Design and synthesis of some 5-substituted-2-(4-(azido or methylsulfonyl)phenyl)-1h-indole derivatives as selective cyclooxygenase (cox-2) inhibitors

Article abstract of DOI:10.3797/scipharm.0805-20

A group of 5-substituted-2-(4-azido or (methylsulfonyl)phenyl)-1H-indoles were designed and synthesized as selective cyclooxygenase (COX-2) inhibitors. In vitro COX-1 and COX-2 isozyme inhibition studies were carried out to investigate the effect of different substituents (H, F, CI, Me, OMe) at C-5 position and different pharmacophore groups (azido or methylsulfonyl) at para position of phenyl ring at C-2 position of the 1H-indole ring on COX-2 selectivity and potency. The structure-activity relationship study of these compounds indicated that the introduction of a methoxy substituent at C-5 position and 4-(methylsulfonyl) phenyl group at C-2 position of the 1H-indole ring (compound 4e) had the best COX-2 selectivity (S.I = 291.2). A molecular modeling study where 4e was docked in the binding site of COX-2 showed that the methylsulfonyl group at para position of phenyl ring is oriented in the vicinity of the COX-2 secondary pocket. Osterrechische Apotheker- Verlagsgedellschaft m.b.H.

Full text of DOI:10.3797/scipharm.0805-20

Sci Pharm. 2008; 76: 361–376
doi:10.3797/scipharm.0805-20
361
© Österreichische Apotheker-Verlagsgesellschaft m. b. H., Vienna, Austria
Reproduction is permitted for non-commercial purposes.
Design and Synthesis of Some 5-Substituted-2-(4-(azido or
methylsulfonyl)phenyl)-1H-indole Derivatives as Selective
Cyclooxygenase (COX-2) Inhibitors
1
1
Afshin ZARGHI * 1, Azar TAHGHIGHI , Zohreh SOLEIMANI ,
2
3
4
Bahram DARAIE , Orkideh Gorban DADRASS , Mehdi HEDAYATI
1 Department of Medicinal Chemistry, School of Pharmacy,
Shahid Beheshti University (M.C), P.O. Box: 14155-6153, Tehran/ Iran
2 Department of Toxicology, School of Medical Sciences,
Tarbiat Modares University, Tehran/ Iran
3 School of Pharmacy, Azad University, Tehran/ Iran
4 Endocrine research center, Shahid Beheshti University (M.C), Tehran/ Iran
Abstract
A group of 5-substituted-2-(4-azido or (methylsulfonyl)phenyl)-1H-indoles were
designed and synthesized as selective cyclooxygenase (COX-2) inhibitors. In vitro
COX-1 and COX-2 isozyme inhibition studies were carried out to investigate the
effect of different substituents (H, F, Cl, Me, OMe) at C-5 position and different
pharmacophore groups (azido or methylsulfonyl) at para position of phenyl ring at
C-2 position of the 1H-indole ring on COX-2 selectivity and potency. The structure-
activity relationship study of these compounds indicated that the introduction of a
methoxy substituent at C-5 position and 4-(methylsulfonyl) phenyl group at C-2
position of the 1H-indole ring (compound 4e) had the best COX-2 selectivity (S.I =
291.2). A molecular modeling study where 4e was docked in the binding site of
COX-2 showed that the methylsulfonyl group at para position of phenyl ring is
oriented in the vicinity of the COX-2 secondary pocket.
* Corresponding author: Fax: +98-21-88795008.
E-mail: azarghi@yahoo.com (A. Zarghi).

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A. Zarghi et al.:
Keywords
2-Phenyl-1H-indoles • COX-2 inhibitors • SAR
Introduction
Cyclooxygenase (COX) also know as prostaglandin synthase (PGH) is a
potent mediator of inflammation. Nonsteroidal anti-inflammatory drugs (NSAIDs)
bind to cyclooxygenase thereby inhibiting the production of prostaglandins.
However, inhibition of COXs may lead to undesirable side effects. Nowadays, it is
well established that there are at least two COX isozymes, COX-1 and COX-2 [1].
The constitutive COX-1 isozyme is produced in a variety of tissues and appears to
be important to the maintenance of physiological functions such as gastric
protection and vascular homeostasis [2]. Alternatively, the COX-2 isozyme is
induced by mitogenic and proinflammatory stimuli linking its involvement to
inflammatory processes [3].Thus, selective inhibition of COX-2 over COX-1 is
useful for the treatment of inflammation and inflammation-associated disorders with
reduced gastrointestinal toxicities when compared with NSAIDs. In addition to the
role of COX-2 in rheumatoid arthritis and osteoarthritis, it is also implicated in colon
cancer and angiogenesis [4, 5]. Recent studies have shown that the progression of
Alzheimer’s disease is reduced among some users of NSAIDs. Chronic treatment
with selective COX-2 inhibitors may therefore slow the progress of Alzheimer’s
disease without causing gastrointestinal damage [6]. Diarylheterocycles, and other
central ring pharmacophore templates, have been extensively studied as selective
COX-2 inhibitors. All these molecules possess 1,2 diaryl substitution on a central
heterocyclic or carbocyclic ring system (see structures A–F in Chart 1) [7–13].
Recently, we reported several investigations describing the design, synthesis and
COX inhibitory activities of a novel class of compounds possessing an acyclic 1,3-
diarylprop-2-en-1-one structural template [14, 15]. For example, the acyclic (E) 1,3-
diphenylprop-2-en-1-ones possessing a 4-methylsulfonyl or 4-azido COX-2

Design and Synthesis of Some 5-Substituted-2-(4-(azido …
363
pharmacophore group at the C-1 phenyl ring (see structure F) exhibited highly
selective COX-2 inhibition.
SO2NH2
SO2Me
N
S
N
F3C
N
O
Me
F
Celecoxib (
A
)
B
( )
SO2NH2
SO2Me
Me
Cl
O
N
N
N
Me
Valdecoxib (
C
)
D
Etoricoxib ( )
SO2NHCOCH3
O
O
O
F
R
(R=SO2Me or N3)
F
E
Chart 1. Representative examples of selective COX-2 inhibitors
As part of our ongoing program to design new types of selective COX-2
inhibitors, we now report the synthesis, some structure-activity relationships, and a
molecular modeling study for a group of 2-phenyl-1H-indoles possessing a COX-2
azido or SO2Me pharmacophore at the para-position of phenyl ring in conjunction
with an 1H-indole ring having different substituents at C-5 position.

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A. Zarghi et al.:
Results and Discussion
1. Chemistry
The target 2-(4-(methylsulfonyl or azido)phenyl)-1H-indole derivatives were
synthesized using a Fischer-indole synthesis as shown in Scheme 1. Accordingly,
warming an ethanolic mixture of 4-methylsulfonylacetophenone (1) [16] and an
appropriate phenylhydrazine (2) on a water bath in presence of few amounts of
acetic acid gave 4-methylsulfonylacetophenone phenylhydrazone (3) (50–89%).
Cyclization of 3 by polyphosphoric acid at 120 oC afforded the 2-(4-(methylsulfonyl)
phenyl)-1H-indoles (4, 60–92%) [17, 18]. Similarly, 2-(4-aminophenyl)-1H-indole
derivatives 5 (40–62%) were synthesized and the amino group was converted to
azido group by diazotation with sodium nitrite and hydrochloric acid and then
treatment with sodium azide to obtain 2-(4-(azido)phenyl)-1H-indoles 6 (55–68%)
[15]. The purity of all products was determined by thin layer chromatography using
several solvent systems of different polarity. All compounds were pure and stable.
1
The compounds were characterized by H nuclear magnetic resonance, infrared,
mass spectrometry and CHN analysis.
H
N
O
N
X
EtOH
AcOH
H2NHN
X
H3CO2S
H3CO2S
+
CH3
CH3
1
2
3
4a, X=H
X
4b, X=F
PPA
SO2CH3
4c, X=Cl
N
H
4d, X=CH3
4e, X=OCH3
X
X
HNO2
NaN3
N3
NH2
N
H
N
H
5a, X=H
5b, X=F
6 ,
a X=H
6b, X=F
5c, X=OCH3
6c, X=OCH3
Sch. 1.

Design and Synthesis of Some 5-Substituted-2-(4-(azido …
365
2. Enzyme Inhibitory Activity
The ability of the 2-phenyl-1H-indoles 4a–e and 6a–c to inhibit the COX-1 and
COX-2 isozymes was determined using chemiluminescent enzyme assays as
previously described [13] (see enzyme inhibition data in Table 1.). In vitro COX-
1/COX-2 inhibition studies showed that compounds containing methylsufonyl
pharmacophore group 4a–e were selective inhibitors of the COX-2 isozyme with
IC50 values in the highly potent 0.08 to 0.26 μM range, and COX-2 selectivity
indexes (S.I.) in the 30.5 to 291.2 range. The structure-activity relationship study of
these compounds indicated that the order of COX-2 selectivity was OMe>F >Me,Cl
>H. These results showed that the nature of substituent at C-5 position of the 1H-
indole ring has an important role on selectivity and potency. Replacing the
methylsulfonyl group with an azido pharmacophore group in these compounds (6a–
6c) decreased either selectivity or potency. According to these results, 5-methoxy-
2-(4-(methylsulfonyl) phenyl)-1H-indole 4e was the most potent (IC50 = 0.08 μM),
and selective (S.I. >291) COX-2 inhibitor among the synthesized compounds.
These data suggest that the compound 4e should inhibit the synthesis of
inflammatory prostaglandins via the cyclooxgenase pathway at sites of
inflammation and be devoid of ulcerogenicity due to the low COX-1 inhibitory
activity.

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A. Zarghi et al.:
Tab. 1. In vitro COX-1 and COX-2 Enzyme Inhibition Data
X
Y
N
H
Compound
X
Y
IC50 (μM)a
COX-2
S.I.b
30.5
COX-1
7.9
COX-2
0.26
4a
H
F
SO2CH3
SO2CH3
SO2CH3
SO2CH3
SO2CH3
N3
4b
12.5
20.1
13.5
23.3
10.8
10.5
15.5
24.3
0.10
0.22
0.14
0.08
4.25
1.85
1.62
0.06
125
91.3
96.4
291.2
2.54
5.68
9.57
405
4c
Cl
4d
Me
OMe
H
4e
6a
6b
F
N3
6c
OMe
N3
Celecoxib
a Values are mean values of two determinations acquired using an ovine
COX-1/COX-2 assay kit, where the deviation from the mean is < 10% of
the mean value.
b In vitro COX-2 selectivity index (COX-1 IC50/ COX-2 IC50).
3. Docking study
The orientation of the highly potent and selective COX-2 inhibitor, 5-methoxy-
2-(4-(methylsulfonyl)phenyl)-1H-indole 4e in the COX-2 active site was examined
by a docking experiment (Fig. 1) [18]. This molecular modeling shows that it binds
in the primary binding site such that the C-2 para-SO2Me substituent inserts into the
secondary pocket present in COX-2. One of the O-atoms of p-SO2Me forms a
hydrogen binding interaction with hydroxyl group (OH) of Tyr355 (distance = 4.8 Ǻ).
The NH of the central 1H-indole ring forms a hydrogen bond (distance = 3.4 Ǻ) with
the C=O group of Val349. It addition, the oxygen atom of methoxy substituent at C-5
position of the 1H-indole ring can form hydrogen binding interaction with hydroxyl
group (OH) of Tyr348 (distance <6 Ǻ) which may explain the high potency of
compound 4e compared with other derivatives. These observations together with

Design and Synthesis of Some 5-Substituted-2-(4-(azido …
367
experimental results provide a good explanation for the potent and selective
inhibitory activity of 4e.
Fig. 1. Compound 4e 5-methoxy-2-(4-(methylsulfonyl)phenyl)-1H-indole docked in
the active site of murine COX-2 isozyme.
Experimental
1. Chemistry
Melting points (mp) were determined using a Thomas Hoover capillary
apparatus (Philadelphia, USA). Infrared spectra were acquired on a Perkin-Elmer
1420 ratio recording spectrometer. A Bruker FT-500 MHz instrument (Brucker
1
Biosciences, USA) was used to acquire HNMR spectra; chloroform-D, DMSO-D6
and methanol-D4 were used as solvents. Mass spectra were acquired with a
Finnigan TSQ-70 mass spectrometer. Electron-impact ionization was performed at
o
an ionizing energy of 70 eV; the source temperature was 250 C. Elemental
analyses were carried out with a Perkin Elmer Model 240-C apparatus (Perkin
Elmer, Norwalk, CT, USA). The results of the elemental analyses (C,H,N) were

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A. Zarghi et al.:
within ± 0.4% of the calculated amounts. All chemicals and reagents were obtained
from Aldrich (USA) or Merck (Germany) and were used without further purification.
General procedure for preparation of (E)-1-(4-substituted-phenyl)-2-(1-(4-
(methylsulfonyl)phenyl)ethylidene)hydrazines (3)
An ethanolic mixture of 4-methylsulfonylacetophenone 1 (4 mmol) and an
appropriate phenylhydrazine 2 (4 mmol) was heated on a water bath in presence of
few amounts of acetic acid for 1 hour to give 4-methylsulfonyl acetophenone
phenylhydrazone 3. The obtained product was separated, dried and recrystallized
from ethanol (Yields: 50–89%).
(1E)-1-{1-[4-(Methylsulfonyl)phenyl]ethylidene}-2-phenylhydrazine (3a)
Yield: 89%; mp: 175 °C; IR (KBr): ν (cm-1) 3310 (NH), 1300, 1150 (SO2), Mass,
m/z (%): 288.3 (M+, 70), 273.1 (20), 208.1 (20), 196.1 (40), 117.1 (50), 92.1(100),
77.1 (50).
(2E)-1-(4-Fluorophenyl)-2-{1-[4-(methylsulfonyl)phenyl]ethylidene}hydrazine
(3b)
Yield: 68%; mp: 179 °C; IR (KBr): ν (cm-1) 3300 (NH), 1300, 1160 (SO2), Mass,
m/z (%): 306.2 (M+, 30), 264.5 (20), 227.0 (20), 149.1 (30), 109.1 (100), 83.1 (90).
(2E)-1-(4-chlorophenyl)-2-{1-[4-(methylsulfonyl)phenyl]ethylidene}hydrazine
(3c)
Yield: 70%; mp: 194–195 °C; IR (KBr): ν (cm-1) 3280 (NH), 1310, 1150 (SO2),
Mass, m/z (%): 322.2 (M+, 10), 279.6 (20), 213.1 (20), 156.1 (30), 138.1 (100),
111.1 (50), 77.1 (50).
(2E)-1-(4-methylphenyl)-2-{1-[4-(methylsulfonyl)phenyl]ethylidene}hydrazine
(3d)
Yield: 62%; mp: 138–139 °C; IR (KBr): ν (cm-1) 3290 (NH), 1300, 1150 (SO2),
Mass, m/z (%): 302.2 (M+, 10), 273.2 (30), 222.1 (20), 156.1 (40), 119.2 (100), 91.2

Design and Synthesis of Some 5-Substituted-2-(4-(azido …
369
(60), 77.1 (30).
(2E)-1-(4-methoxyphenyl)-2-{1-[4-(methylsulfonyl)phenyl]ethylidene}hydrazine
(3e)
Yield: 50%; mp: 142–143 °C; IR (KBr): ν (cm-1) 3300 (NH), 1300, 1150 (SO2),
Mass, m/z (%): 318.3 (M+, 10), 303.3 (20), 239.1 (30), 165.6 (30), 122.2 (80), 92.1
(50), 79.1 (100).
General procedure for preparation of 5-substituted-2-(4-(methyl sulfonyl)-
phenyl)-1H-indoles (4)
4 mmol of 3 was added to polyphosphoric acid (5g) and the mixture was
o
heated at 120 C for 30 min. After this time, the mixture was cooled and poured in
100 ml cold water. The solid product was filtered and boiled with 100 ml of ethanol.
The hot mixture is treated with a little decolourising carbon and filtered through a
pre-heated Buchner funnel; wash the residue with 40 ml of hot ethanol. Cool the
combined filtrates to room temperature, filter off the 2-phenylindole and wash it with
20 ml of cold alcohol. The obtained product was dried and recrystallized from
ethanol (Yields: 60–92%).
2-[4-(Methylsulfonyl)phenyl]-1H-indole (4a)
Yield: 92%; mp: 219–220 °C; IR (KBr): ν (cm-1) 3290 (NH), 1300, 1150 (SO2);
1H NMR (chloroform-D): δ (ppm) 3.01 (s, 3H, SO2CH3), 6.89 (s, 1H, indole H-3),
7.01 (m, 1H, indole H-5), 7.13 (m, 1H, indole H-6), 7.37 (d, 1H, Indole H-4, J= 8.1
Hz), 7.55 (d, 1H, indole H-7, J= 8.1 Hz), 7.88 (d, 2H, 4-methylsulfonyl phenyl H-2 &
H-6, J = 8.5 Hz), 7.93 (d, 2H, 4-methylsulfonyl phenyl H-3 & H-5, J = 8.5 Hz), 10.76
(s, 1H, NH) ; Ms: m/z (%): 271.2 (M+, 100), 208.1 (35), 192.2 (95), 165.1 (40), 139.1
(20), 95.7 (30), 89.1 (40). Anal. Calcd. for C15H13NO2S: C, 66.40; H, 4.83; N, 5.16.
Found: C, 66.65; H, 4.62; N, 5.19.
5-Fluoro-2-[4-(methylsulfonyl)phenyl]-1H-indole (4b)
1
Yield: 85%; mp: 243 °C; IR (KBr): ν (cm-1) 3260 (NH), 1300, 1160 (SO2); H

370
A. Zarghi et al.:
NMR (chloroform-D): δ (ppm) 3.02 (s, 3H, SO2CH3), 6.84 (s, 1H, indole H-3), 7.09-
7.17 (m, 3H, indole H-4, H-6 & H-7), 7.89 (d, 2H, 4-methylsulfonyl phenyl H-2 & H-
6, J = 8.4 Hz), 7.90 (d, 2H, 4-methylsulfonyl phenyl H-3 & H-5, J = 8.4 Hz), 11.06
(s, 1H, NH); Ms: m/z (%): 289.2 (M+, 70), 226.2 (50), 210.2 (100), 198.2 (40), 183.2
(70), 158.2 (30), 107.1 (50), 91.2 (40). Anal. Calcd. for C15H12NO2FS: C, 62.27; H,
4.18; N, 4.44. Found: C, 62.55; H, 4.32; N, 4.35.
5-Chloro-2-[4-(methylsulfonyl)phenyl]-1H-indole (4c)
1
Yield: 88%; mp: 254 °C; IR (KBr): ν (cm-1) 3230 (NH), 1300, 1150 (SO2); H
NMR (chloroform-D): δ (ppm) 3.01 (s, 3H, SO2CH3), 6.76 (s, 1H, indole H-3), 6.99
(d, 1H, indole H-7, J = 8.4 Hz), 7.25 (d, 1H, indole H-6, J = 8.4 Hz), 7.44 (s, 1H,
indole H-4), 7.83 (d, 2H, 4-methylsulfonyl phenyl H-2 & H-6, J = 8.5 Hz), 7.87 (d,
2H, 4-methylsulfonyl phenyl H-3 & H-5, J = 8.5 Hz), 11.09 (s, 1H, NH); Ms: m/z (%):
305.1 (M+, 40), 242.2 (40), 226.2 (50), 191.2 (100), 163.2 (60), 149.2 (30), 158.2
(30), 95.6.1 (60), 76.1 (50). Anal. Calcd. for C15H12NO2ClS: C, 58.92; H, 3.96; N,
4.58. Found: C, 59.15; H, 4.12; N, 4.35.
5-Methyl-2-[4-(methylsulfonyl)phenyl]-1H-indole (4d)
Yield: 68%; mp: 110–111 °C; IR (KBr): ν (cm-1) 3270 (NH), 1310, 1150 (SO2);
1H NMR (chloroform-D): δ (ppm) 2.28 (s, 3H, CH3), 3.03 (s, 3H, SO2CH3), 6.64 (s,
1H, indole H-3), 6.79 (s, 1H, indole H-4), 6.86 (d, 1H, Indole H-6, J= 8.3 Hz), 6.99
(d, 1H, indole H-7, J= 8.3 Hz), 7.81 (d, 2H, 4-methylsulfonyl phenyl H-2 & H-6, J =
8.5 Hz), 7.84 (d, 2H, 4-methylsulfonyl phenyl H-3 & H-5, J = 8.5 Hz), 10.72 (s, 1H,
NH); Ms: m/z (%): 285.2 (M+, 30), 238.2 (20), 209.1 (20), 183.0 (30), 134.1 (100),
107.1 (40), 92.1 (60), 77.1 (50). Anal. Calcd. for C16H15NO2S: C, 67.34; H, 5.30; N,
4.91. Found: C, 67.65; H, 5.12; N, 4.85.
5-Methoxy-2-[4-(methylsulfonyl)phenyl]-1H-indole (4e)
Yield: 60%; mp: 118–120 °C; IR (KBr): ν (cm-1) 3250 (NH), 1300, 1150 (SO2);
1H NMR (chloroform-D): δ (ppm) 3.03 (s, 3H, SO2CH3), 3.65 (s, 3H, OCH3), 6.61 (s,
1H, indole H-3), 6.74 (s, 1H, indole H-4), 6.81 (d, 1H, Indole H-6, J= 8.3 Hz), 6.97

Design and Synthesis of Some 5-Substituted-2-(4-(azido …
371
(d, 1H, indole H-7, J= 8.3 Hz), 7.81 (d, 2H, 4-methylsulfonyl phenyl H-2 & H-6, J =
8.5 Hz), 7.84 (d, 2H, 4-methylsulfonyl phenyl H-3 & H-5, J = 8.5 Hz), 10.72 (s, 1H,
NH); Ms: m/z (%): 301.5 (M+, 30), 273.7 (20), 219.5 (30), 183.0 (40), 152.1 (50),
104.0 (100), 89.1 (50). Anal. Calcd. for C16H15NO3S: C, 63.77; H, 5.02; N, 4.65.
Found: C, 63.95; H, 4.82; N, 4.37.
General procedure for preparation of 5-substituted-2-(4-aminophenyl)-1H-
indoles (5)
The compounds 5a–5c were prepared according to the procedure as
described for 4. The obtained products were crystallized from ethanol (Yields: 40–
62%).
4-(1H-Indol-2-yl)aniline (5a)
1
Yield: 60%; mp: 201–202 °C; IR (KBr): ν (cm-1) 3300, 3250 (NH2); H NMR
(chloroform-D): δ (ppm) 6.65 (d, 2H, 4-aminophenyl H-3 & H-5, J = 8.3 Hz), 6.81 (s,
1H, indole H-3), 7.01 (m, 1H, indole H-5), 7.12 (m, 1H, indole H-6), 7.30-7.48 (m,
2H, indole H-4 & H-7), 7.24 (d, 2H, 4-amino phenyl H-2 & H-6, J = 8.3 Hz), 10.61 (s,
1H, NH).
4-(5-Fluoro-1H-indol-2-yl)aniline (5b)
Yield: 43%; mp: 215–216 °C; IR (KBr): ν (cm-1) 3310, 3260 (NH2);
1H NMR (chloroform-D): δ (ppm) 6.68 (d, 2H, 4-aminophenyl H-3 & H-5, J = 8.2
Hz), 6.76 (s, 1H, indole H3), 7.02-7.21 (m, 3H, indole H-4, H-6 & H-7), 7.25 (d, 2H,
4-aminophenyl H-2 & H-6, J = 8.2 Hz), 10.73 (s, 1H, NH).
4-(5-Methoxy-1H-indol-2-yl)aniline (5c)
1
Yield: 40%; mp: 171–172 °C; IR (KBr): ν (cm-1) 3340, 3250 (NH2); H NMR
(chloroform-D): δ (ppm) 3.53 (s, 3H, OCH3), 6.55 (d, 2H, 4-aminophenyl H-3 & H-5,
J = 8.2 Hz),6.66 (s, 1H, indole H-3), 6.70 (s, 1H, indole H-4), 6.79 (d, 1H, indole H-
6, J= 8.3 Hz), 6.92 (d, 1H, indole H-7, J= 8.3 Hz), 7.23 (d, 2H, 4-aminophenyl H-2 &
H-6, J = 8.2 Hz), 10.53 (s, 1H, NH).

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A. Zarghi et al.:
General procedure for preparation of 5-substituted-2-(4-(azido) phenyl)-1H-
indoles (6)
6 mmol of 5 was added to 10 ml of cold water and 5 ml of hydrochloric acid
(12N) and the mixture was stirred at r.t. for 1 hr. After this time, the mixture was
o
cooled (0 C) and a solution of 6 mmol sodium nitrite in 5 ml water was added
slowly to the mixture. Then 6 mmol sodium azide in 5 ml water was added to
reaction medium. The solid product was filtered, washed with water and crystallized
from ethanol (Yields: 55-68%).
2-(4-Azidophenyl)-1H-indole (6a)
Yield: 68%; mp: 120–121 °C; IR (KBr): ν (cm-1) 3270 (NH), 2120 (N3); 1H NMR
(chloroform-D): δ (ppm) 6.85 (s, 1H, indole H-3), 7.01 (m, 1H, indole H-5), 7.13 (m,
1H, indole H-6), 7.32-7.50 (m, 2H, indole H-4 &H-7), 7.55 (d, 2H, 4-azidophenyl H-2
& H-6, J = 8.3 Hz), 7.85 (d, 2H, 4-azidophenyl H-3 & H-5, J = 8.5 Hz), 10.56 (s, 1H,
NH) ; Anal. Calcd. for C14H10N4: C, 71.78; H, 4.30; N, 23.92. Found: C, 71.65; H,
4.02; N, 23.79.
2-(4-Azidophenyl)-5-fluoro-1H-indole (6b)
Yield: 60%; mp: 135–136 °C; IR (KBr): ν (cm-1) 3260 (NH), 2140 (N3); 1H NMR
(chloroform-D): δ (ppm) 6.80 (s, 1H, indole H3), 7.05-7.25 (m, 3H, indole H-4, H-6 &
H-7), 7.56 (d, 2H, 4-azidophenyl H-2 & H-6, J = 8.4 Hz), 7.88 (d, 2H, 4-azidophenyl
H-3 & H-5, J = 8.4 Hz), 10.95 (s, 1H, NH); Anal. Calcd. for C14H9N4F: C, 66.66; H,
3.60; N, 22.21. Found: C, 66.85; H, 3.82; N, 22.35.
2-(4-Azidophenyl)-5-methoxy-1H-indole (6c)
1
Yield: 55%; mp: 70–71 °C; IR (KBr): ν (cm-1) 3250 (NH), 2110 (N3); H NMR
(chloroform-D): δ (ppm) 3.55 (s, 3H, OCH3), 6.61 (s, 1H, indole H-3), 6.71 (s, 1H,
indole H-4), 6.80 (d, 1H, indole H-6, J= 8.2 Hz), 6.95 (d, 1H, indole H-7, J= 8.2 Hz),
7.60 (d, 2H, 4-azidophenyl H-2 & H-6, J = 8.4 Hz), 7.80 (d, 2H, 4-azidophenyl H-3 &
H-5, J = 8.4 Hz), 10.72 (s, 1H, NH); Anal. Calcd. for C15H12N4O: C, 68.17; H, 4.58;
N, 21.20. Found: C, 68.45; H, 4.72; N, 21.36.

Design and Synthesis of Some 5-Substituted-2-(4-(azido …
373
2. In vitro cyclooxygenase (COX) inhibition assays
The ability of the test compounds listed in Table 1 to inhibit ovine COX-1 and
COX-2 (IC50 value, μM) was determined using chemiluminescent enzyme assays
kit (catalog number 560101, Cayman Chemical, Ann Arbor, MI, USA) according to
our previously reported method [13].
3. Molecular modeling (docking) studies
Docking studies were performed using Autodock software Version 3.0. The
coordinates of the X-ray crystal structure of the selective COX-2 inhibitor SC-558
bound to the murine COX-2 enzyme was obtained from the RCSB Protein Data
Bank (1cx2) and hydrogens were added. The ligand molecules were constructed
using the Builder module and were energy minimized for 1000 iterations reaching a
convergence of 0.01 kcal/mol Å. The energy minimized ligands were superimposed
on SC-558 in the PDB file 1cx2 after which SC-558 was deleted. The purpose of
docking is to search for favorable binding configuration between the small flexible
ligands and the rigid protein. Protein residues with atoms greater than 7.5 Å from
the docking box were removed for efficiency. Searching is conducted within a
specified 3D docking box using annealing based on the Monte Carlo method and
MMFF94 molecular mechanics force field for 8000 iterations. These docked
structures were very similar to the minimized structures obtained initially. The
quality of the docked structures was evaluated by measuring the intermolecular
energy of the ligand-enzyme assembly [19].
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Received May 27th, 2008
Accepted (after revision) July 7th, 2008
Available online at www.scipharm.at July 8th, 2008