Design, synthesis and computational validation of novel benzimidazole/indole-based PPARα and PPAR? partial agonists

Article abstract of DOI:10.1007/s12039-013-0489-4

The design and synthesis of benzimidazolyl and indolyl linked α-alkoxy phenylpropanoic acid derivatives and the β-keto ester analogues in an effort to develop novel peroxisome proliferator activated receptors ligands expected to exhibit PPARα and PPAR? pa

Full text of DOI:10.1007/s12039-013-0489-4

c
J. Chem. Sci. Vol. 125, No. 6, November 2013, pp. 1555–1571. ꢀ Indian Academy of Sciences.
Design, synthesis and computational validation of novel
benzimidazole/indole-based PPARα and PPARγ partial agonists
RAMAN K VERMAa,∗, PRITHWISH GHOSHa, VIJAY KUMARa and LALIT K WADHWAb
aSynthetic Organic and Medicinal Chemistry Laboratory, Department of Chemistry, Punjabi University,
Patiala 147 002, India
bInd-Swift Laboratories Limited (Research and Development Centre), Plot No. E-5, Industrial Area, Phase-2,
SAS Nagar, Mohali 160 055, India
e-mail: raman_verma58@yahoo.com
MS received 28 June 2012; revised 15 March 2013; accepted 4 July 2013
Abstract. The design and synthesis of benzimidazolyl and indolyl linked α-alkoxy phenylpropanoic acid
derivatives and the β-keto ester analogues in an effort to develop novel peroxisome proliferator activated recep-
tors ligands expected to exhibit PPARα and PPARγ partial agonism in the management of hyperglycemia
and hyperlipidemia for the treatment of type 2 diabetes is reported. Computational validation of the designed
molecules through activity prediction and docking studies showed expected results.
Keywords. β-keto ester; α-alkoxy acid; PPAR; partial agonism.
1. Introduction
they demonstrated beneficial impact over individual
PPAR agonists by improving lipid and glucose homeo-
stasis both, safety had been a critical issue and derailed
their development because of adverse toxicity profiles.
Muraglitazar and tesaglitazar (figure 1) though reached
advanced phases of clinical trials but were noted to pro-
duce several cardiovascular risks and carcinogenicity.4,5
Disappointingly, full PPAR agonists have been
plagued by certain adverse side effects. On the up side,
partial PPAR agonists have the potential to retain the
desired efficacy and beneficial effects of full PPAR ago-
nists while diminishing the unwanted effects.6 In vitro
studies by researchers from Astellas and Roche also
indicated that their PPARγ partial agonists activate
pathways that ameliorate insulin resistance without
stimulating fat accumulation in adipocytes.7,8
Partial agonism to both PPARα and PPARγ recep-
tors by dual activators may provide a solution result-
ing in the desirable responses and reducing the adverse
effects caused by the individual agonists for the treat-
ment of T2DM. 3D QSAR methods combined with
docking studies provide valuable insights to determine
the significant structural features required for optimum
activity in designing of new candidates. The subse-
quent prediction and comparative analysis of activities
and binding affinities of the designed molecules help
to select most suitable candidates for further studies.
The work reported here presents such an approach.
The design (maintaining the structural requirements
of PPAR ligands), prediction of PPARα and PPARγ
Type 2 diabetes mellitus is a disease of complex patho-
genesis and pleiotropic clinical manifestations. The
greatest clinical challenge in this disease is the preven-
tion of long term complications, many of which involve
cardiovascular problems. The peroxisome proliferator-
activated receptor α and γ isoforms are pharmaceutical
targets for therapeutic intervention as they can poten-
tially ameliorate not only the hyperglycemia of diabetes
but also the dyslipidemia that is characteristic of this
disorder.1 Activation of PPARα reduces triglycerides
and is involved in regulation of energy homeostasis.
Activation of PPARγ causes insulin sensitization and
enhances glucose metabolism. The development of
multimodal drugs which can reduce hyperglycemia and
concomitantly inhibit the progression of secondary car-
diovascular complications offer valuable therapeutic
option.2 PPARα activators primarily improve dyslipi-
demia, whereas thiazolidinediones are potent PPARγ
activators that improve insulin resistance though are not
devoid of side effects.3
The PPARα/γ dual agonists (figure 1) are devel-
oped to increase insulin sensitivity and simultaneously
prevent diabetic cardiovascular complications.3 Among
the dual activators, glitazars elicited high hopes and
deep disappointment as potential new drugs. Although
∗For correspondence
1555

1556
Raman K Verma et al.
O
O
OH
O
O
OH
HN
HN
N
O
N
O
O
O
Farglitazar
GW 409544
OH
O
N
O
O
O
OH
O
O
O
O
N
O
N
S
O
LY 510929
Muraglitazar
O
O
O
O
S
OH
OH
N
O
O
O
O
O
Tesaglitazar
NND 9
O
O
O
OH
O
HN
N
OH
O
N
O
O
O
DRF 2725
GW7845
Figure 1. Molecular structure of some well-studied PPAR dual agonists.
activities, prediction of binding affinities of a set of spectrometer, respectively at RSIC, Panjab University,
novel molecules as PPARα/γ partial agonists and their Chandigarh. LCMS of the compounds were recorded on
syntheses have been reported in the present work.
LCMS LCQ Finnigan Matt (APCI +ve mode) at Cen-
tral Instrumentation Lab, NIPER, SAS Nagar, Mohali,
Punjab. GCMS and elemental analysis of these com-
pounds were carried out on Shimadzu GCMS-QP2010
Plus and Vario Micro CHN Elemental Analyzer, respec-
tively at Instrumental Laboratory, Department of Chem-
istry, Punjabi University, Patiala.
2. Experimental
2.1 Materials and methods
All the chemicals used were purchased from Aldrich
and Sdfine chemicals. The melting/boiling points
reported here were recorded using an open conc. sul-
phuric acid bath and are uncorrected. The infrared
and 1H NMR spectra of the reported compounds
were recorded on Perkin-Elmer Spectrum RX FTIR
Spectrophotometer, and AC400F, 400 MHz Bruker
2.2 Synthetic procedures for the lhs units
2.2a (1-Methyl-1H-benzimidazol-2-yl)methanol (com-
pound 1, scheme 1): N-methyl-1,2-phenylenediamine
dihydrochloride (11.700 g, 60 mmol), glycolic acid
(17 mL, 180 mmol, 65% aqueous solution) and water
O
NH2.HCl
N
N
H
b
a
N
O
N
OH
NHCH3.HCl
1a
1
Scheme 1. Reagents and conditions: (a) glycolic acid, water, reflux; (b) 4-fluorobenzaldehyde, NaH, DMF, 0–25◦C.

Design, synthesis and computational validation of novel benzimidazole and indole
1557
(42 mL) were combined, and refluxed for 90 min. The mp 108–110◦C; FTIR (KBr): 3600–3400, 2962, 2929,
reaction mixture was basified with dilute ammonia 2850, 1612, 1515, 1468, 1399, 745; 1H NMR (CDCl3)
solution under ice cold condition after cooling to room δ: 7.58 (d, J = 7.9 Hz, 1H), 7.32 (m, 1H), 7.23 (m, 1H),
temperature. The grey solid separated was collected 7.10 (m, 1H), 6.45 (s, 1H), 4.80 (s, 2H), 3.80 (s, 3H).
under suction, washed with cold water, and which upon
recrystallization from methanol gave (8.75 g, 90%) of
1a: mp 145–147◦C; FTIR (KBr): 3660, 3450–3200,
2.3 General procedure for the syntheses of heterocyclyl
3142, 2950, 2842,1 548, 1482, 1434, 1357, 739 cm−1;
1H NMR (CDCl3+DMSO-d6) δ: 7.69 (m, 1H), 7.27
(m, 3H), 4.89 (s, 2H), 3.82 (s, 3H).
linked benzaldehydes (compounds 1a and 2b)
To a stirred suspension of sodium hydride (1.4 mmol,
60% w/w dispersion) in dry DMF (20 mL) was added
1/2a (1.2 mmol) in dry DMF (5 mL) at 0◦C, and the
2.2b Ethyl 1-methyl-1H-indole-2-carboxylate (com- mixture was stirred for 30 min at rt (ca. 30◦C). A solu-
pound 2, scheme 2): To a stirred solution of sodium tion of 4-fluorobenzaldehyde (1.3 mmol) in dry DMF
hydride (1.100 g, 27.5 mmol, 60% w/w) in dry (5 mL) was added drop-wise over 15 min at 0◦C, and
DMF (100 ml) was added ethyl indole-2-carboxylate stirred for 24 h at rt. The reaction mixture was quenched
(4.160 g, 22 mmol) at 2–5◦C, and the mixture was with water and extracted with EtOAc (3 × 30 mL).
stirred for 30 min at room temperature (rt) (ca. 30◦C). The combined organic extracts were washed with brine,
A solution of iodomethane (3.750 g, 26.4 mmol) in dry dried over anhydrous Na2SO4, and concentrated. The
DMF (5 mL) was added drop-wise over 15 min at 2– residue was chromatographed to achieve the target
5◦C, and stirred for 28 h at rt. The reaction mixture benzaldehyde.
was quenched with ice-water, and extracted with EtOAc
(3 × 25 mL). The combined organic extracts were
2.3a 4-[(1-Methyl-1H-benzimidazol-2-yl)methoxy]ben-
zaldehyde (compound 1a, scheme 1): Yield: 30%.
Mp: 120–122◦C; FTIR (KBr): 2926, 2823, 2733, 1697,
1601, 1577, 1482, 1430, 1363, 1247,1005, 828 cm−1;
1H NMR (CDCl3) δ: 9.9 (s, 1H), 7.83 (m, 3H), 7.39
(m, 3H), 7.24 (d, J = 8.8 Hz, 2H), 5.59 (s, 2H), 3.94
(s, 3H) ; GCMS (m/z): 266 [M]+, 145; Anal. Calcd
for C16H14N2O2: C (72.16%), H (5.30%), N (10.52%);
Found: C (72.51%), H (5.57%), N (10.19%).
washed with brine and water, dried, and concentrated.
The crude product was treated with hexane to obtain
the pure product 2 as a white solid (3.35 g, 75%): mp
68–70◦C; FTIR (KBr): 2982, 2850, 1703, 1515, 1469,
1
1400, 1378, 1251, 1087, 747 cm−1; H NMR (CDCl3)
δ: 7.67 (d, J = 7.9 Hz, 1H), 7.40 (m, 1H), 7.33 (m, 1H),
7.30 (s, 1H), 7.14 (m, 1H), 4.37 (q, J = 7.1 Hz, 2H),
4.08 (s, 3H), 1.41 (t, J = 7.2 Hz, 3H).
2.2c (1-Methyl-1H-indol-2-yl)methanol (compound 2a,
scheme 2): To a stirred suspension of lithium alu- 2.3b 4-[(1-Methyl-1H-indol-2-yl)methoxy]benzalde-
minium hydride (7.600 g, 200 mmol) in THF (100 mL) hyde (compound 2b, scheme 2): Yield: 30%. Mp:
was added 2 (4.060 g, 20 mmol) in THF (5 mL), 158–160◦C; FTIR (KBr): 2933, 2823, 2733, 1697,
1
and the mixture was stirred at room temperature (ca. 1598, 1506, 1468, 1380, 1244, 1160, 828 cm−1; H
30◦C) for 36 h. The reaction mixture was quenched NMR (CDCl3) δ: 9.90 (s, 1H), 7.86 (d, J = 8.7 Hz,
with ice water, acidified with 2N- HCl, and extracted 2H), 7.62 (d, J = 7.8 Hz, 1H), 7.34 (m, 1H), 7.27
with ethyl acetate (3 × 20 ml). The combined organic (m, 2H), 7.13 (d, J = 8.8 Hz, 2H), 6.63 (s, 1H), 5.29
extracts were dried over sodium sulphate and concen- (s, 2H), 3.82 (s, 3H) ; LCMS (m/z): 266 [M+1]+;
trated to give white solid and which upon recrystal- Anal. Calcd for C17H15NO2: C (76.96%), H (5.70%), N
lization from ethyl acetate gave (3.06 g, 95%) of 2a: (5.28%); Found: C (76.58%), H (5.55%), N (5.60%).
O
O
O
O
O
a
H
b
c
N
H
N
N
OH
N
O
2
2b
2a
Scheme 2. Reagents and conditions: (a) NaH, DMF, MeI, rt; (b) LAH, THF, rt; (c) 4-fluorobenzaldehyde, NaH,
DMF, 0–25◦C.

1558
Raman K Verma et al.
2.4 Synthetic procedures for the rhs units
(overlapped t, J = 7.1 Hz, 3H+3H); GCMS (m/z):
248 [M]+, 233; Anal. Calcd for C14H16O4: C(67.73%),
H(6.50%); Found: C(68.11%), H(6.78%).
2.4a General procedure for the syntheses of 3a and
3b: A solution of p-anisaldehyde (8.16 g, 60 mmol)
and methyl acetoacetate/ethyl acetoactate (60 mmol)
in toluene (150 mL) containing a catalytic quantity of
piperidinium acetate (2 mL) was refluxed in a Dean-
Stark trap for 16 h. After cooling to room temperature,
the solution was concentrated. The residue was purified
by column chromatography using a mixture of EtOAc
and hexane (1:3) to give 3a/b as brown viscous mass.
2.4d General procedure for the syntheses of 4a and
4b: To a solution of 3a/b (12.8 mmol) in DCM at
0◦C was added BBr3 in DCM (13 mL, 1M solution)
drop-wise while stirring and stirring continued for two
h at 0◦C and the at rt for 16 h. The contents treated
with ice cold water and the organic layers separated,
washed with brine, dried over sodium sulphate, filtered
and solvent evaporated and the residue purified by col-
umn chromatography EtOAc/Hexane (1:4) to yield the
target demethylated β-ketoester (4a/b) as yellow solid.
2.4b Methyl 2-(4-methoxy benzylidene)-3-oxobutanoate
(compound 3a, scheme 3): Yield: 40.0%. FTIR
(CHCl3): 2981, 2841, 1734, 1640, 1027, 845 cm−1; 1H
NMR (CDCl3) mixture of geometric isomers, δ: 7.45
(superimposed s, 1H+1H), 7.33 (d, J = 8.7 Hz, 2H),
7.28 (d, J = 8.9 Hz, 2H), 6.84 (d, J = 8.8 Hz, 2H), 2.31
(s, 3H), 6.82 (d, J = 9.3 Hz, 2H), 3.79 (superimposed s,
3H+3H), 3.75 (s, 3H), 3.74 (s, 3H), 2.32 (s, 3H); GCMS
(m/z): 234 [M]+, 219, 203; Anal. Calcd for C13H14O4:
C(66.66%), H(6.02%); Found: C(66.51%). H(6.20%).
2.4e Methyl 2-(4-hydroxybenzylidene)-3-oxobutanoate
(compound 4a, scheme 3): Yield: 37%. Mp: 152–
155◦C; FTIR (KBr): 3349, 2987, 2940, 1731, 1645,
1
1572, 1168, 1026, 856 cm−1; H NMR (CDCl3) mix-
ture of E and Z isomers, δ: 7.55 (s, 1H), 7.44 (s, 1H),
7.26 (d, J = 8.7 Hz, 2H), 7.23 (d, J = 8.7 Hz, 2H), 6.75
(d, J = 8.7 Hz, 2H), 6.74 (d, J = 8.7 Hz, 2H), 5.47
(s, 1H), 5.27 (s, 1H), 3.80 (s, 3H), 3.75 (s, 3H), 2.33
(s, 3H), 2.31 (s, 3H); GCMS (m/z): 220 [M]+, 205, 189,
160; Anal. Calcd for C12H12O4: C(65.45%), H(5.49%);
Found: C(65.27%), H(5.33%).
2.4c Ethyl 2-(4-methoxybenzylidene)-3-oxobutanoate
(compound 3b, scheme 3): Yield: 38%. FTIR (CHCl3):
2981, 2841, 1726, 1659, 1120, 1058, 830 cm−1;
1HNMR (CDCl3) mixture of geometric isomers, δ: 7.50
(s, 1H), 7.41 (s, 1H), 7.33 (d, J = 8.8 Hz, 2H), 7.26 (d,
J = 8.8 Hz, 2H), 6.80 (overlapped d, J = 8.8 Hz, 2H), 2.4f Ethyl 2-(4-hydroxybenzylidene)-3-oxobutanoate
4.27 (q, J = 7.1 Hz, 2H), 4.18 (q, J = 7.1 Hz, 2H), 3.73 (compound 4b, scheme 3): Yield: 35%. Mp: 134–
(s, 3H), 3.72 (s, 3H), 2.30 (s, 3H), 2.29 (s, 3H), 1.22 136◦C; FTIR (KBr): 3360, 2982, 1715, 1665, 1114,
H
O
O
O
R'
R'
R'
O
O
a
O
b
+
O
O
R
O
O
O
R
5a/b
O
O
R
3a/b
p-anisaldehyde
MAA/EAA
code
R
R’
3a-6a Me Me
3b-6b Me Et
c
c
O
O
R'
R'
O
O
HO
O
6a/b
R
code
7a
7b
X
N
N
R
R’
HO
O
4a/b
R
Me Me
Me Et
8a CH Me Me
8b CH Me Et
1/2a
d
d
1/2a
O
O
R
R'
9a
9b
N
N
Me Me
Me Et
R'
X
O
X
N
O
10a CH Me Me
10b CH Me Et
N
O
O
R
O
O
9a-10b
7a-8b
Scheme 3. Reagents and conditions: (a) Piperidinium acetate, toluene, reflux; (b) Pd/C, H2, 20psi, rt; (c) BBr3 in
DCM, 0–25◦C; (d) DEAD, Ph3P, THF, rt.

Design, synthesis and computational validation of novel benzimidazole and indole
1559
1
1043, 834 cm−1; HNMR (CDCl3) mixture of geomet- 2.4k Methyl 2-(4-hydroxybenzyl)-3-oxobutanoate (com-
ric isomers (1:3), δ: 7.59 (s, 1H), 7.49 (s, 1H), 7.37 pound 6a, scheme 3): Yield: 35%. FTIR (CHCl3):
1
(d, J = 8.6 Hz, 2H+2H), 7.29 (d, J = 8.6 Hz, 2H), 3348, 2980, 2837, 1741, 1714, 1034, 849 cm−1; H
6.83 (d, J = 8.7 Hz, 2H), 6.80 (d, J = 8.7 Hz, 2H, NMR (CDCl3)δ: 7.02 (d, J = 8.5 Hz, 2H), 6.73 (d, J =
Ar), 4.36 (q, J = 7.1 Hz, 2H), 4.29 (q, J = 7.2 Hz, 8.5 Hz, 2H), 5.49 (s, 1H), 3.75 (t, J = 7.8 Hz, 1H), 3.70
2H), 2.40 (s, 3H), 2.39 (s, 3H), 1.32 (overlapped t, J = (s, 3H), 3.09 (d, J = 7.7 Hz, 2H), 2.17 (s, 3H); GCMS
7.1 Hz, 3H+3H); GCMS (m/z): 234 [M]+, 219; Anal. (m/z): 223 [M+1]+, 207, 190, 147; Anal. Calcd for
Calcd for C13H14O4: C(66.66%), H(6.02%); Found: C12H14O4: C(64.85%), H(6.35%); Found: C(64.66%),
C(66.14%), H(6.58%).
H(6.52%).
2.4g General procedure for the syntheses of 5a
and 5b: A solution of 3a/b (12 mmol) in methanol
(80 mL) in the presence of 10% palladium on charcoal
(0.5 g) was shaken under an atmosphere of hydrogen
(20 psi) in a Parr catalytic hydrogenator at room tem-
perature until hydrogen uptake ceased (> 20 h). The
solution was filtered through celite, and the filtrate was
evaporated under a vacuum. The residue was chro-
matographed eluting with a mixture of ethyl acetate and
hexane (1:4) to give 4a/b as pale yellow viscous mass.
2.4l Ethyl 2-(4-hydroxybenzyl)-3-oxobutanoate (com-
pound 6b, scheme 3): Yield: 35%. FTIR (CHCl3):
3437, 2931, 1732, 1710, 1219, 1614, 1516, 1446, 1153,
1
1056, 826 cm−1; HNMR (CDCl3), δ: 7.02 (d, J =
8.5 Hz, 2H), 6.72 (d, J = 8.5 Hz, 2H), 4.12 (q, J =
7.2 Hz, 2H), 3.74 (t, J = 7.7 Hz, 1H), 2.18 (s, 3H), 3.08
(d, J = 7.7 Hz, 2H), 1.21 (t, J = 7.1 Hz, 3H); GCMS
(m/z): 236 [M]+, 193, 163; Anal. Calcd for C13H16O4:
C(66.09%), H(6.83%); Found: C(66.44%), H(6.65%).
2.5 General procedure for the syntheses of final
β-ketoester based NCEs (compounds 7a–10b)
2.4h Methyl 2-(4-methoxybenzyl)-3-oxobutanoate (com-
pound 5a, scheme 3): Yield: 67.8%. FTIR (CHCl3):
1
2981, 2837, 1734, 1650, 1033, 833 cm−1; H NMR
A solution of diethyl azodicarboxylate (0.9 mmol) and
triphenylphosphine (0.9 mmol) in THF (5 mL) at 0◦C
was added dropwise to a stirred mixture of 1/2a
(0.6 mmol) and 4a/b or 6a/b (0.72 mmol) in THF
(20 mL) at 0◦C. The reaction was stirred at 0◦C for
an hour and then at rt for 16 h and the solvent
removed in vacuo to dryness. The residue was taken
up in ethyl acetate/ water (2:1). The organic layer
was separated, dried over sodium sulphate, filtered
and the solvent evaporated under reduced pressure. The
residue was chromatographed using a mixture of either
methanol and dichloromethane (1:99) (for 7a/b and
9a/b) or EtOAC and hexane (1:4) (for 8a/b and 10a/b)
to give of the coupled product (7a/b or 8a/b or 9a/b
or 10a/b).
(CDCl3)δ: 7.08 (d, J = 8.7 Hz, 2H), 6.81 (d, J =
8.7 Hz, 2H), 3.75 (t, J = 6.9 Hz, 1H), 3.71 (s, 3H), 3.69
(s, 3H), 3.10 (d, J = 7.6 Hz, 2H), 2.17 (s, 3H); GCMS
(m/z): 236 (M.+), 205, 193, 177; Anal. Calcd for
C13H16O4: C(66.09%), H(6.83%); Found: C(66.17%),
H(6.97%).
2.4i Ethyl 2-(4-methoxybenzyl)-3-oxobutanoate (com-
pound 5b, scheme 3): Yield: 70%. FTIR (CHCl3):
2981, 2837, 1739, 1716, 1248, 1110, 1063, 823 cm−1;
1HNMR (CDCl3)δ: 7.09 (d, J = 8.6 Hz, 2H), 6.80
(d, J = 8.6 Hz, 2H), 4.14 (q, J = 7.1 Hz, 2H), 3.77
(s, 3H), 3.73 (t, J = 7.6 Hz, 1H), 3.09 (d, J = 7.7 Hz,
2H), 2.18 (s, 3H), 1.21 (t, J = 8.00 Hz, 3H); GCMS
(m/z): 250 [M]+, 207; Anal. Calcd for C14H18O4:
C(67.18%), H(7.25%); Found: C(66.74%), H(6.92%).
2.5a Methyl 2-{4-[(1-methyl-1H-benzimidazol-2-yl)
methoxy]benzylidene}-3-oxobutanoate (compound 7a,
scheme 3): Yield: 22.6%. Mp: 161–163◦C; FTIR
(KBr): 2917 and 2850, 1735, 1630, 1092, 844 cm−1; 1H
NMR (CDCl3) mixture of E and Z isomers, δ: 7.78 (m,
1H), 7.71 (m, 1H), 7.53 (s, 1H), 7.42 (s, 1H), 7.32 (d,
J = 8.9 Hz, 2H+2H), 7.27 (m, 3H+3H), 7.04 (d, J =
8.9 Hz, 2H), 7.01 (d, J = 8.9 Hz, 2H), 5.36 (s, 2H), 5.35
(s, 2H), 3.78 (s, 3H), 3.75 (s, 3H), 3.82 (s, 3H), 3.81
(s, 3H), 2.32 (s, 3H), 2.28 (s, 3H); LCMS (m/z): 366
[M++2], 365 [M+1]+; Anal. Calcd for C21H20N2O4:
C(69.22%), H(5.53%), N(7.69%); Found: C(69.34%),
H(5.61%), N(7.75%).
2.4j General procedure for the syntheses of 6a and 6b:
To a solution of 5a/b (12.8 mmol) in DCM at 0◦C was
added BBr3 in DCM (13 mL, 1M solution) drop-wise
while stirring and stirring continued for two h at 0◦C
and the at rt for 16 h. The contents treated with ice cold
water and the organic layers separated, washed with
brine, dried over sodium sulphate, filtered and solvent
evaporated and the residue purified by column chro-
matography EtOAc/Hexane (1:4) to yield the target
demethylated β-ketoester (6a/b) as colourless viscous
mass.

1560
Raman K Verma et al.
2.5b Ethyl 2-acetyl-3-[4-(1-methyl-1H-benzimidazol- 3.87 (s, 3H), 3.76 (s, 3H), 3.64 (d, J = 4.6 Hz, 1H), 3.27
2-ylmethoxy)-phenyl]-acrylate (compound 7b, scheme 3): (d, J = 16.88 Hz, 1H), 3.10 (d, J = 16.92 Hz, 1H), 2.42
Yield: 20%. Mp: 145–148◦C; FTIR (KBr): 2960, 2851, (s, 3H); LCMS (m/z): 405 [M++39], 366 [M]+, 261;
1
1714, 1695, 1258, 1174, 1103, 799 cm−1; HNMR Anal. Calcd for C21H22 N2O4: C(68.84%), H(6.05%),
(CDCl3) mixture of geometric isomers, δ: 7.75 (m, N(7.65%). Found: C(68.59%), H(6.23%), N(7.52%).
1H+1H), 7.51 (s, 1H), 7.41 (s, 1H), 7.35 (superimposed
d, J = 8.6 Hz, 2H+2H), 7.28 (m, 3H), 7.03 (overlapped
2.5f Ethyl 2-[4-(1-Methyl-1H-benzimidazol-2-ylmethoxy)-
d, J = 9.1 Hz, 2H+2H), 5.41 (s, 2H), 5.40 (s, 2H), 4.27
benzyl]-3-oxo-butyrate (compound 9b, scheme 3):
(q, J = 7.1 Hz, 2H), 4.23 (q, J = 7.1 Hz, 2H), 3.86
(s, 3H), 3.84 (s, 3H), 2.32 (s, 3H), 2.30 (s, 3H), 1.25
(t, J = 7.1 Hz, 3H), 1.21 (t, J = 7.1 Hz, 3H); LCMS
(m/z): 379 [M+1]+; Anal. Calcd for C22H22 N2O4:
C(69.83%), H(5.87%); Found: C(69.45%), H(6.09%).
Yield: 20%. Mp: 119-122◦C; FTIR (KBr): 2925, 2853,
1738, 1714, 1461, 1241, 1155, 1112, 1040, 854 cm−1;
1HNMR (CDCl3)δ: 7.77 (d, J = 7.2 Hz, 1H), 7.32
(m, 3H), 7.08 (d, J = 8.7 Hz, 2H), 6.97 (d, J =
8.7 Hz, 2H), 5.35 (s, 2H), 4.10 (q, J = 7.2 Hz, 2H),
3.88 (s, 3H), 3.73 (t, J = 7.6 Hz 1H), 3.07 (d, J =
7.6 Hz, 2H), 2.29 (s, 3H), 1.17 (t, J = 7.20 Hz, 3H);
LCMS (m/z): 404 [M++23], 381 [M+1]+, 380 [M]+;
Anal. Calcd for C22H24 N2O4: C(69.46%), H(6.36%),
N(7.36%); Found: C(69.91%), H(6.74%), N(6.95%).
2.5c Methyl-2-{4-[(1-methyl-1H-indol-2-yl)methoxy]
benzylidene}-3-oxobutanoate (compound 8a, scheme 3):
Yield: 15.3%. Mp: 142–144◦C; FTIR (KBr): 2922 and
1
2851, 1735, 1638, 1240, 1043, 800 cm−1; H NMR
(CDCl3) mixture of E and Z isomers, δ: 7.63 (s,
1H+1H), 7.61 (d, J = 8.0 Hz, 1H+1H), 7.37 (d, J =
8.8 Hz, 2H+2H), 7.34 (m, 1H+1H), 7.25 (m, 1H+1H),
7.11 (m, 1H+1H), 7.01 (d, J = 8.8 Hz, 2H+2H), 6.61
(s, 1H+1H), 5.23 (s, 2H), 5.22 (s, 2H), 3.83 (s, 3H),
3.82 (s, 3H), 3.79 (superimposed s, 3H+3H), 2.38 (s,
3H), 2.36 (s, 3H); LCMS (m/z): 386 [M++23], 365
[M++2], 364 [M+1]+; Anal. Calcd for C22H21NO4:
C(72.71%), H(5.82%), N(3.85%); Found: C(72.63%),
H(5.57%), N(3.68%).
2.5g Methyl 2-{4-[(1-methyl-1H-indol-2-yl)methoxy]
benzyl}-3-oxobutanoate (compound 10a, scheme 3):
Yield: 14.5%. Mp: 122–124◦C; FTIR (KBr): 2917 and
1
2849, 1730, 1637, 1216, 1103, 847 cm−1; H NMR
(CDCl3)δ: 7.44 (d, J = 8.4 Hz, 1H), 7.37 (d, J =
8.8 Hz, 2H), 7.20 (m, 2H), 7.11 (m, 1H), 6.93 (d, J =
8.8 Hz, 2H), 6.68 (s, 1H), 5.26 (s, 2H), 3.86 (s, 3H), 3.78
(t, J = 7.0 Hz, 1H), 3.63 (s, 3H), 3.48 (d, J = 7.2 Hz,
2H), 2.28 (s, 3H); LCMS (m/z): 365 [M]+, 322, 285;
Anal. Calcd for C22H23NO4: C(72.31%), H(6.34%),
N(3.83%); Found: C(72.49%), H(6.51%), N(3.72%).
2.5d Ethyl 2-acetyl-3-[4-(1-methyl-1H-indol-2-ylmethoxy)-
phenyl]-acrylate (compound 8b, scheme 3): Yield:
22.5%. Mp: 128–131◦C FTIR (KBr): 2983, 2852, 1731,
2.5h Ethyl 2-[4-(1-methyl-1H-indol-2-ylmethoxy)-
benzyl]-3-oxo-butyrate (compound 10b, scheme 3):
Yield: 18%. Mp: 107–110◦C; FTIR (KBr): 2923, 2852,
1
1715, 1242, 1145, 1108, 859 cm−1; HNMR (CDCl3)
mixture of geometric isomers, δ: 7.55 (s, 1H), 7.53
(s, 1H), 7.43 (m, 1H+1H), 7.40 (d, 1H+1H), 7.31 (d,
J = 8.8 Hz, 2H), 7.27 (d, J = 8.5 Hz, 2H), 7.05 (m,
1H+1H), 6.96 (m, 1H+1H), 6.94 (overlapped d, J =
8.8 Hz, 2H+2H, Ar), 6.54 (superimposed s, 1H+1H,
Ar), 5.16 (s, 2H), 5.15 (s, 2H), 4.29 (q, J = 7.2 Hz,
2H), 4.22 (q, J = 7.1 Hz, 2H), 3.72 (superimposed s,
3H+3H), 2.33 (s, 3H), 2.31 (s, 3H), 1.25 (overlapped t,
J = 7.2 Hz, 3H+3H); LCMS (m/z): 378 [M+1]+, 364;
Anal. Calcd for C23H23NO4: C(73.19%), H(6.14%),
N(3.71%); Found: C(73.44%), H(6.52%), N(3.98%).
1
1740, 1714, 1235, 1177, 1075, 823 cm−1; HNMR
(CDCl3)δ: 7.60 (d, J = 7.8 Hz, 1H), 7.10 (m, 1H), 7.33
(m, 1H), 7.07 (d, J = 8.6 Hz, 2H), 6.91 (d, J = 8.6 Hz,
2H), 5.15 (s, 2H), 4.13 (q, J = 7.1 Hz, 2H), 3.79 (s,
3H), 3.75 (m, 1H), 3.09 (d, J = 7.5 Hz, 2H), 2.30
(s. 3H), 1.20 (t, J = 7.2 Hz, 3H); LCMS (m/z): 380
[M+1]+, 379 [M]+, 333; Anal. Calcd for C23H25NO4:
C(72.80%), H(6.64%), N(3.69%); Found: C(73.15%),
H(6.83%), N(4.01%).
2.6 Synthetic procedures for the preparation
of the final α-alkoxy propanoic acid based
NCEs (compounds 14a and 14b)
2.5e Methyl 2-{4-[(1-methyl-1H-benzimidazol-2-yl)methoxy]
benzyl}-3-oxobutanoate (compound 9a, scheme 3):
Yield: 18.0%. Mp: 135–138◦C; FTIR (KBr): 2918 and
2.6a General procedure for the syntheses of 11a
and 11b: To a slurry of (methoxymethyl)triphenyl-
phosphonium chloride (2.7 g, 0.008 mol) and diiso-
propylamine (0.76 mL, 0.006 mol) in THF (20 mL)
1
2850, 1730, 1711, 1240, 1067, 846 cm−1; H NMR
(CDCl3)δ: 7.68 (m, 1H), 7.32 (m, 3H), 6.89 (d, J =
8.68 Hz, 2H), 6.71 (d, J = 8.60 Hz, 2H), 5.33 (s, 2H),

Design, synthesis and computational validation of novel benzimidazole and indole
1561
was added a 2.5 M n-butyllithium solution in hexane 1H), 5.16 (s, 2H), 5.17 (s, 2H), 3.80 (d, J = 7.0 Hz,
(2.6 mL, 6 mmol), at −10◦C. After 1 h at −10◦C a solu- 1H), 3.80 (s, 3H), 3.79 (s, 3H), 3.75 (s, 3H), 3.66
tion of 1a/2b (4 mmol) in THF (4 mL) was added. (s, 3H); LCMS (m/z): 294 (M+1) ; Anal. Calcd for
The mixture was allowed to warm to rt over 2 h, then C19H19NO2: C(77.79%), H(6.53%), N(4.77%); Found:
poured into water (20 mL), and extracted with ether (3 C(77.24%), H(6.87%), N(5.26%).
× 20 mL). The combined extracts were washed with
brine, dried over sodium sulphate, and concentrated.
The required product 11a/b (1:2 mixture of geometri-
cal isomers) was isolated as a white solid by column
chromatography using a mixture of hexane and ethyl
2.6d General procedure for the syntheses of
the acetals 12a and 12b: A solution 11a/b
(2.5 mmol) and p-toluenesulphonic acid monohydrate
(0.026 mmol) in iso-Butyl alcohol (7 mL) was heated to
acetate.
reflux overnight. The solvent was removed, the residue
was taken up in ethyl acetate, and the solution was
washed with 5% sodium bicarbonate and brine, dried
over sodium sulphate, and concentrated to get 12a/b as
yellow viscous oil which slowly solidified on standing.
2.6b 2-({4-[2-Methoxyethenyl]phenoxy}methyl)-1-
methyl-1H-benzimidazole (compound 11a, scheme 4):
Yield: 34.2%. Mp: 101◦C; FTIR (KBr):3033, 2930
1
and 2860, 1653, 1243, 1094, 766, 670 cm−1; H NMR
(CDCl3)δ: mixture of geometrical isomers, 7.84 (m,
2H), 7.50 (d, J = 7.0 Hz, 2H), 7.33 (m, 6H), 7.15
(d, J = 7.0 Hz, 2H), 7.00 (d, J = 7.0 Hz, 2H), 6.91
(d, J = 13.0 Hz, 1H), 6.05(d, J = 7.0 Hz, 1H), 5.75
(d, J = 13.0 Hz, 1H), 5.43 (s, 2H), 5.41 (s, 2H) 5.15
(d, J = 7.0 Hz, 1H), 3.90 (s, 3H), 3.89 (s, 3H), 3.74
(s, 3H), 3.65 (s, 3H); LCMS (m/z): 295 [M+1]+;
Anal. Calcd for C18H18N2O2: C(73.45%), H(6.16%),
N(9.52%); Found: C(73.24%), H(6.35%), N(9.26%).
2.6e 2-[4-(2,2-Diisobutoxy-ethyl)-phenoxymethyl]-1-
methyl-1H-benzimidazole (compound 12a, scheme 4):
Yield: 65.0%. Mp: 110◦C; FTIR (KBr): 3053, 2956
1
and 2872, 1253, 1234, 1064, 1039, 743, 570 cm1; H
NMR (CDCl3)δ: 7.77 (d, 1H), 7.31 (m, 3H), 7.16 (d,
J = 8.6 Hz, 2H), 6.98 (d, J = 8.6 Hz, 2H ) 5.35 (s,
2H), 4.53 (t, 1H), 3.86 (s, 3H), 3.37 (dd, J = 6.5 Hz
and 9.1 Hz, 2H), 3.13 (dd, J = 6.5 Hz and 9.06 Hz,
2H), 2.84 (d, 2H), 1.78 (m, 2H), 0.86 (d, 6H), 0.84
(d, 6H); LCMS (m/z): 411 [M+1]+; Anal. Calcd for
C25H34N2O3: C(73.14%), H(8.35%), N(6.82%); Found:
C(73.55%), H(8.12%), N(6.51%).
2.6c 2-({4-[2-Methoxyethenyl]phenoxy}methyl)-1-
methyl-1H-indole (compound 11b, scheme 4): Yield:
32.0%. Mp: 108–109◦C; FTIR (KBr): 3035, 2932
and 2800, 1645, 1233, 1114, 752, 635 cm−1; 1H 2.6f 2-[4-(2, 2-Diisobutoxy-ethyl)-phenoxymethyl]-1-
NMR (CDCl3)δ: mixture of geometrical isomers, 7.67 methyl-1H-indole (compound 12b, scheme 4): Yield:
(m, 2H), 7.61 (d, 2H), 7.54 (d, J = 8.2 Hz, 2H), 7.53 65%. Mp: 120–122◦C; FTIR (KBr): 3062, 2948 and
(m, 1H), 7.32 (d, J = 8.2 Hz, 2H), 7.23 (m, 2H), 7.21 2862, 1246, 1231, 1116, 753, 638 cm1; 1H NMR
(d, J = 8.8 Hz, 2H), 7.16 (m, 1H), 7.08 (d, J = 8.8 Hz, (CDCl3)δ: 7.51 (d, 1H), 7.24 (d, 1H), 7.14 (m, 2H),
2H), 6.94 (d, J = 13.0 Hz, 1H), 6.58 (superimposed s, 7.03 (d, J = 8.6 Hz, 2H), 6.67 (d, J = 8.6 Hz, 2H), 6.38
2H), 6.06 (d, J = 7.0 Hz, 1H), 5.78 (d, J = 13,0 Hz, (s, 1H), 4.58 (s, 2H), 4.47 (t, J = 5.6 Hz, 1H), 3.71 (s,
O
O
O
X
N
X
H
X
O
b
a
O
O
N
O
N
12a/b
11a/b
1a/2b
c
O
CN
OH
X
code
a
b
X
N
CH
O
O
X
O
d
O
N
13a/b
N
14a/b
Scheme 4. Reagents and conditions: (a) Ph3P+CH2OMe Cl−, LDA, THF, −10◦C; (b) isobutanol; (c) TMSCN,
BF3-DCM; (d) NaOH, H2O-EtOH.

1562
Raman K Verma et al.
3H), 3.31 (dd, J = 6.5 Hz and 9.1 Hz, 2H), 3.07 washed with brine, dried over sodium sulphate, and
(dd, J = 6.5 Hz and 9.1 Hz, 2H), 2.77 (d, 2H), 1.71 concentrated. The crude product was recrystallized
(m, 2H), 1.18 (d, 12H); LCMS (m/z): 410 [M+1]+; from ethyl acetate/hexane and to obtain 14a/b as a
Anal. Calcd for C26H35NO3: C(76.25%), H(8.61%), white solid.
N(3.42%); Found: C(76.55%), H(8.37%), N(3.51%).
2.6k 2-Isobutoxy-3-[4-(1-methyl-1H-benzimidazole-2-
ylmethoxy)-phenyl]-propionic acid: (compound 14a,
scheme 4): Yield: 70.0%. Mp: 167–168◦C; FTIR
(KBr): 3400, 2900, 2800, 1655, 1238, 1050, 825
2.6g General procedure for the syntheses of the
cyanides 13a and 13b: To a solution of 12a/b
(0.3 mmol) in dichloromethane (8 mL) were added
trimethylsilyl cyanide (0.11 mL, 0.9 mmol) and boron
trifluoride etherate (0.008 g, 0.075 mmol). After 1 h the
solution was diluted with dichloromethane, washed
with 5% sodium bicarbonate, water, and brine, dried
over sodium sulphate, and concentrated. The crude
product was purified by column chromatography elut-
ing with a mixture of hexane and ethyl acetate and
13a/b was isolated as an off white solid.
1
765 cm−1; H NMR (DMSO-d6)δ: 7.63 (d, 1H), 7.56
(d, 1H), 7.27 (t, 1H), 7.20 (t, 1H), 7.13 (d, J = 6.8 Hz,
2H), 7.00 (d, J = 7.4 Hz, 2H) 5.27 (s, 2H), 3.83 (s,
3H), 3.71 (t, 1H), 3.37 (dd, J = 6.5 Hz and 9.1 Hz,
2H), 2.84 (d, 2H), 1.6848 (m, 1H), 0.72 (d, 6H); LCMS
(m/z): 383 [M+1]+; Anal. Calcd for C22H26N2O4:
C(69.09%), H(6.85%), N(7.32%); Found: C(69.33%),
H(6.56%), N(7.50%).
2.6l 2-Isobutoxy-3-[4-(1-methyl-1H-indole-2-ylmethoxy)-
phenyl]-propionic acid: (compound 14b, scheme 4):
Yield: 67%. Mp: 175–177◦C; FTIR (KBr): 3430, 2927,
2.6h 2-Isobutoxy-3-[4-(1-methyl-1H-benzimidazole-
2-ylmethoxy)-phenyl]-propionitrile (compound 13a,
scheme 4): Yield: 33.0%. Mp: 115–117◦C; FTIR
(KBr): 2900, 2800, 2300, 1600, 1240, 1026, 900,
1
744 cm−1; H NMR (CDCl3)δ:7.85 (d, 1H), 7.40 (m,
Table 1. Designed NCEs.
3H), 7.21 (d, J = 8.6 Hz, 2H), 7.06 (d, J = 8.6 Hz,
2H), 5.53 (s, 2H), 4.18 (t, 1H), 3.96 (s, 3H), 3.49 (dd,
J = 8.6 and 6.6 Hz), 3.17 (dd, J = 8.6 Hz and 6.5 Hz,
2H), 3.05 (overlapped dd, 2H, J = 6.7 and 2.9), 1.86
(m, 1H), 0.86 (d, 6H); LCMS (m/z): 364 [M+1]+;
Anal. Calcd for C22H25 N3O2: C(72.70%), H(6.93%),
N(11.56%); Found: C(72.48%), H(7.23%), N(11.22%).
O
R'
Z
O
X
Y
O
R
n
N
Compound
code
2.6i 2-Isobutoxy-3-[4-(1-methyl-1H-indole-2-ylmethoxy)-
phenyl]-propionitrile (compound 13b, scheme 4):
Yield: 31.0%. Mp: 130–132◦C; FTIR (KBr): 2954,
2873, 2322, 1612, 1253, 1032, 922, 749 cm−1; 1H NMR
(CDCl3)δ:7.58 (d, 1H), 7.48 (m, 2H), 7.32 (d, 2H),
7.22 (d, J = 8.1 Hz, 2H), 7.10 (d, J = 7.9 Hz, 2H),
6.45 (s, 1H), 4.82 (s, 2H), 4.18 (t, J = 6.8, 1H), 3.81
(s, 3H), 3.49 (dd, J = 8.6 and 6.6 Hz, 1H), 3.17 (dd,
J = 8.6 Hz and 6.5 Hz, 1H), 3.05 (overlapping dd, J =
6.7 and 2.9, 2H), 1.85 (m, 1H), 0.87 (d, 6H); LCMS
(m/z): 364 [M+2]+; Anal. Calcd for C23H26N2O2:
C(76.21%), H(7.23%), N(7.73%); Found: C(75.88%),
H(7.35%), N(8.12%).
n
Y
X
R
Rꢁ
Z*
7ꢁa
7a
2
1
2
1
2
1
2
1
2
1
2
1
2
1
2
1
2
1
2
1
N
N
N
C=O
C=O
C=O
C=O
C=O
C=O
C=O
C=O
C=O
C=O
C=O
C=O
C=O
C=O
C=O
C=O
O
Me
Me
Me
Me
Me
Me
Me
Me
Me
Me
Me
Me
Me
Me
Me
Me
iBu
iBu
iBu
iBu
Me
Me
Et
db
db
db
db
db
db
db
db
sb
sb
sb
sb
sb
sb
sb
sb
sb
sb
sb
sb
7ꢁb
7b
N
Et
8ꢁa
8a
CH
CH
CH
CH
N
N
N
Me
Me
Et
8ꢁb
8b
Et
9ꢁa
9a
Me
Me
Et
9ꢁb
9b
N
Et
10ꢁa
10a
10ꢁb
10b
14ꢁa
14a
14ꢁb
14b
CH
CH
CH
CH
N
N
CH
CH
Me
Me
Et
Et
H
H
H
H
2.6j General procedure for the syntheses of the acids
14a and 14b: A mixture of 13a/b (0.09 mmol),
ethanol (7 mL), and 6 N sodium hydroxide (0.5 mL)
was heated to reflux for 3 h. Water (2 mL) was
added, and the solution was acidified with concentrated
hydrochloric acid (6 mL) and then extracted with ethyl
O
O
O
acetate (2 × 7 mL). The combined organic layers were *db= double bond, sb= single bond

Design, synthesis and computational validation of novel benzimidazole and indole
1563
1
2832, 1656, 1240, 1038, 840, 760 cm−1; H NMR Farglitazar, extracted from PPARγ crystal structure
(DMSO-d6)δ: 7.65 (d, 1H), 7.48 (d, 1H), 7.30 (t, 2H), (PDB code 1FM9) by the ‘build molecule’ mod-
7.15 (d, J = 6.7 Hz, 2H), 6.99 (d, J = 7.4 Hz, 2H), ule of Sybyl7.3.16 After the energy optimization of
6.34 (s, 1H), 5.36 (s, 2H), 3.89 (s, 3H), 4.98 (t, J = the sketched molecules by Powell method (using the
5.8 Hz, 1H), 4.27 (dd, J = 6.5 Hz and 9.1 Hz, 2H), default parameters, Gasteiger–Marsili charges have
2.36 (d, 2H), 1.75 (m, 1H), 0.87 (d, 6H); LCMS (m/z): been assigned), they were all subjected to activity pre-
382 [M+1]+; Anal. Calcd for C23H27NO4: C(72.42%), diction by the developed PPARα, PPARγ and PPAR
H(7.13%), N(3.67%); Found: C(72.13%), H(6.66%), dual CoMFA models.9 The predicted activities in terms
N(4.15%).
of pEC50 values are listed in table 2. The ketoester
molecules in ‘R’ configuration whereas the α-alkoxy
acid molecules in ‘S’ were predicted for identical and
optimum alignment (figures 9, 10).
2.7 Design of NCEs as PPARα/γ partial agonists
and prediction of PPARα and PPARγ activities
The novel molecules were designed by thoroughly
studying the structural features required for partial ago-
nism to both PPARα and PPARγ obtained from con-
tour analysis of the developed PPARα and PPARγ
3D-QSAR CoMFA models.9 The critical observation
of the structural features of the highly potent dual
agonist farglitazar and PPARγ full agonist rosiglita-
zone also aided to the design of the new molecules
(table 1) expected to be PPARα/γ partial agonists.
The designed molecules were modelled onto the ligand,
2.8 Molecular docking studies
The sketched molecules (some standard dual activators
and designed molecules) were docked into ligand bind-
ing active site of PPARγ crystal structure by the Surflex
Dock method. The surflex dock score (total score) and
the G score value for best docked conformation of
each molecule were recorded (table 2). The number of
hydrogen bonding interactions of the docked ligands
with the active site and the amino acid residues involved
Table 2. Predicted PPAR activities and binding affinities at PPARγ active site of the synthesized NCEs and standard
molecules.
Compound‡
Predicted α pEC50
Predicted γ pEC50
Predicted dual pEC50
Total score
G-score*
Farglitazar
LY 510929
GW409544
DRF 2725
GW 7845
NND 9
7ꢁa
6.307
8.418
6.125
5.799
5.912
6.230
6.176
6.093
6.225
6.159
6.387
6.121
6.325
6.143
6.457
5.783
6.165
5.971
6.400
6.198
6.367
6.114
6.706
6.135
6.490
6.275
9.542
8.768
9.491
6.471
9.301
6.609
6.727
6.634
6.782
6.673
7.213
6.605
7.109
6.649
7.197
6.720
6.903
6.360
7.210
6.762
7.055
6.402
7.519
6.528
7.189
6.568
16.418
17.092
15.348
12.076
14.988
12.797
12.857
12.785
12.987
12.828
13.524
12.062
13.301
12.657
13.529
12.375
13.075
12.204
13.449
12.906
13.236
12.397
14.029
12.470
13.400
12.643
11.62
8.85
9.35
8.08
8.72
7.06
6.46
4.37
7.05
5.77
5.64
4.43
5.47
4.71
5.25
3.56
1.34
4.79
4.82
5.69
3.69
6.71
7.88
6.93
7.25
8.06
−390.56
−301.54
−363.39
−289.41
−356.52
−302.76
−254.12
−218.91
−280.81
−221.81
−271.34
−242.49
−278.49
−260.76
−208.26
−216.53
−332.76
−177.43
−251.90
−236.34
−254.44
−266.91
−294.91
−295.49
−281.33
−306.42
7a
8ꢁa
8a
9ꢁa
9a
10ꢁa
10a
7ꢁb
7b
8ꢁb
8b
9ꢁb
9b
10ꢁb
10b
14ꢁa
14a
14ꢁb
14b
‡The benzyl ketoester molecules are in ‘R’ configuration and α-alkoxy acid molecules in ‘S’ configuration
*G score of the best docked conformation

1564
Raman K Verma et al.
Table 3. The amino acid residues involved in hydrogen bonding interactions with the
ligands at the PPARγ active site (1FM9).
Compound
Amino acid residues (no. of H-bonding interactions)
Total no. of H-bonds
Farglitazar
GW409544
LY 510929
DRF 2725
GW 7845
NND 9
7a
7b
8a
8b
9a
S 289 (1), H 323 (1), H 449 (1), Y 473 (1)
S 289 (1), H 323 (1), H 449 (1), Y 473 (1)
Y 327 (1), H 449 (1), Y 473 (2)
S 289 (1), H 449 (1), Y 473 (1)
S 289 (1), H 323 (1), H 449 (1), Y 473 (1)
S 289 (1), H 449 (1), Y 473 (1)
S 342 (1)
4
4
4
3
4
3
1
1
1
1
1
1
1
1
3
3
S 342 (1)
ARG288 (1)
S 342 (1)
S 289 (1)
S 342
S 289 (1)
S 289 (1)
9b
10a
10b
14a
S 289 (2), H 323 (1)
Y 473 (2), H 449 (1)
14b
were also found (table 3) and compared with that of the to the steric and electronic requirements and were sub-
standard molecules.
sequently predicted for their activities (tables 1 and 2).
Two benzfused heterocycles namely; benzimidazole
and indole, popular for their versatile pharmacological
potential, were taken according to design guided by the
analysis of the CoMFA contours and chemical structure
analysis of the known standard PPAR molecules for the
hydrophobic part to reduce the extending length of the
hydrophobic unit (figures 3–8) unlike a phenyl oxazole
of farglitar or muraglitazar; thiophenyl oxazole of LY
510929; a tricyclic phenoxazine of ragaglitazar or car-
bazole of NND9 (figures 5 and 6). Fusion of the five and
six-membered rings of the hydrophobic part of fargli-
tazar to get a benzfused heterocycle (figure 6) decreases
the extending length of the hydrophobic unit (figures 7
and 8). The heterocyclic left hand side part of full ago-
nist rosiglitazone can also be structurally modified by
joining the heteroatom of the N-methyl pyridyl moie-
ty to the carbon atom adjacent to the N-Me group of
the spacer to obtain a benzfused heterocycle benzimi-
dazole with one heteroatom substituted with a methyl
group (figure 6). The bioisosteric replacement of the
unsubstituted nitrogen with a ‘CH’ group gives rise to
other benzfused heterocycle indole with the heteroatom
substituted with a methyl group (figure 6). Such hetero-
cyclic scaffolds reported here contributed to the reduc-
tion of PPARα and PPARγ activities compared to the
previously known molecules. The heteroatom (nitro-
gen) of the heterocycles with methyl group substitution
was desirable to suppress electron richness (red rhom-
bohedral contour on the left hand side in the PPARα
and PPARγ models) simultaneously rendering less bulk
in the region (yellow contour on the left hand side of
3. Results and discussion
PPARα/γ dual agonists mainly the tyrosine and
propanoic acid derivatives usually possess essential
pharmacophoric elements10–12 i.e.; an acidic group or
a hydrogen bonding part attached to a central flat aro-
matic ring, a linker and a large hydrophobic fragment
and adopts a bioactive U-shapped conformation for
receptor binding13 (figure 2). We have previously
reported the development of three 3D-QSAR CoMFA
models namely; PPARα, PPARγ and PPAR dual, using
a set of known dual agonists (tyrosine and α-alkoxy/
aryloxy propanoic acid derivatives) for which in vitro
PPAR transactivation assay activities are reported.9
From the analysis of the steric and electrostatic contours
resulted from the models, a set of molecules expected to
be PPARα/γ partial agonists were designed according
flat aromatic ring
linker
Hydrogen
bonding
part
Bioactive 'U'-shape
Figure 2. The pharmacophore.

Design, synthesis and computational validation of novel benzimidazole and indole
1565
Figure 3. Steric and electrostatic solid contours of the PPARα model9
(Farglitazar shown as the standard ligand, special features for the design of
the reported NCEs as partial agonists have been highlighted).
Figure 4. Steric and electrostatic solid contours of the PPARγ model9
(Farglitazar shown as the standard ligand, special features for the design of
the reported NCEs as partial agonists have been highlighted).
PPARγ model) as found from observation and analysis were as expected and supported that methyleneoxy,
of the contours9 (figures 3, 4, 7 and 8) and also keeping linker is preferred over ethyleneoxy for partial ago-
in view the housability of the ligands at the receptor site. nism (table 2). The effect of longer and shorter spacer
The length of the two carbon linker (as reported in far- (ethyleneoxy and methyleneoxy, respectively) has been
glitazar, ragaglitazar, tesaglitazar, etc.) was decreased to shown in figures 9 and 10. It can be observed that
one carbon to impart further constraint to the designed the hydrophobic units (left hand side) of the molecules
molecules. Although NCEs with ethyleneoxy as well with ethyleneoxy spacer (table 1) enters into the green
as methyleneoxy linker were predicted for their PPAR steric contour which actually favours the increase
activities and binding affinities and results obtained in activities of the molecules whereas heterocyclic

1566
Raman K Verma et al.
X= O/ C=O
R’= H/ Me
R= iBu/ Me/Et
Y= N/ CH
linker length shortened
to impart constraint
3
double bond effects
constraint to rhs
O
128.9 3.0 cm
replacement
by N/CH
O
OH
Z= single bond/
double bond
O
COOH
HN
O
N
3
3
92.4 3.0 cm
198.1 3.0 cm
O
fusion
3
O
111.6 3.0 cm
Y
N
O
N-Me: electrostatic
contour analysis
O
Analysis of CoMFA
3
167.5 3.0 cm
contours and
Farglitazar- potent dual agonist
O
3
58.8 3.0 cm
structures of the
O
standards molecules
O
O
S
N
Z
X
NH
N
O
R
O
3
145.3 3.0 cm
O
OR'
linked and shift of heteroatom to obtain
benz fused pyrole or imidazole heteroccycle
O
proposed novel
PPARα/γ partial agonists
Rosiglitazone- potent PPARγ agonist
Figure 5. Design of the acyclic analogs of oxazolidenedione and isoxazoli-
denedione as PPARα and PPARγ partial agonists: structural modification of
the hydrophobic part of the template Farglitazar (highly potent dual agonist)
and Rosiglitazone (highly potent PPARγ agonist) to reach to the conclusion
of introducing benzfused imidazole or pyrole (also guided and supported by
CoMFA steric and electrostatic contours) as the hydrophobic units in the design
of partial PPARα/γ activators. The effect of reducing the size by incorporating
alkoxy/alkanoyl group on the total volume of the hydrogen bonding part is also
shown. (The numbers in blue and violet indicate calculated molar volume of the
respective fragment.)
required to maintain
bioactive conformation
OH
short linker
OR'
Ester
or acid
O
O
O
O
HN
O
Contour
and
structure
analysis
X
O
X
Y
N
N
R
R
H
X= O/ C=O
R= smaller alkyl
(iBu/Me) for
partial agonism
R’= H/ Me/Et
i
R= Bu/ Me
X= carbonyl/ O
Y= N/ CH
Structural modification of the template
PPAR partial agonists
Figure 6. Pharmacophoric modifications of the template for the design of the α-
alkoxy phenyl propanoic acid and β-acetyl phenyl propanoic acid methyl/ethyl
ester based NCEs (PPAR partial agonists).
part of the molecules with methyleneoxy spacer reduces the activity in considerable amount; we selected
remains away from the green contours of the PPARα isobutyloxy (figures 5 and 6) to get a moderate and
and PPARγ models (figures 7 and 8). The flat aromatic medium effect. This was also supported by the steric
ring was kept intact while design so as to maintain the contours (green contour on the right hand side) of the
bioactive ‘U’ conformation. We observed that a bulkier PPARα and PPARγ models (figures 3, 4, 7 and 8). The
group (phenoxy, benzyloxy) at the α-position of the prediction of activities with the models gave expected
acid group contributes mainly in increasing the PPARγ results (table 2). The modifications consequently dimin-
activity. Smaller alkyl groups exert less effect on the ished the overall dual activity too (table 2). A steri-
activity. Dual molecules with α-ethoxy are known to cally less bulky β-ketoester (methyl acetoacetate/ethyl
have lesser PPARγ activity compared to their α-aryloxy acetoacetate) group as the hydrogen bonding part
counterparts. The incorporation of ethoxy group into (figures 5 and 6) also gave predicted results in favour
the hydrogen bonding part (as in NND9, Ragaglitazar) of partial agonism. Blue contours can be observed in

Design, synthesis and computational validation of novel benzimidazole and indole
1567
Figure 7. The reported NCEs and the template within the steric and elec-
trostatic transparent contours of the PPARα model (farglitazar shown in
orange, the special modifications into the standard have been highlighted).
Figure 8. The reported NCEs and the template within the steric and elec-
trostatic transparent contours of the PPARγ model (farglitazar shown in
orange, the special modifications into the standard have been highlighted).
case of both the models near to the nitrogen atom molecule at γ -postion with respect to the amino group
of secondary amino group on the right hand side of on the right hand side but it is away from the blue con-
the template (figures 3 and 4) which indicate positive tour (figures 3 and 4) and when the carbonyl group is
potential in this region is favourable for enhancing kept at the β-position with respect to the ester group
PPARα and PPARγ activities, but if electron richness in the designed molecules the carbonyl oxygen atom
is provided in the region that will exert a negative approaches near to the blue region (figures 7 and 8). The
effect upon the enhancement of activities. A carbonyl antihypoglycemic activity of the 1,3-dicarbonyl com-
group in place of the amino group in the designed pounds has been previously investigated thoroughly and
molecules (figures 7 and 8) served the purpose well reported.14 The heterocyclyl linked benzyl β-ketoester
and contributed to the reduction of activities. Though based molecules along with their benzylidene analogs
a carbonyl group can also be noticed in the template were predicted for their activities (table 2) as the

1568
Raman K Verma et al.
(a)
(b)
Figure 9. The reported NCEs and the template (farglitazar: orange)
within the steric and electrostatic contours (transparent) of the CoMFA
models,14 the effects of increasing the length of the spacer are indicated.
Reported β-keto ester based NCEs: (a) PPARα model and (b) contours,
PPARγ model.
benzylidines are also reported to be active and show introduced in a subset of designed molecules intention-
euglycemic activity.15 The benzylidene 1,3-diesters are ally to understand the effect on reduction of activities
also reported to show antihypoglycemic activity.14 The by the modification. The designed molecules exhibited
double bond can also have an effect of imparting con- appreciable partial agonism as evident from the pre-
straint to the right hand side hydrogen bonding frag- dicted activity data values which are lesser compared
ments of the designed molecules. As the diesters are to that of the standard dual agonists like farglitazar,
reported to be active in both PPARα and PPARγ and LY510929, GW7845 etc (table 2). The molecules with
also exhibit lesser activities as compared to the tyrosine methyleneoxy spacer were found to be of lesser pre-
and α-alkoxy dihydrocinnamic acid based agonists,14 dicted activities compared to the molecules with ethyle-
β-ketoester was decided upon to be incorporated in the neoxy spacer and hence preferred over the latter for
designed molecules as a part of the hydrogen bond- selection for synthesis. The lesser predicted activities
ing fragment. Electron-rich group indicating the pres- of the molecules with methyleneoxy spacer may be
ence of an acid was a requirement for enhancement of attributed to the shortened length of the spacer which
activity according to contour analysis.9 Ester group was in turn reduces the distance between the hydrophobic

Design, synthesis and computational validation of novel benzimidazole and indole
1569
(a)
(b)
Figure 10. The reported NCEs and the template (farglitazar: orange)
within the steric and electrostatic contours (transparent) of the CoMFA
models,14 the effects of increasing the length of the spacer are indicated.
Reported α-alkoxy acid based NCEs: (a) contours, PPARα model and (b)
contours, PPARγ model.
part and the hydrogen bonding tail and introduces they exhibited lesser number of hydrogen bond inter-
a constraint to the molecules that helps lesser bind- actions as compared to the previously discussed dual
ing interactions at the receptor site compared to the agonists (table 3). From the predicted activities and
molecules with ethyleneoxy spacer as well as the stan- binding affinities it is evident that the molecules with
dard molecules. Smaller hydrophobic and hydrogen methyleneoxy linker exhibit lesser activities and bind-
bonding units with moderate bulk were introduced ing affinities compared to their ethyleneoxy counter-
to impart features of partial agonism to the designed parts in almost all the cases so the molecules with
NCEs. The feature of partial agonism of the NCEs methyleneoxy linker were selected as better partial
was further validated computationally by the dock- agonists for synthesis. The syntheses and characteri-
ing studies at PPARγ X-ray crystal structure. This zation of the α-isobutoxy propanoic acid based and
showed less binding affinities of the designed NCEs the β-ketoester based compounds are reported in the
to the PPARγ active site as compared to the previ- present work.
ously reported dual agonists as evident from the lesser
The ketoester final NCEs were achieved by first
docking score and Gold score16,17 values (table 2) and synthesizing the left hand side (lhs) alcohol units

1570
Raman K Verma et al.
(schemes 1 and 2) and then right hand side (rhs) phe- The isobutoxy cyanides (13a/b) were obtained in
nolic units (scheme 3) followed by coupling the two appreciable yields by reacting 12a/b with trimethylsi-
units by Mitsunobu reaction (scheme 3). The final lyl cyanide. Finally, the α-alkoxy acid based final
α-alkoxy acids were achieved from the aldehydes NCEs (14a/b) were achieved in excellent yields by
(1a/2b) obtained from the lhs alcohols (1/2a) by a hydrolysing the cyanides (13a/b).
sequence of four steps of synthesis (scheme 4).
The benzimidazolyl linked aldehyde (1a) was pre-
pared by the synthetic route as shown in scheme 1.
4. Conclusion
N-methyl-1, 2-phenylene diamine dihydrochloride was
cyclised drastically with glycolic acid to furnish the
We report here the syntheses and characterization, ben-
zimidazole and indole linked benzyl based α-alkoxy
corresponding hydroxyl methyl compound (1) in excel-
propanoic acids and benzylidene and benzyl based β-
lent yield. This was reacted with 4-fluorobenzaldehyde
ketoesters as partial PPARα/γ agonists as anti type 2
diabetic compounds. The activities and binding affini-
ties at individual PPAR of synthesized molecules were
predicted to support the design of the molecules with
to afford the aldehyde (1a). The hydroxyl methyl
compound (2a) was prepared by a sequence from
commercially available ethyl indole-2-carboxylate via
N-methylation and subsequent reduction (scheme 2).
The yields of the N-methylated product (2a) and the
reduced product (2a) were very good. The indolyl
linked aldehyde (2b) was prepared from (2a) in a simi-
lar way as shown in scheme1 for (1a). The prepared
compounds (1–2b) were characterized and confirmed
by IR, 1HNMR and mass spectroscopy.
expected partial agonism.
Acknowledgements
The authors are thankful to Head, Department of Chem-
istry, Punjabi University and are also grateful to the
Director, Regional Sophisticated Instrumentation Cen-
tre (RSIC), Panjab University, Chandigarh and Direc-
tor, National Institute of Pharmaceutical Education and
Research (NIPER), SAS Nagar, Mohali, Punjab for
extending the facilities for the analysis of various com-
pounds reported in this paper. We greatly acknowledge
the financial support from IndSwift Labs. Ltd., SAS
Nagar, Mohali, Punjab for the ISLL-Punjabi Univer-
sity Collaborative Research Project, and providing the
research fellowship to two of the authors VK and PG
and for the timely guidance and support.
The ketoesters rhs units (4a/b and 6a/b) were syn-
thesized as shown in scheme 3. Commercially avail-
able p-anisaldehyde and methyl acetoacetate/ethyl ace-
toacetate were condensed by Knoevenagel rection in
the presence of a base to yield the methoxy benzyli-
dene compounds 3a/b which were reduced catalyti-
cally in a Parr hydrogenator to get the methoxy benzyl
compounds 5a/b. Demethylation of 3a/b and 5a/b
with boron tribromide gave the corresponding pheno-
lic benzylidene-based and phenolic benzyl-based com-
pounds (4a/b and 6a/b, respectively) which are the rhs
units for the synthesis of the β-ketoester based final
NCEs. The methoxy benzylidenes 3a/b and hydroxyl
benzylidenes 4a/b were obtained as mixture of geomet-
ric isomers which was clearly indicated by their PMR
spectra. 4a/b and 6a/b were coupled with the lhs units
1a and 2a by Mitsunobu process to finally synthesize
the β-ketoester based final NCEs (7a–10b, scheme 3).
The benzylidene β-ketoester-based final NCEs (7a–8b)
were also obtained as mixture of geometrical isomers
as evident from their PMR spectra and was as expected.
The efficient syntheses of the α-alkoxy acids have
been shown in scheme 4. The benzimdazolyl linked
aldehyde (1a) and the indolyl linked benzaldehyde (2b)
were treated (separately) with methoxymethyl triph-
enylphosphonim chloride in the presence of a strong
base lithium diisopropyl amine (prepared in situ by
mixing butyl lithium and isopropyl amine at low tem-
perature) to get 11a/b in good yields. The diacetals
12a/b were synthesized from 11a/b by refluxing
with isobutanol catalysed by p-toluenesuphonic acid.
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