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(Received for publication, January 4, 1996; and in revised form, February 19,
1996) From the
Human P450 2C19 is selective for 4`-hydroxylation of S-mephenytoin and 5-hydroxylation of omeprazole, while the
structurally homologous P450 2C9 has low activity toward these
substrates. To identify the critical amino acids that determine the
specificity of human P450 2C19, we constructed chimeras of P450 2C9
replacing various proposed substrate binding sites (SRS) with those of
P450 2C19 and then replaced individual residues of P450 2C9 by
site-directed mutagenesis. The 339 NH
The P450 ( P450 2C19 is a member of the human CYP2C
subfamily, which includes four structurally related
enzymes(6) . P450 2C9 and 2C19 are the most highly conserved of
these forms, showing 91% structural identity, but have very distinctive
substrate specificities. For example P450 2C19, which is polymorphic in
man, is the principal enzyme responsible for the stereoselective
4`-hydroxylation of S-mephenytoin (7) and is highly
selective for the 5-hydroxylation of the popular anti-ulcer drug
omeprazole(46) . The structurally related P450 2C9 exhibits
little activity toward either of these substrates, but exhibits a high
turnover number for hydroxylation of tolbutamide and phenytoin and
specifically 7-hydroxylates S-warfarin(6) . The
present studies were designed to elucidate the key amino acids that
determine the marked specificity of P450 2C19 for omeprazole and S-mephenytoin. Since none of the mammalian P450 enzymes
have been crystallized, the experimentally derived three-dimensional
crystal structures of the bacterial enzymes, P450cam, P450BM-3, and
P450terp, have served as models for predicting their structure and
function. The current paradigm for such predictions has focused on
alignment-based sequence similarities, Gotoh (13) predicted six potential substrate recognition
sites (SRS) in the mammalian family 2 P450 enzymes based on an
alignment with bacterial P450cam whose substrate-binding residues have
been identified by x-ray crystallography and analysis of mutations that
altered substrate specificity in experimental studies of the P450 2
subfamily. For example, site-directed mutagenesis studies have shown
that the substrate and regiospecificity of the 2C subfamily of
cytochrome P450 can be altered by substitution of critical amino acid
residues at positions 112 to 115, 301, 359,
364(14, 15, 16, 17, 18, 19) .
Replacement of residues 117, 209, 365, and 481 in the 2A subfamily (5, 20, 21, 22, 23) as well
as residues 114, 206, 302, 363, 367, and 478 (24, 25, 26, 27, 28) in the
2B subfamily and residue 380 (29) in 2D1 have also been
documented to alter substrate or regiospecificity. To identify key
amino acid residues responsible for the marked specificity of human
P450 2C19 for two key substrates, omeprazole and S-mephenytoin, we constructed a total of 24 chimeras and
mutant enzymes from the structurally related P450 2C9. Constructs were
expressed in a yeast cDNA expression system. Initial chimeras replaced
regions of P450 2C9 with similar segments of P450 2C19, using
restriction enzymes sites located outside the six putative substrate
binding domains proposed by Gotoh(13) . Subsequently, we used
primary sequence alignment and comparative analysis of amino acid
variations within the appropriate segments of the human P450 2C
proteins to identify residues that might play a role in the substrate
specificity of P450 2C19. Site-directed mutagenesis was then used to
identify key residues responsible for the substrate specificity of P450
2C19.
Figure 1:
Schematic
representation of the chimeric constructs (A) and
site-directed mutants (B) of P450 2C9 and P450 2C19. A, the restriction enzyme sites utilized for chimeras and
putative SRS (numbered 1-6) are indicated at the
appropriate sites of P450 2C9 (top). Solid thin lines of the chimeras represent segments of P450 2C19, while bars represent the segments of P450 2C9. The site of an I99H mutation
in a 2C9/2C19
Figure 2:
Omeprazole 5-hydroxylase activity of
chimeras of P450 2C9 and P450 2C19 expressed in yeast. Construction of
chimeras is shown in Fig. 1. The omeprazole hydroxylase activity
was measured as described under ``Experimental
Procedures.''
Figure 3:
Omeprazole 5-hydroxylase activities of
site-directed mutants of P450 2C9. Omeprazole hydroxylase activity is
given as the means ± S.E. The single mutations are numbered m1-m5, with amino acid substitutions indicated in parentheses, and m134, m145, m1345,
and m1245 represent the corresponding multiple mutants. Three
other mutant enzymes, m2 (S451F), m34, and m45 (not shown), did not
affect omeprazole hydroxylase activity.
Figure 4:
Model showing omeprazole docked in the
substrate-binding pocket of P450cam. Thr
Figure 5:
Analysis of the contribution of His
We next sequentially modified
amino acids in this region to those of the corresponding residues in
P450 2C19 as shown in Fig. 1B. Six amino acids of P450
2C19 (three conservative and three nonconservative changes) differ from
those of P450 2C9 between amino acids 160 and 227, with five of these
mapping within 20 tandem amino acid residues of the carboxyl end of
SRS-2. Mutations Lys
Figure 6:
S-Mephenytoin 4`-hydroxylase
activity of chimeric and mutant CYP2C9 proteins expressed in yeast.
Chimeras and mutants are identical to those shown in Fig. 2and Fig. 5. None of the other mutants shown in Fig. 1B, Fig. 3, and Fig. 4increased
mephenytoin hydroxylase activity (data not
shown).
Volume 271,
Number 21,
Issue of May 24, 1996 pp. 12496-12501
©1996 by The American Society for Biochemistry and Molecular Biology, Inc.
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS AND DISCUSSION
FOOTNOTES
ACKNOWLEDGEMENTS
REFERENCES
-terminal amino acid
residues (SRS-1-SRS-4) and amino acids 160-383
(SRS-2-SRS-5) of P450 2C19 conferred omeprazole 5-hydroxylase
activity to P450 2C9. In contrast, the COOH terminus of P450 2C19
(residues 340-490 including SRS-5 and SRS-6), residues
228-339 (SRS-3 and SRS-4) and residues 292-383 (part of
SRS-4 and SRS-5) conferred only modest increases in activity. A single
mutation Ile
His increased omeprazole 5-hydroxylase
to
51% of that of P450 2C19. A chimera spanning residues
160-227 of P450 2C19 also exhibited omeprazole 5-hydroxylase
activity which was dramatically enhanced by the mutation Ile
His. A combination of two mutations, Ile
His and Ser
Pro, converted P450 2C9
to an enzyme with a turnover number for omeprazole 5-hydroxylation,
which resembled that of P450 2C19. Mutation of Pro
Thr enhanced this activity. Residue 99 is within SRS-1, but amino acids
220 and 221 are in the F-G loop and outside any known SRS. Mutation of
these three amino acids did not confer significant S-mephenytoin 4`-hydroxylase activity to P450 2C9, although
chimeras containing SRS-1-SRS-4 and SRS-2-SRS-5 of P450
2C19 exhibited activity toward this substrate. Our results thus
indicate that amino acids 99, 220, and 221 are key residues that
determine the specificity of P450 2C19 for omeprazole.
)cytochromes represent a ubiquitous
superfamily of monooxygenases, which metabolize a vast array of
endogenous and exogenous
substrates(1, 2, 3) . Multiple P450 enzymes
appear to have arisen from a single ancestral gene by duplication and
diverged by mutation and gene conversion to produce families of
structurally related enzymes with overlapping but often distinct
substrate specificities. The regio- and stereoselectivity of specific
enzymes for particular substrates appears to be encoded in certain
defined regions of the primary sequence. Considerable progress has been
made in recent years in elucidating the structural determinants of
substrate specificity(4) . In some cases, substrate specificity
between highly related members of the same subfamily has been shown to
be defined by a few critical residues or even a single amino
acid(5) .
- and
-secondary
structure, hydropathy indices, computerized modeling based on the
crystal structures of the bacterial P450 enzymes and protein
engineering using chimeric constructs and site-directed
mutagenesis(8, 9, 10, 11, 12) .
Although the amino acid sequences of the soluble bacterial P450 differ
considerably from those of the membrane-bound mammalian P450 enzymes,
these methods have proven resourceful in identifying regions that
determine the substrate specificities of the mammalian proteins.
Chemicals and Reagents
Restriction and
modification enzymes were purchased from New England Biolabs and
sequenase sequencing kits and deoxyadenosine
5`-[
S]thiotriphosphate from Amersham Life
Sciences.
C-Labeled omeprazole (53 mCi/mmol), a gift from
Glaxo Research and Development (Hertfordshire, United Kingdom (UK)),
was unstable and therefore periodically purified to
98%
homogeneity by HPLC and stored at -70 °C under absolute
ethanol.
C-Labeled S-mephenytoin (20.7 mCi/mmol)
was prepared as described previously(7) . Purified P450
reductase was obtained from Human Biologics Inc., Phoenix, AZ.Plasmids
The cloning of P450 2C9 and P450 2C19
into the yeast vector pAAH5 has been described previously(30) .
To facilitate restriction enzyme manipulations, the modified cDNAs were
recloned in both orientations in the HindIII site of pUC19.
P450 2C9/2C19 hybrid clones were constructed by ligation of homologous
fragments of the cDNA inserts. All plasmids were propagated in Escherichia coli DH5
(Life Technologies Inc.) and
recombinant DNA identified by sequencing. The modified cDNAs were
excised, inserted into pAAH5 vector, and recombinants in the correct
orientation selected by restriction mapping and sequencing of the
5`-cloning junctions.Site-directed Mutagenesis
Amino acid changes were
introduced in P450 2C9 and the 2C9/2C19 hybrids using synthetic
oligonucleotides (Table 1) containing the desired point mutations
and a second primer, which abolished a unique restriction site in the
pAAH5 plasmid. The procedure was essentially as described by Deng and
Nickoloff (31) with minor modifications. The concentration of
the plasmid selection oligonucleotide was reduced 5-fold in the
annealing reaction. After extension with unmodified T7 DNA polymerase,
the product was purified by Sephadex G50 spin column chromatography.
BMH71-18, a mismatch repair-deficient bacteria strain, was transformed.
Plasmid DNA isolated from the pooled colonies was digested to linearize
non-mutated clones prior to retransformation in DH5
cells.
Individual colonies were sequenced to confirm incorporation of the
mutagenic primers.
Transformation of Yeast and Preparation of Recombinant
Microsomes
The protease-deficient Saccharomyces cerevisiae strain 334 (MAT
pep4-3 prb1-1122
ura3-52 leu2-3 leu2-1222 reg1-501 gal11)
was transformed with recombinant plasmids and Leu
transformants selected as described
previously(30, 32) . Microsomes were isolated from
transformed yeast cells grown in synthetic broth, which did not contain
leucine(32) , to mid-logarithmic growth phase essentially as
described by Oeda et al.(33) with minor
alterations(30) . Microsomal protein concentration (34) and P450 content (35) were determined as described
previously.Enzymatic Assays
S-Mephenytoin
4`-hydroxylation was assayed as described previously (7) except
that cytochrome b
was not added to the reactions.
To assay omeprazole 5-hydroxylase, recombinant yeast microsomes were
preincubated at 37 °C for 5 min with purified P450 reductase (100
units/10 pmol of P450) and dilaurophosphatidylcholine (0.3 µg/pmol
of P450) and then placed on ice.
C-Labeled omeprazole (400
µM, 22 mCi/mmol) was added to 50 mM HEPES buffer
(pH 7.4) containing 0.1 mM EDTA and 1.5 mM MgCl
. The reaction was preincubated at 37 °C with
shaking for 5 min, initiated by addition of NADPH (2 mM), and
terminated with equal volume of methanol after 15 min. After
centrifugation, products were analyzed by reverse phase HPLC using an
isocratic solvent phase consisting of 45 parts methanol and 55 parts
water. Detection and quantitative analysis of radioactive peaks was
accomplished through an on-line radiochemical detector.Modeling and Structural Alignments
Omeprazole was
docked into two structures using the molecular modeling package SYBYL
at the Molecular Modeling Laboratory, University of North Carolina,
Chapel Hill, NC. The first structure was a model for P450 2B1 described
by Szklar et al.(19) , which is based on the x-ray
structures of P450cam, P450terp, and P450BM-3. The second structure was
that of P450cam. Omeprazole was docked into the binding pockets of both
structures by requiring C19 of omeprazole to be 3-4 Å from
the heme iron and rotating the substrate to minimize Van der Waals
contacts with the protein. P450 2C9 and P450 2C19 were aligned with
P450cam using GAP from the Wisconsin GCG package with standard
defaults.
Chimeras
Twenty-four chimeric 2C9/2C19 and
mutant P450 2C9 proteins were analyzed for their ability to hydroxylate
omeprazole and S-mephenytoin. The structures of the chimeras
and their relationships to the SRS proposed by Gotoh (13) are
shown in Fig. 1A. The 2C9/2C19
chimera exhibited only a slight increase in omeprazole
5`-hydroxylase activity over the wild-type P450 2C9, suggesting that
the carboxyl terminus of P450 2C19 has relatively minor influence on
its capacity to metabolize omeprazole (Fig. 2). Although this
region encompasses SRS-5 and SRS-6, it contains some of the most highly
conserved P450 domains including the heme-binding region. P450
cytochromes 2C9 and 2C19 differ by only 11 amino acids in this
152-residue domain, with a preponderance of conservative replacements.
It is, therefore, not surprising that this region conferred only a
small increase in omeprazole hydroxylase activity. In contrast, the
chimeric 2C19
/2C9 protein exhibited the largest
(13-fold) increase in omeprazole 5-hydroxylase activity. The 2C19
segment of this chimera spanned the putative SRS-1-SRS-4 with 31
nonidentical residues, including 16 nonsynonymous changes. A nearly
comparable increase was observed with the 2C9/2C19
chimera spanning SRS-2-SRS-5 of 2C19. The 2C19 region of
these two chimeras overlap from residues 160-339, suggesting that
this region may be requisite to substrate specificity. The
2C19
/2C9 chimera contained 12 amino acid changes
at the NH
-terminal end, which were not present in the
2C9/2C19
chimera, presumably accounting for the
slightly higher activity of the former protein. Two other chimeric
proteins containing only parts of the 160-383 fragment of 2C19, i.e. 2C9/2C19
(containing SRS-3 and
SRS-4) and 2C9/2C19
(containing SRS-5 and part
of SRS-4), exhibited a smaller increase (3-7-fold) in omeprazole
hydroxylase activity than the 2C9/2C19
chimera,
suggesting that the region spanning residues 160-227 of P450 2C19
could be involved in substrate specificity.
chimera is indicated by a diamond. B, site-directed mutants of P450 2C9. The
amino acids shown above the construct represent those of P450 2C9 which
were mutated to the corresponding residues of P450 2C19 shown below the
construct. The region 198-240 between SRS-2 and SRS-3 is expanded
below. Residues that affected omeprazole hydroxylase activity are
represented by diamonds.
Mutants
We initially generated five single amino
acid mutants I99H (m1), Y243D (m3), M257I (m5), L362I (m4), and S451F
(m2) and combinations of these mutations (m34, m45, m134, m145, m1245,
and m1345) in P450 2C9 (Fig. 1B). Each amino acid was
mutated to the corresponding amino acid in P450 2C19. The amino acids
were chosen as residues that might be involved in substrate recognition
based on alignment with P450cam and mouse 2A4/5 and selection of amino
acids in P450 2C19 that were unique compared to other members of the
P450 2C subfamily. Ile
His was chosen because it is
the only difference between P450 cytochromes 2C9 and 2C19 in SRS-1, and
His
is unique to P450 2C19. Ile
is a unique
amino acid in P450 2C19. Tyr
Asp is a unique
nonsynonymous amino acid change near SRS-3. Ile
corresponds to contact residue Val
in P450cam and
is the only unique amino acid in SRS-5. Ser
Phe is
a unique nonsynonymous change located between SRS-5 and SRS-6. Of the
single amino acid mutants, only I99H (Ile
His) in
SRS-1 increased omeprazole 5`-hydroxylase activity markedly (Fig. 3). The other mutations had essentially no effect.
Multiple mutants containing the Ile
His mutation
had comparable activity to that of I99H. In contrast, multiple mutants
m34 and m45, which did not contain the Ile
His
mutation, exhibited no increase in omeprazole hydroxylase activity
(data not shown). Residue 99 maps to the interhelical region of B and
B` helices, three residues from the NH
terminus of B`,
which comprises part of the substrate-contact loop in the structure of
P450cam (36, 37, 38) . Many mutations that
alter the substrate specificity of members of the 2A, 2B, and 2C
subfamilies of cytochrome P450 map to the B`-C interhelical region near
the carboxyl terminus of
SRS-1(5, 39, 40, 41, 42, 43) .
Three-dimensional analysis of P450cam, P450terp, and P450BM-3 suggests
that this substrate-contact loop, the largest in P450, extends from
proximal end of the
1-5 sheet through the distal end of the
B`-C coil(8) . His
of P450 2C19 corresponds to
Pro
of P450cam in the alignment of Gotoh(13) ,
which is one of three amino acids in SRS-1 that contact camphor.
Moreover, it represents the only amino acid change between P450 2C9 and
P450 2C19 in SRS-1 and is the only residue in SRS-1 that is unique to
P450 2C19. This change involves the replacement of a nonpolar,
hydrophobic isoleucine with a polar and possibly charged histidine
residue. This polar histidine has the capacity for hydrogen bonding. It
is possible that the residue is involved in substrate binding or
alternatively changes the configuration of the active site. Comparison
of P450 2C19 with a three-dimensional model of P450 2B1 (19) predicts that this amino acid would be approximately 15
Å from the center of the substrate binding pocket. Alternatively,
when omeprazole is docked into binding pocket in the three-dimensional
model of P450cam, we find that Pro
(which aligns with
His
in 2C19) is near the docked substrate (approximately 6
Å) as shown in Fig. 4. Moreover, the adjacent Phe
of P450cam is even closer to the substrate (
2 Å).
Thus, the effect of the Ile
His mutation is
consistent with this model.
is the highly
conserved Thr in the I helix. The heme is shown in red, amino
acid residues in blue, and substrate in black.
Analysis of Residues 160-227
Analysis of the
chimeric data indicated that amino acids 160-227 may also play a
crucial role in the specificity of P450 2C19 for omeprazole. We
therefore constructed a 2C9/2C19
chimera and an
identical construct containing an Ile
His mutation.
The 2C9/2C19
chimera exhibited a 7-fold
increase in omeprazole 5-hydroxylase activity compared to P450 2C9 (Fig. 5). Moreover, when combined with the an Ile
His mutation, this chimera exhibited a dramatic 38-fold
increase in activity. The activity of this mutated chimera was even
greater than that of native P450 2C19.
and region 160-227 of 2C19 to omeprazole 5-hydroxylase
activity using chimeras and site-directed mutants. The construction of
the 2C9/2C19
chimera is shown in Fig. 1.
A second 2C9/2C19
chimera contained the
Ile
His mutation. Individual amino acids in the
160-227 region were mutated in P450 2C9 in combination with the
Ile
His mutation as shown in Fig. 1B. Values represent means ±
S.E.
Arg (K206R), Leu
Val (L208V), Pro
Thr (P221T), and
Ser
Thr in combination with Ile
His did not increase omeprazole 5`-hydroxylase activity
over that of I99H alone (Fig. 5), indicating that these residues
are not the critical amino acids in this region. However, mutation of
the polar serine at position 220 to a nonpolar hydrophobic proline
residue (Ser
Pro) increased activity to
90%
of that of P450 2C19. When a second nonconservative mutation was made
in the tandem residue at position 221 (P221T) in conjunction with S220P
and I99H, the omeprazole hydroxylase activity of the triple mutant
(I99H/S220P/P221T) was equivalent to that of P450 2C19. Sequence
alignment indicates that residues 220 and 221 reside midway between the
COOH-terminal end of the F-helix and the NH
-terminal end of
G-helix in the interhelical loop, outside of any known substrate
binding sites. This region corresponds to the F-G helical turn. This
region is extremely variable in length in the P450 superfamily, and
bacterial P450cam contains no amino acids corresponding to Pro
or Thr
of P450 2C19. The three-dimensional model of
P450 2B1 would predict that these amino acids are far from the
substrate-binding pocket; however, it has been suggested that this
region may form a flexible lid over the substrate-binding pocket and
thus form part of the substrate access
channel(8, 11) . Proline residues give loops greater
flexibility. Therefore, the introduction of Pro
may
refold the F-G loop and change accessibility to the active site or
bring these residues closer to the substrate pocket. Interestingly, Uno
and Imai (44) reported that residues 210-262, which
contain part of the same domain, cooperate with amino acids
90-125 to confer substrate specificity to laurate
(
-1)-hydroxylase P450 2C2. Several other investigators have also
identified important key residues in or near this domain, including
residue 209 of mouse 2A5 as well as 206 and 209 of rat
2B1(5, 20, 22, 26, 45) .
The present results clearly show that residues 220 and 221, which are
in the F-G loop of human P450 2C19 and outside the SRS proposed by
Gotoh(13) , are critical determinants of omeprazole hydroxylase
activity.S-Mephenytoin 4`-Hydroxylase Activity
Somewhat
surprisingly, S-mephenytoin hydroxylase activity did not
parallel omeprazole hydroxylase activity in the various chimeras and
mutants. As shown in Fig. 6, only two chimeric proteins,
2C19
/2C9 and 2C9/2C19
,
exhibited significant increases in S-mephenytoin hydroxylase
activity over P450 2C9. Activities of these proteins were
30% of
that of P450 2C19. Furthermore, S-mephenytoin hydroxylase
activity was not detected in any of the mutant proteins (data not
shown). The differences in activity of the His
mutants
toward S-mephenytoin and omeprazole could be due to the fact
that although S-mephenytoin is a smaller molecule (16 heavy
atoms) than omeprazole (24 heavy atoms), it is more branched. The side
chain of histidine can potentially interact with both omeprazole and
mephenytoin since it has the capacity for hydrogen bonding, whereas
this cannot happen with isoleucine. When S-mephenytoin is
docked with the 4-position of the phenyl ring replacing the 5-position
of omeprazole (Fig. 4), the remaining rings of both molecules
would be placed in an orientation that could allow strong hydrogen
bonding with His
. However, the branched structure of S-mephenytoin may require additional three-dimensional
accommodation in the active site. These results suggest that
specificity of P450 2C19 for S-mephenytoin may require a more
complex enzyme configuration than that for omeprazole, possibly
involving multiple substrate recognition domains acting in concert.
Conclusions
Chimeric proteins and amino acid
mutations have been widely used to determine critical residues
responsible for substrate specificity of closely related P450 proteins.
We have utilized this approach to identify amino acids that are
critical determinants of omeprazole 5-hydroxylase activity of human
P450 2C19. We first identified regions important in substrate
specificity by analyzing the catalytic activity of chimeras and then
sequentially replaced individual residues in P450 2C9 by site-directed
mutagenesis. We have identified three key amino acids at positions 99,
220, and 221, which are critical determinants of omeprazole
5-hydroxylase activity. These residues map to SRS-1 and the F-G loop.
)
We express our gratitude to Glaxo Research and
Development (Hertfordshire, UK) for the generous gift of
C-labeled omeprazole. We also thank Dr. James R. Halpert,
University of Arizona, Tucson, for generously providing the coordinates
for a structural model of cytochrome P450 2B1 (19) and for a
preprint of a manuscript in press(19) . We thank Tamara
McIntyre, Heath LeFevers, and Angela Stanley for HPLC analysis of
omeprazole metabolites.
©1996 by The American Society for Biochemistry and Molecular Biology, Inc.
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D. J. Fraser, Y. Q. He, G. R. Harlow, and J. R. Halpert Use of Chimeric Enzymes and Site-Directed Mutagenesis for Identification of Three Key Residues Responsible for Differences in Steroid Hydroxylation between Canine Cytochromes P-450 3A12 and 3A26 Mol. Pharmacol., February 1, 1999; 55(2): 241 - 247. [Abstract] [Full Text] |
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G. C. Ibeanu, J. A. Goldstein, U. Meyer, S. Benhamou, C. Bouchardy, P. Dayer, B. I. Ghanayem, and J. Blaisdell Identification of New Human CYP2C19 Alleles (CYP2C19*6 and CYP2C19*2B) in a Caucasian Poor Metabolizer of Mephenytoin J. Pharmacol. Exp. Ther., September 1, 1998; 286(3): 1490 - 1495. [Abstract] [Full Text] |
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H. Yamazaki, K. Inoue, P. M. Shaw, W. J. Checovich, F. P. Guengerich, and T. Shimada 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., November 1, 1997; 283(2): 434 - 442. [Abstract] [Full Text] |
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