The 2′-trifluoromethyl analogue of indomethacin is a potent and selective COX-2 inhibitor

Article abstract of DOI:10.1021/ml400066a

Indomethacin is a potent, time-dependent, nonselective inhibitor of the cyclooxygenase enzymes (COX-1 and COX-2). Deletion of the 2′-methyl group of indomethacin produces a weak, reversible COX inhibitor, leading us to explore functionality at that position. Here, we report that substitution of the 2′-methyl group of indomethacin with trifluoromethyl produces CF ₃-indomethacin, a tight-binding inhibitor with kinetic properties similar to those of indomethacin and unexpected COX-2 selectivity (IC ₅₀ mCOX-2 = 267 nM; IC₅₀ oCOX-1 > 100 μM). Studies with site-directed mutants reveal that COX-2 selectivity results from insertion of the CF₃ group into a small hydrophobic pocket formed by Ala-527, Val-349, Ser-530, and Leu-531 and projection of the methoxy group toward a side pocket bordered by Val-523. CF₃-indomethacin inhibited COX-2 activity in human head and neck squamous cell carcinoma cells and exhibited in vivo anti-inflammatory activity in the carrageenan-induced rat paw edema model with similar potency to that of indomethacin.

Full text of DOI:10.1021/ml400066a

Letter
pubs.acs.org/acsmedchemlett
The 2′-Trifluoromethyl Analogue of Indomethacin Is a Potent and
Selective COX‑2 Inhibitor
Anna L. Blobaum,† Md. Jashim Uddin,† Andrew S. Felts, Brenda C. Crews, Carol A. Rouzer,
and Lawrence J. Marnett*
The A. B. Hancock Jr. Memorial Laboratory for Cancer Research, Departments of Biochemistry, Chemistry, and Pharmacology,
Vanderbilt Institute of Chemical Biology, Center in Molecular Toxicology, and Vanderbilt-Ingram Cancer Center, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
S
* Supporting Information
ABSTRACT: Indomethacin is a potent, time-dependent, non-
selective inhibitor of the cyclooxygenase enzymes (COX-1 and
COX-2). Deletion of the 2′-methyl group of indomethacin
produces a weak, reversible COX inhibitor, leading us to explore
functionality at that position. Here, we report that substitution of
the 2′-methyl group of indomethacin with trifluoromethyl produces
CF3−indomethacin, a tight-binding inhibitor with kinetic properties
similar to those of indomethacin and unexpected COX-2 selectivity
(IC50 mCOX-2 = 267 nM; IC50 oCOX-1 > 100 μM). Studies with
site-directed mutants reveal that COX-2 selectivity results from
insertion of the CF3 group into a small hydrophobic pocket formed by Ala-527, Val-349, Ser-530, and Leu-531 and projection of
the methoxy group toward a side pocket bordered by Val-523. CF3−indomethacin inhibited COX-2 activity in human head and
neck squamous cell carcinoma cells and exhibited in vivo anti-inflammatory activity in the carrageenan-induced rat paw edema
model with similar potency to that of indomethacin.
KEYWORDS: Cyclooxygenase, inflammation, nonsteroidal anti-inflammatory drug, coxib, prostaglandin, arachidonic acid
yclooxygenase (COX) enzymes, which catalyze the
The use of indomethacin is limited by its gastrointestinal
Cconversion of arachidonic acid (AA) to prostaglandin toxicity and its inhibition of platelet function leading to
increased bleeding times.10,11 A significant component of both
of these side effects results from the ability of indomethacin to
H2, are the pharmacological targets of nonsteroidal anti-
inflammatory drugs (NSAIDs).1 The two COX isoforms, COX-
inhibit COX-1. Thus, multiple attempts to decrease the COX-1
inhibitory activity of indomethacin have been reported. Since
the COX-2 active site is approximately 25% larger than that of
COX-1, indomethacin analogues have been synthesized that
increase its size by, e.g., lengthening the carboxylic acid side
chain or augmenting the steric bulk of the acyl group attached
to the indole nitrogen.12 In addition, many different amides and
esters of indomethacin exhibit significant COX-2 selectivity,
and this approach has been used to construct COX-2-targeted
molecular imaging agents.13,14
1 and COX-2, have high sequence identity (60%), very similar
three-dimensional structures, and nearly indistinguishable
kinetic parameters with AA as substrate.2 COX-1 is
constitutively expressed in most tissues and is involved in the
production of prostaglandins that mediate basic cellular
housekeeping functions. In most contexts, COX-2 is an
inducible enzyme, the expression of which is activated by
cytokines, mitogens, endotoxin, and tumor promoters. The
anti-inflammatory and analgesic properties of traditional
NSAIDs are primarily due to inhibition of COX-2.3
Several years ago, our laboratory reported that deletion of the
2′-methyl group on the indole ring of indomethacin produces a
des-methyl derivative that is a weak, reversible inhibitor of
COX-2 and, to some extent, COX-1.15 The explanation for the
loss of COX inhibitory activity resulting from deletion of the 2′-
methyl group is provided by the crystal structure of a complex
of indomethacin with COX-2.16 The 2′-methyl inserts into a
hydrophobic pocket comprising Ala-527, Val-349, Ser-530, and
Leu-531 (Figure 1C). Mutations of Val-349 to Ala or Leu alter
Indomethacin is a potent NSAID that exhibits an
approximately 15-fold higher selectivity for COX-1 relative to
COX-2 (Figure 1).4−7 It is a slow, tight-binding inhibitor that
establishes a rapidly reversible equilibrium with the enzyme
followed by a slow transition to a much more tightly bound
COX-indomethacin complex. Formation of the tightly bound
complex is responsible for indomethacin’s strong COX
inhibitory activity.4 Indomethacin is a powerful anti-inflamma-
tory agent and a strong tocolytic.8 It also exhibits anticancer
activity as suggested by a report demonstrating that
indomethacin significantly increased the lifespan of a group of
terminally ill patients suffering from a range of cancers, mainly
gastrointestinal.9
Received: February 16, 2013
Accepted: March 24, 2013
© XXXX American Chemical Society
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Figure 2. Synthesis of CF3−indomethacin from CF3−levulinic acid
lactone.
detected the desired CF3−indomethacin by mass spectrometry
of the reaction mixture of 1-(4-methoxyphenyl)-1-(4-
chlorobenzoyl)hydrazine hydrochloride and the lactone. The
success of this approach suggests that a significant lactone
impurity in commercial CF3-levulinic acid may have accounted
for our occasional ability to synthesize CF3−indomethacin
using the more traditional synthetic route.
Mass spectral analysis (Figure S1, Supporting Information,
shown for CF3−indomethacin), one-dimensional proton NMR
spectroscopy (Figures S2 and S3, Supporting Information,
shown for CF3−indomethacin), and HPLC analysis were
performed on each of the reaction intermediates and final
products to confirm both the structure and purity of the
compounds. Each was shown by HPLC analysis with
evaporative light scattering detection to elute as a single peak
(>98% pure). Under optimal conditions, the yield of CF3−
indomethacin from the reaction of the hydrazine and the
lactone was 20%; however, the synthesis was reproducible, and
sufficient amounts of material could be generated for
subsequent testing.
Following a 3 min equilibration of purified and hematin-
reconstituted mouse or human COX-2 (mCOX-2 or hCOX-2)
or ovine COX-1 (oCOX-1) at 37 °C, CF3−indomethacin and
[1-14C]-AA were added simultaneously and incubated for 30 s.
No significant enzyme inhibition was observed over a wide
range of inhibitor and substrate concentrations, indicating that
CF3−indomethacin is not a pure competitive inhibitor of COX
(data not shown). Next, CF3−indomethacin was preincubated
with purified COX enzymes using a protocol designed to
evaluate time-dependent inhibition. Figure 3A shows the
inhibition curve for indomethacin itself. As expected,
indomethacin was a potent and nonselective inhibitor of
mCOX-2, hCOX-2, and oCOX-1, with IC50 values of 127, 180,
and 27 nM, respectively, consistent with previous reports.15 In
contrast, Figure 3B shows that CF3−indomethacin potently and
selectively inhibited both mCOX-2 and hCOX-2 (IC50 = 267
and 388 nM, respectively) with no appreciable effect on oCOX-
1 up to very high inhibitor concentrations (100 μM).
Figure 1. Structures of indomethacin and trifluoromethyl-indometha-
cin (A). Representation of indomethacin in the active site of mouse
COX-2 (B) and a space-filling model of the methyl-binding pocket in
mouse COX-2 for indomethacin comprising Ala-527, Val-349, Ser-530,
and Leu-531 (C).
the size of the pocket and lead to an increase or decrease,
respectively, in the potency of indomethacin.15
The importance of the 2′-methyl group in mediating slow,
tight-binding of indomethacin prompted us to explore other
functionality at this position. These efforts led to the discovery
of 2′-trifluoromethyl-indomethacin (CF3−indomethacin), in
which the 2′-methyl group was replaced by a CF3 group
(Figure 1). This modest chemical change results in a very
significant and unexpected shift in the selectivity of COX
inhibition, creating a molecule that is a highly potent, slow,
tight-binding inhibitor of COX-2 lacking significant COX-1
inhibitory activity. Here, we describe the synthesis, inhibitory
mechanism, and pharmacology of CF3−indomethacin.
We initially attempted to synthesize CF3−indomethacin
through the condensation of 1-(4-methoxyphenyl)-1-(4-
chlorobenzoyl)hydrazine hydrochloride with CF3-levulinic
acid using a classic Fisher indole synthesis approach. Although
this route occasionally yielded the desired product, it proved to
be unreliable, affording a phenylhydrazone derivative with no
cyclization to the intended indole on most attempts. This led us
to investigate a number of alternative approaches, including a
Fisher indole synthesis starting with CF3-levulinic acid and 2-
methyl-1-(4-methoxyphenyl)-1-(4-chlorobenzoyl) hydrazine,
synthesized from 1-(4-methoxyphenyl)-1-(4-chlorobenzoyl)-
hydrazine hydrochloride by reaction with paraformaldehyde
followed by reduction with NaBH4. We also attempted
condensation of CF3-levulinic acid with 2-acetyl-1-(4-methox-
yphenyl)-1-(4-chlorobenzoyl)hydrazine. No indole product was
detected in either of these reactions.
Time-dependent inhibition of COX enzymes is most simply
described by the two-stage equilibrium summarized in eq 1.4
To evaluate the magnitude of the steps in this equilibrium, the
dependence of COX inhibition by CF3−indomethacin on
preincubation time and inhibitor concentration was deter-
mined. The decrease in substrate conversion at different
inhibitor concentrations was plotted against the preincubation
times and fit to a single-exponential decay with a plateau to
determine a value for kobs. The dependence of kobs on inhibitor
concentration is represented by eq 2, where KI corresponds to
the inhibitor concentration that yields a kobs value equal to half
the limiting kobs, and k2 represents the limiting forward rate
We hypothesized that failure of indole formation was due to
the electron-withdrawing effect of the CF3 group, which
disfavors tautomerization of the hydrazone to the enamine
intermediate required for cyclization to the indole product. To
address this problem, we designed a synthetic route utilizing the
reaction of the hydrazine with CF3-levulinic acid lactone in
hopes that direct formation of the enamine could occur without
the intermediacy of the hydrazone (Figure 2). Consistently, we
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Figure 3. Inhibition of purified oCOX-1, mCOX-2 and hCOX-2 by
indomethacin (INDO) and CF3−indomethacin (CF3−INDO). The
IC50 values of indomethacin for oCOX-1, mCOX-2 and hCOX-2 were
27, 127, and 180 nM, respectively. The corresponding IC50 values of
CF3−indomethacin were >4 μM, 267 nM, and 388 nM, respectively.
Figure 4. Kinetics of the time-dependent inhibition of hCOX-2 by
CF3−indomethacin (CF3−INDO). Individual kobs values were
obtained from a plot of the decrease in AA conversion versus
preincubation time (A) and plotted against inhibition concentration
(B) to calculate the kinetic constants, KI, k2, and k−2.
constant for inhibition. The reverse rate constant, k−2, is equal
to the y-intercept and is zero for compounds that display
extremely tight binding.
Table 1. Inhibition of COX Enzymes by Indomethacin and
CF3−Indomethacin
a
a
enzyme
INDO IC50
127 nM
27 nM
CF3−INDO IC50
E + I XooY [EI] Xkoo2Y EI*
k1
wt mCOX-2
wt oCOX-1
mV349A
mV349I
267 nM
k−1
k−2
(1)
(2)
71 nM (1.8↑)
315 nM (2.5↓)
1.34 μM (10.6↓)
220 nM (1.7↓)
120 nM (2.2↑)
163 μM (6.1↓)
kobs = ((k2[I])/(KI + [I])) + k−2
where KI = k−1/k1.
mV349L
mS530A
mR120A
mR120Q
mY355F
mV523I
Figure 4A shows the kinetics for the time- and concentration-
dependent inhibition of wild-type hCOX-2 by CF3−indome-
thacin. Inhibition proceeded rapidly, and plateaus were reached
at short time points for the higher inhibitor concentrations. The
time-dependent inhibition curve for hCOX-2 approached 0%
remaining activity at higher inhibitor concentrations, indicating
tight binding to the enzyme by CF3−indomethacin. Interest-
ingly, CF3−indomethacin interacted with hCOX-2 with a
greater affinity than indomethacin, as indicated by a lower KI
(1.5 0.26 μM versus 13 2.3 μM, respectively). The forward
rate constants (k2) were similar between indomethacin (0.061
0.004 s−1) and CF3−indomethacin (0.020 0.001 s−1). A
reverse rate constant (k−2) was not determinable for either
compound. Similar results were demonstrated for wild-type
mCOX-2 (data not shown).
The crystal structure of indomethacin complexed with COX-
2 shows that the carboxyl group of the inhibitor hydrogen
bonds and ion pairs with Tyr-355 and Arg-120 at the
constriction site at the base of the active site (Figure 1B). In
contrast, some carboxylic acid-containing inhibitors, including
diclofenac and lumiracoxib, bind to COX-2 in an orientation
that places their carboxylates at the top of the active site,
allowing them to form hydrogen bonds with Ser-530 and Tyr-
385.17,18 Table 1 shows that a Ser-530 to Ala mutation has little
effect on the IC50 value observed for CF3−indomethacin,
indicating an orientation similar to that of indomethacin.
435 nM (1.6↓)
1.56 μM (5.8↓)
>4 μM (15↓)
326 nM (2.6↓)
475 nM (3.7↓)
a
Indomethacin (INDO) and CF3−indomethacin (CF3−INDO) were
screened against purified wild-type (wt) oCOX-1, mCOX-2, and the
indicated mCOX-2 mutants as described in the Experimental
Procedures in the Supporting Information. Values in parentheses
indicate the fold increase or decrease in IC50 values for the mutants
compared to wt mCOX-2. Dashed lines indicate that no inhibition was
observed for inhibitor concentrations of up to 100 μM.
Kinetics studies of inhibition by esterified NSAIDs or of site-
directed mutants of Arg-120 have revealed that carboxylic acid-
containing, time-dependent NSAIDs (e.g., indomethacin and
flurbiprofen) form an ion-pair and/or hydrogen bond with Arg-
120 and that this interaction is critical for inhibition. For COX-
2, this interaction plays a role but is less important for inhibitor
binding and potency than it is for COX-1.4,7,19,20 Table 1 shows
that both indomethacin and CF3−indomethacin are unable to
inhibit an Arg-120 to Ala mutant or a Tyr355 to Phe mutant of
COX-2, suggesting that the carboxylate of each inhibitor
interacts with those residues at the constriction site. An R120Q
mutant eliminates a potential ion-pair interaction with the
inhibitors but retains the ability to hydrogen bond. Both
C
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indomethacin and CF3−indomethacin were able to inhibit the
R120Q mutant, although the potency of inhibition was
decreased by nearly 3-fold and 6-fold, respectively, indicating
the importance of both hydrogen bonding and ion-pairing in
the inhibition of COX by these compounds.
This is contrary to expectations because indomethacin is a
more potent inhibitor against COX-1 than COX-2.7 The
reduced sensitivity of V523I to indomethacin inhibition is a
reminder that a drug’s action on its target reflects the ensemble
of multiple interactions in the binding site and is rarely dictated
by the interaction with a single protein residue.
Having determined its key molecular determinants of COX-2
inhibition, we next evaluated CF3−indomethacin’s ability to
inhibit COX-2 in intact cells. For these studies, we selected
1483 human head and neck squamous cell carcinoma cells that
express high levels of the enzyme. Cells were pretreated with
varying concentrations of CF3−indomethacin for 30 min
followed by incubation with [1-14C]AA for 20 min. In this
assay, CF3−indomethacin inhibited COX-2-dependent AA
oxygenation with an IC50 value of 0.15 μM.
Finally, we assessed the in vivo anti-inflammatory activity of
CF3−indomethacin in the footpads of rats injected with
carrageenan. CF3−indomethacin or indomethacin was admin-
istered orally in corn oil at 1 h postcarrageenan injection, and
footpad volume was measured 2 h later. The results showed
that both CF3−indomethacin and indomethacin exhibited anti-
inflammatory activity with EC50 values of 1.7 mg/kg and 1.0
mg/kg, respectively (Figure 5). The highest concentration of
As noted above, the potent, time-dependent inhibition of
COX by indomethacin is attributed to the insertion of the 2′-
methyl group of the inhibitor into a small hydrophobic pocket
comprising four residues (Ala-527, Val-349, Ser-530, and Leu-
531). Mutation of Val-349 to Ala enlarges the pocket and
increases the potency of indomethacin 3-fold, whereas mutation
to Leu reduces the pocket size and decreases the potency of the
inhibitor by 16-fold. A Val-349 to Ile mutant resembles wild-
type enzyme.15 A similar, though more severe, trend was
observed for CF3−indomethacin with regard to mutating Val-
349 (Table 1), suggesting that the trifluoromethyl group of
CF3−indomethacin also inserts into or interacts with the
residues in the hydrophobic pocket.
The first X-ray crystal structures solved for hCOX-2 showed
that there is an overall difference in the size and shape of the
COX-2 active site compared to that of COX-1.16,21 The nearly
25% larger active site of COX-2 is accounted for by a side
pocket resulting from a Val-523 substitution (Ile in COX-1) in
the active site and by Arg-513 and Val-434 substitutions (His-
513 and Ile-434, respectively, in COX-1) in the secondary shell.
This side pocket is the primary determinant of inhibition of the
diarylheterocycle class of COX-2-selective inhibitors (e.g.,
celecoxib and rofecoxib). The crystal structure of mCOX-2
with the celecoxib analogue SC-558 reveals that the
sulfonamide group of the inhibitor binds in the side pocket
adjacent to Val-523.16 Mutagenesis of Val-523 to Ile in COX-2
abolishes the selectivity of diarylheterocycle inhibitors.22,23
Thus, the current data suggest that the selective, time-
dependent step in diarylheterocycle-mediated inhibition of
COX-2 is most likely the insertion of the methylsulfonyl or
sulfonamide group of the inhibitor into the pocket adjacent to
Val-523 in COX-2. This is precluded in COX-1 by the extra
steric bulk of Ile-523.
The cumulative results of the site-directed mutagenesis
studies described above suggested that CF3−indomethacin
binds to COX-2 in essentially the same orientation as
indomethacin and that the two inhibitors share the same
molecular determinants of inhibition. However, this conclusion
was contradicted by results from a V523I mutant that clearly
differentiated CF3−indomethacin and indomethacin. As noted
above, V523I is a conserved COX-2 → COX-1 amino acid
change that has a dramatic effect on the binding of
diarylheterocycles such as celecoxib and rofecoxib to COX-
2.22,23 Although the V523I mutant COX-2 was sensitive to
inhibition by indomethacin, the mutation resulted in a 3.7-fold
reduction in inhibitor potency compared to wild-type enzyme.
This reduction in potency was much more striking for CF3−
indomethacin (>15-fold) (Table 1). The 5-methoxy group of
indomethacin is located near Val-523, but it does not insert into
the side pocket.16 Thus, the reduced inhibition of the V523I
mutant by indomethacin may arise from steric interactions with
the bulky Ile residue. The greater loss of activity observed with
CF3−indomethacin suggests that the larger trifluoromethyl
group at the 2′ position displaces the indole ring toward the
center of the active site and puts more pressure on the 5-
methoxy-Ile-523 interaction in the mutant. It is noteworthy that
the V523I mutant is less sensitive to inhibition by indomethacin
even though it represents a COX-2 → COX-1 substitution.
Figure 5. In vivo anti-inflammatory activity of indomethacin and CF3−
indomethacin in the rat paw edema model. Carageenan was injected
into one paw, then 1 h later indomethacin or CF3−indomethacin was
administered by oral gavage. Paw volume was measured 2 h later.
▲
●
.
Indomethacin, ; CF3−indomethacin,
indomethacin tested was 2 mg/kg because previous studies in
Sprague−Dawley rats had indicated substantial gastric erosion
and bleeding at higher doses. CF3−indomethacin was tested up
to 10 mg/kg with no evidence of gastrointestinal bleeding. In
fact, once testing was complete, the CF3−indomethacin-treated
animals were maintained overnight for further observation. The
animals appeared healthy, and no passage of blood from the
gastrointestinal tract was observed.
In conclusion, we report here the remarkable finding that
replacement of the 2′-methyl group of indomethacin with
trifluoromethyl completely eliminates COX-1 inhibitory activity
while retaining potent, time-dependent inhibition of COX-2.
The KI for initial binding to COX-2 is approximately 9-fold
lower for CF3−indomethacin than for indomethacin, but the k2
is 3-fold slower. Thus, the k2/KI for CF3−indomethacin (0.013
s−1 μM) is approximately 3-fold greater than the k2/KI for
indomethacin (0.0046 s−1 μM). CF3−indomethacin inhibits
COX-2 oxygenation of AA in cultured human head-and-neck
(1483) cancer cells and is equipotent to indomethacin as an
inhibitor of edema in the rat footpad model of inflammation.
Given its comparable effects to indomethacin on COX-2
combined with its inability to inhibit COX-1, CF3−
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ASSOCIATED CONTENT
* Supporting Information
■
S
Experimental procedures and spectral data for CF3−indome-
thacin. This material is available free of charge via the Internet
at http://pubs.acs.org.
AUTHOR INFORMATION
Corresponding Author
*(L.J.M.) E-mail: larry.marnett@vanderbilt.edu.
■
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†These authors contributed equally to this work.
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Funding
This work was supported by a grant from the National
Institutes of Health (CA89450).
Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
We are grateful to Matt Windsor for assistance with molecular
graphics.
■
ABBREVIATIONS
■
indomethacin, 2-(1-(4-chlorobenzoyl)-5-methoxy-2′-methyl-
1H-indol-3-yl)ethanoic acid; CF3−indomethacin, 2-(1-(4-chlor-
obenzoyl)-5-methoxy-2′-trifluoromethyl-1H-indol-3-yl)-
ethanoic acid; COX, cyclooxygenase; AA, arachidonic acid;
NSAID, nonsteroidal anti-inflammatory drug
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