Park.

Performed data analysis: Ryu, B.Y. Park, Kim, S.H. Park, K.D. Park, Ahn, and Yun.

Wrote or contributed to the writing of the manuscript: Ryu, K.D. Park, and Yun.

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References

Abelö A, Andersson TB, Antonsson M, Naudot AK, Skånberg I, Weidolf L (2000)

Stereoselective metabolism of omeprazole by human cytochrome P450 enzymes. Drug

Metab Dispos 28:966-972.

Atrakchi AH (2009) Interpretation and considerations on the safety evaluation of human drug

metabolites. Chem Res Toxicol 22:1217-1220.

Butler CF, Peet C, Mason AE, Voice MW, Leys D, Munro AW (2013) Key mutations alter the

cytochrome P450 BM3 conformational landscape and remove inherent substrate bias. J

Biol Chem 288:25387-25399.

Butler CF, Peet C, McLean KJ, Baynham MT, Blankley RT, Fisher K, Rigby SE, Leys D,

Voice MW, Munro AW (2014) Human P450-like oxidation of diverse proton pump

inhibitor drugs by "gatekeeper" mutants of flavocytochrome P450 BM3. Biochem J

460:247-259.

Folli U, Iarossi D, Mucci A, Taddei F (1995) Internal rotation around single bonds and

conformational preferences in heterocyclic analogues of benzyl methyl sulphoxide

studied with NMR techniques. J Mol Struct 350:115-128.

Furuta T, Shirai N, Sugimoto M, Nakamura A, Hishida A, Ishizaki T (2005) Influence of

CYP2C19 pharmacogenetic polymorphism on proton pump inhibitor-based therapies.

Drug Metab Pharmacokinet 20:153–167.

Goldstein JA (2001) Clinical relevance of genetic polymorphisms in the human CYP2C

subfamily. Br J Clin Pharmacol 52:349–355.

Julsing MK, Cornelissen S, Buhler B, Schmid A (2008) Heme-iron oxygenases: powerful

industrial biocatalysts? Curr Opin Chem Biol 12:177-186.

This article has not been copyedited and formatted. The final version may differ from this version.DMD Fast Forward. Published on July 9, 2014 as DOI: 10.1124/dmd.114.058636

at ASPE

T Journals on N

ovember 23, 2020

dmd.aspetjournals.org

Dow

nloaded from

Page 16: Regioselective Hydroxylation of Omeprazole Enantiomers by ...dmd.aspetjournals.org/content/dmd/early/2014/07/09/... · 7/9/2014  · peptic ulcer disease, gastroesophageal reflux

DMD #58636

16

Li XQ, Weidolf L, Simonsson R, Andersson TB (2005) Enantiomer/enantiomer interactions

between the S- and R- isomers of omeprazole in human cytochrome P450 enzymes:

major role of CYP2C19 and CYP3A4. J Pharmacol Exp Ther 315:777-787.

Kang JY, Ryu SH, Park SH, Cha GS, Kim DH, Kim KH, Hong AW, Ahn T, Pan JG, Joung

YH, Kang HS, Yun CH (2014) Chimeric cytochromes P450 engineered by domain

swapping and random mutagenesis for producing human metabolites of drugs. Biotechnol

Bioeng 111:1313-1322.

Kawabata H, Habu Y, Tomioka H, Kutsumi H, Kobayashi M, Oyasu K, Hayakumo T, Mizuno

S, Kiyota K, Nakajima M, Kimoto K, Inokuchi H, Kawai K (2003) Effect of different

proton pump inhibitors, differences in CYP2C19 genotype and antibiotic resistance on the

eradication rate of Helicobacter pylori infection by a 1-week regimen of proton pump

inhibitor, amoxicillin and clarithromycin. Aliment Pharmacol Therap 17:259–264.

Kim DH, Kim KH, Kim DH, Liu KH, Jung HC, Pan JG, Yun CH (2008) Generation of

human metabolites of 7-ethoxycoumarin by bacterial cytochrome P450 BM3. Drug

Metab Dispos 36:2166-2170.

Kobayashi K, Chiba K, Tani M, Kuroiwa Y, Ishizaki T (1994) Development and preliminary

application of a high-performance liquid chromatographic assay for omeprazole

metabolism in human liver microsomes. J Pharm Biomed Anal 12:839-844.

McKeage K, Blick SK, Croxtall JD, Lyseng-Williamson KA, Keating GM (2008)

Esomeprazole: a review of its use in the management of gastric acid-related diseases in

adults. Drugs 68:1571–1607.

Park SH, Kim DH, Kim D, Kim DH, Jung HC, Pan JG, Ahn T, Kim D, Yun CH (2010)

Engineering bacterial cytochrome P450 (P450) BM3 into a prototype with human P450

enzyme activity using indigo formation. Drug Metab Dispos 38:732-739.

This article has not been copyedited and formatted. The final version may differ from this version.DMD Fast Forward. Published on July 9, 2014 as DOI: 10.1124/dmd.114.058636

at ASPE

T Journals on N

ovember 23, 2020

dmd.aspetjournals.org

Dow

nloaded from

Page 17: Regioselective Hydroxylation of Omeprazole Enantiomers by ...dmd.aspetjournals.org/content/dmd/early/2014/07/09/... · 7/9/2014  · peptic ulcer disease, gastroesophageal reflux

DMD #58636

17

Redondo J, Capdevila A, Latorre I (2010) Use of (S)-BINOL as NMR chiral solvating agent

for the enantiodiscrimination of omeprazole and its analogs. Chirality 22:472-478.

Renberg L, Simonsson R, Hoffmann KJ. (1989) Identification of two main urinary

metabolites of [14C]omeprazole in humans. Drug Metab Dispos 17:69-76.

Urlacher VB, Girhard M (2012) Cytochrome P450 monooxygenases: an update on

perspectives for synthetic application. Trends Biotechnol 30:26-36.

Whitehouse CJ, Bell SG, Wong LL (2012) P450(BM3) (CYP102A1): connecting the dots.

Chem Soc Rev 41:1218-1260.

Yamazaki H, Inoue K, Shaw PM, Checovich WJ, Guengerich FP, Shimada T (1997) Different

contributions of cytochrome P450 2C19 and 3A4 in the oxidation of omeprazole by

human liver microsomes: effects of contents of these two forms in individual human

samples. J Pharmacol Exp Ther 283:434-442.

Yang R, Schulman SG, Zavala PJ (2003) Acid-base chemistry of omeprazole in aqueous

solutions. Anal Chim Acta 481:155-164.

Yelle WE, Handley DA (2001) Hydroxyomeprazole compositions and methods. US patent

6,294,586, 2001 Sep 25.

Yun CH, Kim KH, Kim DH, Jung HC, Pan JG (2007) The bacterial P450 BM3: a prototype

for a biocatalyst with human P450 activities. Trends Biotechnol 25:289-298.

Yun CH, Yim SK, Kim DH, Ahn T (2006) Functional expression of human cytochrome P450

enzymes in Escherichia coli. Curr Drug Metab 7:411-429.

Yun CH, Kim SY, Ryu SH, Kang HS (2013) inventors; PCT international. Novel method for

producing metabolites from omeprazole using bacterial cytochrome P450, and

composition for same. World patent WO2013115484, 2013 Aug 8.

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Footnotes

S.H.R. and B.Y.P. contributed equally to this work.

This work was supported by the Basic Science Research Program through the National

Research Foundation of Korea (NRF) and funded by the Ministry of Education [Grant

2013R1A1A2007090].

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Figure legends

FIG 1. Structures of the omeprazole (OMP) enantiomers and their respective metabolites. R-

OMP is primarily metabolized by CYP2C19 for 5’-OH R-OMP. S-OMP is mainly

metabolized by CYP3A4 for 5-O-desmethyl OMP and OMP sulfone, which is further

hydroxylated by CYP2C19. In this study, we observed that both enantiomers are

hydroxylated by CYP102A1 mutants.

FIG 2. Rates of omeprazole (OMP) metabolite production by the 26 CYP102A1 mutants.

Assays were performed for 30 min using 100 μM of either S- or R-OMP. The formation rate

of the 5’-OH OMP metabolite was determined by HPLC. The values are represented as the

mean ± S.E.M. of duplicate measurements.

FIG 3. Conversion of racemic, R-, and S-omeprazole to 5’-hydroxylated metabolites by

CYP102A1 mutant #10. Assays were performed for 1 h using 1 mM of each substrate. HPLC

chromatograms of racemic (A) S- (C), R- (E) omeprazole and their corresponding 5’-OH

metabolites (B, D, and, F, respectively) produced by CYP102A1 mutant #10. The peaks of

the substrate and 5’-OH product are indicated. The UV absorbance was monitored at 302 nm.

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Figure 3

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